1201
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Heigwer F, Zhan T, Breinig M, Winter J, Brügemann D, Leible S, Boutros M. CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries. Genome Biol 2016; 17:55. [PMID: 27013184 PMCID: PMC4807595 DOI: 10.1186/s13059-016-0915-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. RESULTS Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs. CONCLUSION CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld.
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Affiliation(s)
- Florian Heigwer
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Tianzuo Zhan
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
- />Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Marco Breinig
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Jan Winter
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Dirk Brügemann
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Svenja Leible
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
| | - Michael Boutros
- />Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120 Germany
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1202
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Aravalli RN, Steer CJ. Gene editing technology as an approach to the treatment of liver diseases. Expert Opin Biol Ther 2016; 16:595-608. [DOI: 10.1517/14712598.2016.1158808] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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1203
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Wen WS, Yuan ZM, Ma SJ, Xu J, Yuan DT. CRISPR-Cas9 systems: versatile cancer modelling platforms and promising therapeutic strategies. Int J Cancer 2016; 138:1328-36. [PMID: 26044706 DOI: 10.1002/ijc.29626] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/12/2015] [Accepted: 05/28/2015] [Indexed: 12/26/2022]
Abstract
The RNA-guided nuclease CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9) and its variants such as nickase Cas9, dead Cas9, guide RNA scaffolds and RNA-targeting Cas9 are convenient and versatile platforms for site-specific genome editing and epigenome modulation. They are easy-to-use, simple-to-design and capable of targeting multiple loci simultaneously. Given that cancer develops from cumulative genetic and epigenetic alterations, CRISPR-Cas9 and its variants (hereafter referred to as CRISPR-Cas9 systems) hold extensive application potentials in cancer modeling and therapy. To date, they have already been applied to model oncogenic mutations in cell lines (e.g., Choi and Meyerson, Nat Commun 2014;5:3728) and in adult animals (e.g., Xue et al., Nature 2014;514:380-4), as well as to combat cancer by disabling oncogenic viruses (e.g., Hu et al., Biomed Res Int 2014;2014:612823) or by manipulating cancer genome (e.g., Liu et al., Nat Commun 2014;5:5393). Given the importance of epigenome and transcriptome in tumourigenesis, manipulation of cancer epigenome and transcriptome for cancer modeling and therapy is a promising area in the future. Whereas (epi)genetic modifications of cancer microenvironment with CRISPR-Cas9 systems for therapeutic purposes represent another promising area in cancer research. Herein, we introduce the functions and mechanisms of CRISPR-Cas9 systems in genome editing and epigenome modulation, retrospect their applications in cancer modelling and therapy, discuss limitations and possible solutions and propose future directions, in hope of providing concise and enlightening information for readers interested in this area.
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Affiliation(s)
- Wan-Shun Wen
- Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang Province, China
| | - Zhi-Min Yuan
- Cervical Disease Clinic, Jiangsu Huai'an Maternity and Children Hospital, Huai'an, China
| | - Shi-Jie Ma
- Department of Gastroenterology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| | - Jiang Xu
- Department of Rehabilitation, the Affiliated Huai'an Hospital of Xuzhou Medical College and the Second People's Hospital of Huai'an, Huai'an, China
| | - Dong-Tang Yuan
- Department of Orthopedics, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
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1204
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Di Donato V, De Santis F, Auer TO, Testa N, Sánchez-Iranzo H, Mercader N, Concordet JP, Del Bene F. 2C-Cas9: a versatile tool for clonal analysis of gene function. Genome Res 2016; 26:681-92. [PMID: 26957310 PMCID: PMC4864464 DOI: 10.1101/gr.196170.115] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 02/24/2016] [Indexed: 11/24/2022]
Abstract
CRISPR/Cas9-mediated targeted mutagenesis allows efficient generation of loss-of-function alleles in zebrafish. To date, this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation. Here, we show that tissue-specific gene disruption can be achieved by driving Cas9 expression with the Gal4/UAS system. Furthermore, by combining the Gal4/UAS and Cre/loxP systems, we establish a versatile tool to genetically label mutant cell clones, enabling their phenotypic analysis. Our technique has the potential to be applied to diverse model organisms, enabling tissue-specific loss-of-function and phenotypic characterization of live and fixed tissues.
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Affiliation(s)
- Vincenzo Di Donato
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Flavia De Santis
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Thomas O Auer
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Noé Testa
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
| | - Héctor Sánchez-Iranzo
- Department of Cardiovascular Development and Repair, Atherothrombosis and Imaging, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28028 Madrid, Spain
| | - Nadia Mercader
- Department of Cardiovascular Development and Repair, Atherothrombosis and Imaging, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28028 Madrid, Spain
| | - Jean-Paul Concordet
- Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Paris F-75231, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U 934, CNRS UMR3215, F-75005, Paris, France
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1205
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Kalebic N, Taverna E, Tavano S, Wong FK, Suchold D, Winkler S, Huttner WB, Sarov M. CRISPR/Cas9-induced disruption of gene expression in mouse embryonic brain and single neural stem cells in vivo. EMBO Rep 2016; 17:338-48. [PMID: 26758805 PMCID: PMC4772980 DOI: 10.15252/embr.201541715] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 01/08/2023] Open
Abstract
We have applied the CRISPR/Cas9 system in vivo to disrupt gene expression in neural stem cells in the developing mammalian brain. Two days after in utero electroporation of a single plasmid encoding Cas9 and an appropriate guide RNA (gRNA) into the embryonic neocortex of Tis21::GFP knock-in mice, expression of GFP, which occurs specifically in neural stem cells committed to neurogenesis, was found to be nearly completely (≈ 90%) abolished in the progeny of the targeted cells. Importantly, upon in utero electroporation directly of recombinant Cas9/gRNA complex, near-maximal efficiency of disruption of GFP expression was achieved already after 24 h. Furthermore, by using microinjection of the Cas9 protein/gRNA complex into neural stem cells in organotypic slice culture, we obtained disruption of GFP expression within a single cell cycle. Finally, we used either Cas9 plasmid in utero electroporation or Cas9 protein complex microinjection to disrupt the expression of Eomes/Tbr2, a gene fundamental for neocortical neurogenesis. This resulted in a reduction in basal progenitors and an increase in neuronal differentiation. Thus, the present in vivo application of the CRISPR/Cas9 system in neural stem cells provides a rapid, efficient and enduring disruption of expression of specific genes to dissect their role in mammalian brain development.
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Affiliation(s)
- Nereo Kalebic
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Elena Taverna
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Stefania Tavano
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Fong Kuan Wong
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Dana Suchold
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
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1206
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Schook LB, Rund L, Begnini KR, Remião MH, Seixas FK, Collares T. Emerging Technologies to Create Inducible and Genetically Defined Porcine Cancer Models. Front Genet 2016; 7:28. [PMID: 26973698 PMCID: PMC4770043 DOI: 10.3389/fgene.2016.00028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/13/2016] [Indexed: 12/26/2022] Open
Abstract
There is an emerging need for new animal models that address unmet translational cancer research requirements. Transgenic porcine models provide an exceptional opportunity due to their genetic, anatomic, and physiological similarities with humans. Due to recent advances in the sequencing of domestic animal genomes and the development of new organism cloning technologies, it is now very feasible to utilize pigs as a malleable species, with similar anatomic and physiological features with humans, in which to develop cancer models. In this review, we discuss genetic modification technologies successfully used to produce porcine biomedical models, in particular the Cre-loxP System as well as major advances and perspectives the CRISPR/Cas9 System. Recent advancements in porcine tumor modeling and genome editing will bring porcine models to the forefront of translational cancer research.
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Affiliation(s)
- Lawrence B Schook
- University of Illinois Cancer Center, University of Illinois at ChicagoChicago, IL, USA; Department of Animal Sciences, University of Illinois at Urbana-ChampaignChampaign, IL, USA
| | - Laurie Rund
- Department of Animal Sciences, University of Illinois at Urbana-Champaign Champaign, IL, USA
| | - Karine R Begnini
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
| | - Mariana H Remião
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
| | - Fabiana K Seixas
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
| | - Tiago Collares
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
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1207
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Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice. Nat Commun 2016; 7:10770. [PMID: 26916719 PMCID: PMC4773438 DOI: 10.1038/ncomms10770] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/19/2016] [Indexed: 12/19/2022] Open
Abstract
Mouse transgenesis has provided fundamental insights into pancreatic cancer, but is limited by the long duration of allele/model generation. Here we show transfection-based multiplexed delivery of CRISPR/Cas9 to the pancreas of adult mice, allowing simultaneous editing of multiple gene sets in individual cells. We use the method to induce pancreatic cancer and exploit CRISPR/Cas9 mutational signatures for phylogenetic tracking of metastatic disease. Our results demonstrate that CRISPR/Cas9-multiplexing enables key applications, such as combinatorial gene-network analysis, in vivo synthetic lethality screening and chromosome engineering. Negative-selection screening in the pancreas using multiplexed-CRISPR/Cas9 confirms the vulnerability of pancreatic cells to Brca2-inactivation in a Kras-mutant context. We also demonstrate modelling of chromosomal deletions and targeted somatic engineering of inter-chromosomal translocations, offering multifaceted opportunities to study complex structural variation, a hallmark of pancreatic cancer. The low-frequency mosaic pattern of transfection-based CRISPR/Cas9 delivery faithfully recapitulates the stochastic nature of human tumorigenesis, supporting wide applicability for biological/preclinical research. CRISPR/Cas9 technology has been used for genome engineering in vivo. Here, the authors use a transfection technique to deliver multiple guide RNAs to the pancreas of adult mice, allowing genetic screening and chromosome engineering in pancreatic cancer.
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1208
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Beil-Wagner J, Dössinger G, Schober K, vom Berg J, Tresch A, Grandl M, Palle P, Mair F, Gerhard M, Becher B, Busch DH, Buch T. T cell-specific inactivation of mouse CD2 by CRISPR/Cas9. Sci Rep 2016; 6:21377. [PMID: 26903281 PMCID: PMC4763270 DOI: 10.1038/srep21377] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 01/22/2016] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system can be used to mutate target sequences by introduction of double-strand breaks followed by imprecise repair. To test its use for conditional gene editing we generated mice transgenic for CD4 promoter-driven Cas9 combined with guide RNA targeting CD2. We found that within CD4(+) and CD8(+) lymphocytes from lymph nodes and spleen 1% and 0.6% were not expressing CD2, respectively. T cells lacking CD2 carryied mutations, which confirmed that Cas9 driven by cell-type specific promoters can edit genes in the mouse and may thus allow targeted studies of gene function in vivo.
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Affiliation(s)
- Jane Beil-Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Germany
- Institute of Laboratory Animal Science, University of Zurich, Schlieren, Switzerland
| | - Georg Dössinger
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Germany
| | - Johannes vom Berg
- Institute of Laboratory Animal Science, University of Zurich, Schlieren, Switzerland
| | - Achim Tresch
- Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
- Department of Biology, Albertus-Magnus University, Cologne, Germany
| | - Martina Grandl
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Germany
| | - Pushpalatha Palle
- Institute of Laboratory Animal Science, University of Zurich, Schlieren, Switzerland
| | - Florian Mair
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Germany
| | - Thorsten Buch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Germany
- Institute of Laboratory Animal Science, University of Zurich, Schlieren, Switzerland
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1209
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Porlan E, Martí-Prado B, Consiglio A, Fariñas I. Stable and Efficient Genetic Modification of Cells in the Adult Mouse V-SVZ for the Analysis of Neural Stem Cell Autonomous and Non-autonomous Effects. J Vis Exp 2016:53282. [PMID: 26967974 DOI: 10.3791/53282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Relatively quiescent somatic stem cells support life-long cell renewal in most adult tissues. Neural stem cells in the adult mammalian brain are restricted to two specific neurogenic niches: the subgranular zone of the dentate gyrus in the hippocampus and the ventricular-subventricular zone (V-SVZ; also called subependymal zone or SEZ) in the walls of the lateral ventricles. The development of in vivo gene transfer strategies for adult stem cell populations (i.e. those of the mammalian brain) resulting in long-term expression of desired transgenes in the stem cells and their derived progeny is a crucial tool in current biomedical and biotechnological research. Here, a direct in vivo method is presented for the stable genetic modification of adult mouse V-SVZ cells that takes advantage of the cell cycle-independent infection by LVs and the highly specialized cytoarchitecture of the V-SVZ niche. Specifically, the current protocol involves the injection of empty LVs (control) or LVs encoding specific transgene expression cassettes into either the V-SVZ itself, for the in vivo targeting of all types of cells in the niche, or into the lateral ventricle lumen, for the targeting of ependymal cells only. Expression cassettes are then integrated into the genome of the transduced cells and fluorescent proteins, also encoded by the LVs, allow the detection of the transduced cells for the analysis of cell autonomous and non-autonomous, niche-dependent effects in the labeled cells and their progeny.
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Affiliation(s)
- Eva Porlan
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO)
| | - Beatriz Martí-Prado
- Centro de Investigaciones Biomédicas en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Departmento de Biologìa Celular, Universidad de Valencia
| | - Antonella Consiglio
- Institut de Biomedicina de la Universitat de Barcelona (IBUB); Department of Molecular and Translational Medicine, Fibroblast Reprogramming Unit, University of Brescia;
| | - Isabel Fariñas
- Centro de Investigaciones Biomédicas en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Departmento de Biologìa Celular, Universidad de Valencia;
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1210
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CRISPR/Cas9-mediated gene knockout in the mouse brain using in utero electroporation. Sci Rep 2016; 6:20611. [PMID: 26857612 PMCID: PMC4746659 DOI: 10.1038/srep20611] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/08/2016] [Indexed: 01/23/2023] Open
Abstract
The CRISPR/Cas9 system has recently been adapted for generating knockout mice to investigate physiological functions and pathological mechanisms. Here, we report a highly efficient procedure for brain-specific disruption of genes of interest in vivo. We constructed pX330 plasmids expressing humanized Cas9 and single-guide RNAs (sgRNAs) against the Satb2 gene, which encodes an AT-rich DNA-binding transcription factor and is responsible for callosal axon projections in the developing mouse brain. We first confirmed that these constructs efficiently induced double-strand breaks (DSBs) in target sites of exogenous plasmids both in vitro and in vivo. We then found that the introduction of pX330-Satb2 into the developing mouse brain using in utero electroporation led to a dramatic reduction of Satb2 expression in the transfected cerebral cortex, suggesting DSBs had occurred in the Satb2 gene with high efficiency. Furthermore, we found that Cas9-mediated targeting of the Satb2 gene induced abnormalities in axonal projection patterns, which is consistent with the phenotypes previously observed in Satb2 mutant mice. Introduction of pX330-NeuN using our procedure also resulted in the efficient disruption of the NeuN gene. Thus, our procedure combining the CRISPR/Cas9 system and in utero electroporation is an effective and rapid approach to achieve brain-specific gene knockout in vivo.
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1211
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Bakker AC, La Rosa S, Sherman LS, Knight P, Lee H, Pancza P, Nievo M. Neurofibromatosis as a gateway to better treatment for a variety of malignancies. Prog Neurobiol 2016; 152:149-165. [PMID: 26854064 DOI: 10.1016/j.pneurobio.2016.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 12/23/2022]
Abstract
The neurofibromatoses (NF) are a group of rare genetic disorders that can affect all races equally at an incidence from 1:3000 (NF1) to a log unit lower for NF2 and schwannomatosis. Since the research community is reporting an increasing number of malignant cancers that carry mutations in the NF genes, the general interest of both the research and pharma community is increasing and the authors saw an opportunity to present a novel, fresh approach to drug discovery in NF. The aim of the paper is to challenge the current drug discovery approach to NF, whereby existing targeted therapies that are either in the clinic or on the market for other disease indications are repurposed for NF. We offer a suggestion for an alternative drug discovery approach. In the new approach, selective and tolerable targeted therapies would be developed for NF and later expanded to patients with more complex diseases such as malignant cancer in which the NF downstream pathways are deregulated. The Children's Tumor Foundation, together with some other major NF funders, is playing a key role in funding critical initiatives that will accelerate the development of better targeted therapies for NF patients, while these novel, innovative treatments could potentially be beneficial to molecularly characterized cancer patients in which NF mutations have been identified.
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Affiliation(s)
- Annette C Bakker
- Children's Tumor Foundation, 120, Wall Street, 16th Floor, New York 10005, United States
| | - Salvatore La Rosa
- Children's Tumor Foundation, 120, Wall Street, 16th Floor, New York 10005, United States
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, United States
| | - Pamela Knight
- Children's Tumor Foundation, 120, Wall Street, 16th Floor, New York 10005, United States
| | - Hyerim Lee
- Children's Tumor Foundation, 120, Wall Street, 16th Floor, New York 10005, United States
| | - Patrice Pancza
- Children's Tumor Foundation, 120, Wall Street, 16th Floor, New York 10005, United States
| | - Marco Nievo
- Children's Tumor Foundation, 120, Wall Street, 16th Floor, New York 10005, United States.
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1212
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Gutschner T, Haemmerle M, Genovese G, Draetta GF, Chin L. Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair. Cell Rep 2016; 14:1555-1566. [PMID: 26854237 DOI: 10.1016/j.celrep.2016.01.019] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/08/2015] [Accepted: 01/01/2016] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 induces DNA double-strand breaks that are repaired by cell-autonomous repair pathways, namely, non-homologous end-joining (NHEJ), or homology-directed repair (HDR). While HDR is absent in G1, NHEJ is active throughout the cell cycle and, thus, is largely favored over HDR. We devised a strategy to increase HDR by directly synchronizing the expression of Cas9 with cell-cycle progression. Fusion of Cas9 to the N-terminal region of human Geminin converted this gene-editing protein into a substrate for the E3 ubiquitin ligase complex APC/Cdh1, resulting in a cell-cycle-tailored expression with low levels in G1 but high expression in S/G2/M. Importantly, Cas9-hGem(1/110) increased the rate of HDR by up to 87% compared to wild-type Cas9. Future developments may enable high-resolution expression of genome engineering proteins, which might increase HDR rates further, and may contribute to a better understanding of DNA repair pathways due to spatiotemporal control of DNA damage induction.
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Affiliation(s)
- Tony Gutschner
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Monika Haemmerle
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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1213
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Levitz J, Popescu AT, Reiner A, Isacoff EY. A Toolkit for Orthogonal and in vivo Optical Manipulation of Ionotropic Glutamate Receptors. Front Mol Neurosci 2016; 9:2. [PMID: 26869877 PMCID: PMC4735401 DOI: 10.3389/fnmol.2016.00002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/06/2016] [Indexed: 12/16/2022] Open
Abstract
The ability to optically manipulate specific neuronal signaling proteins with genetic precision paves the way for the dissection of their roles in brain function, behavior, and disease. Chemical optogenetic control with photoswitchable tethered ligands (PTLs) enables rapid, reversible and reproducible activation or block of specific neurotransmitter-gated receptors and ion channels in specific cells. In this study, we further engineered and characterized the light-activated GluK2 kainate receptor, LiGluR, to develop a toolbox of LiGluR variants. Low-affinity LiGluRs allow for efficient optical control of GluK2 while removing activation by native glutamate, whereas variant RNA edited versions enable the synaptic role of receptors with high and low Ca2+ permeability to be assessed and spectral variant photoswitches provide flexibility in illumination. Importantly, we establish that LiGluR works efficiently in the cortex of awake, adult mice using standard optogenetic techniques, thus opening the door to probing the role of specific synaptic receptors and cellular signals in the neural circuit operations of the mammalian brain in normal conditions and in disease. The principals developed in this study are widely relevant to the engineering and in vivo use of optically controllable proteins, including other neurotransmitter receptors.
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Affiliation(s)
- Joshua Levitz
- Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Andrei T Popescu
- Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Andreas Reiner
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeley, CA, USA; Department of Biology and Biotechnology, Ruhr-University BochumBochum, Germany
| | - Ehud Y Isacoff
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeley, CA, USA; Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeley, CA, USA; Physical Bioscience Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
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1214
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Nakaya HI, Pulendran B. Vaccinology in the era of high-throughput biology. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0146. [PMID: 25964458 DOI: 10.1098/rstb.2014.0146] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced 'experimental challenge models' in humans.
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Affiliation(s)
- Helder I Nakaya
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil Emory Vaccine Center and Yerkes National Primate Research Center, Atlanta, GA 30329, USA Department of Pathology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Bali Pulendran
- Emory Vaccine Center and Yerkes National Primate Research Center, Atlanta, GA 30329, USA Department of Pathology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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1215
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Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR. Nat Neurosci 2016; 19:517-22. [PMID: 26829649 PMCID: PMC4903018 DOI: 10.1038/nn.4235] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 01/07/2016] [Indexed: 12/16/2022]
Abstract
Recurrent, reciprocal genomic disorders resulting from non-allelic homologous recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human disease, often producing phenotypically distinct syndromes. The genomic architecture of flanking SDs presents a significant challenge for modeling these syndromes; however, the capability to efficiently generate reciprocal copy number variants (CNVs) that mimic NAHR would represent an invaluable modeling tool. We describe here a CRISPR/Cas9 genome engineering method, Single-guide-CRISPR/Cas-targeting-Of-Repetitive-Elements (SCORE), to model reciprocal genomic disorders and demonstrate its capabilities by generating reciprocal CNVs of 16p11.2 and 15q13.3, including alteration of one copy-equivalent of the SDs that mediate NAHR in vivo. The method is reproducible and RNAseq reliably clusters transcriptional signatures from human subjects with in vivo CNV and their corresponding in vitro models. This new approach will provide broad applicability for the study of genomic disorders and, with further development, may also permit efficient correction of these defects.
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1216
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Mei Y, Wang Y, Chen H, Sun ZS, Ju XD. Recent Progress in CRISPR/Cas9 Technology. J Genet Genomics 2016; 43:63-75. [DOI: 10.1016/j.jgg.2016.01.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 12/30/2015] [Accepted: 01/08/2016] [Indexed: 12/26/2022]
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1217
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van de Sluis B. In-vivo genome editing using CRISPR-Cas9 to study lipid metabolism. Curr Opin Lipidol 2016; 27:92-3. [PMID: 26655294 DOI: 10.1097/mol.0000000000000264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Bart van de Sluis
- University of Groningen, University Medical Center Groningen, Molecular Genetics, Groningen, the Netherlands
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1218
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Sakurai T, Kamiyoshi A, Kawate H, Mori C, Watanabe S, Tanaka M, Uetake R, Sato M, Shindo T. A non-inheritable maternal Cas9-based multiple-gene editing system in mice. Sci Rep 2016; 6:20011. [PMID: 26817415 PMCID: PMC4730228 DOI: 10.1038/srep20011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022] Open
Abstract
The CRISPR/Cas9 system is capable of editing multiple genes through one-step zygote injection. The preexisting method is largely based on the co-injection of Cas9 DNA (or mRNA) and guide RNAs (gRNAs); however, it is unclear how many genes can be simultaneously edited by this method, and a reliable means to generate transgenic (Tg) animals with multiple gene editing has yet to be developed. Here, we employed non-inheritable maternal Cas9 (maCas9) protein derived from Tg mice with systemic Cas9 overexpression (Cas9 mice). The maCas9 protein in zygotes derived from mating or in vitro fertilization of Tg/+ oocytes and +/+ sperm could successfully edit the target genome. The efficiency of such maCas9-based genome editing was comparable to that of zygote microinjection-based genome editing widely used at present. Furthermore, we demonstrated a novel approach to create "Cas9 transgene-free" gene-modified mice using non-Tg (+/+) zygotes carrying maCas9. The maCas9 protein in mouse zygotes edited nine target loci simultaneously after injection with nine different gRNAs alone. Cas9 mouse-derived zygotes have the potential to facilitate the creation of genetically modified animals carrying the Cas9 transgene, enabling repeatable genome engineering and the production of Cas9 transgene-free mice.
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Affiliation(s)
- Takayuki Sakurai
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Akiko Kamiyoshi
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Hisaka Kawate
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Chie Mori
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Satoshi Watanabe
- Animal Genome Research Unit, Division of Animal Science, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Megumu Tanaka
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Ryuichi Uetake
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Takayuki Shindo
- Department of Cardiovascular Research, Graduate School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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1219
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Gomez EJ, Gerhardt K, Judd J, Tabor JJ, Suh J. Light-Activated Nuclear Translocation of Adeno-Associated Virus Nanoparticles Using Phytochrome B for Enhanced, Tunable, and Spatially Programmable Gene Delivery. ACS NANO 2016; 10:225-237. [PMID: 26618393 DOI: 10.1021/acsnano.5b05558] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Gene delivery vectors that are activated by external stimuli may allow improved control over the location and the degree of gene expression in target populations of cells. Light is an attractive stimulus because it does not cross-react with cellular signaling networks, has negligible toxicity, is noninvasive, and can be applied in space and time with unparalleled precision. We used the previously engineered red (R)/far-red (FR) light-switchable protein phytochrome B (PhyB) and its R light dependent interaction partner phytochrome interacting factor 6 (PIF6) from Arabidopsis thaliana to engineer an adeno-associated virus (AAV) platform whose gene delivery efficiency is controlled by light. Upon exposure to R light, AAV engineered to display PIF6 motifs on the capsid bind to PhyB tagged with a nuclear localization sequence (NLS), resulting in significantly increased translocation of viruses into the host cell nucleus and overall gene delivery efficiency. By modulating the ratio of R to FR light, the gene delivery efficiency can be tuned to as little as 35% or over 600% of the unengineered AAV. We also demonstrate spatial control of gene delivery using projected patterns of codelivered R and FR light. Overall, our successful use of light-switchable proteins in virus capsid engineering extends these important optogenetic tools into the adjacent realm of nucleic acid delivery and enables enhanced, tunable, and spatially controllable regulation of viral gene delivery. Our current light-triggered viral gene delivery prototype may be broadly useful for genetic manipulation of cells ex vivo or in vivo in transgenic model organisms, with the ultimate prospect of achieving dose- and site-specific gene expression profiles for either therapeutic (e.g., regenerative medicine) or fundamental discovery research efforts.
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Affiliation(s)
- Eric J Gomez
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Karl Gerhardt
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Justin Judd
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Jeffrey J Tabor
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
| | - Junghae Suh
- Department of Bioengineering, ‡Systems, Synthetic, and Physical Biology Program, and §Department of Biochemistry and Cell Biology, Rice University , Houston, Texas 77005, United States
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1220
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Liu T, Shen JK, Li Z, Choy E, Hornicek FJ, Duan Z. Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma. Cancer Lett 2016; 373:109-118. [PMID: 26806808 DOI: 10.1016/j.canlet.2016.01.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 02/07/2023]
Abstract
Sarcomas include some of the most aggressive tumors and typically respond poorly to chemotherapy. In recent years, specific gene fusion/mutations and gene over-expression/activation have been shown to drive sarcoma pathogenesis and development. These emerging genomic alterations may provide targets for novel therapeutic strategies and have the potential to transform sarcoma patient care. The RNA-guided nuclease CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein-9 nuclease) is a convenient and versatile platform for site-specific genome editing and epigenome targeted modulation. Given that sarcoma is believed to develop as a result of genetic alterations in mesenchymal progenitor/stem cells, CRISPR-Cas9 genome editing technologies hold extensive application potentials in sarcoma models and therapies. We review the development and mechanisms of the CRISPR-Cas9 system in genome editing and introduce its application in sarcoma research and potential therapy in clinic. Additionally, we propose future directions and discuss the challenges faced with these applications, providing concise and enlightening information for readers interested in this area.
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Affiliation(s)
- Tang Liu
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States; Department of Orthopaedic, the 2nd Xiangya Hospital of Central South University, 139 Renmin Road, Changsha, Hunan 410011, China
| | - Jacson K Shen
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Zhihong Li
- Department of Orthopaedic, the 2nd Xiangya Hospital of Central South University, 139 Renmin Road, Changsha, Hunan 410011, China
| | - Edwin Choy
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Francis J Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Zhenfeng Duan
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States.
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1221
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Abstract
Immunotherapy is now evolving into a major therapeutic option for cancer patients. Such clinical advances also promote massive interest in the search for novel immunotherapy targets, and to understand the mechanism of action of current drugs. It is projected that a series of novel immunotherapy agents will be developed and assessed for their therapeutic activity. In light of this, in vivo experimental mouse models that recapitulate human malignancies serve as valuable tools to validate the efficacy and safety profile of immunotherapy agents, before their transition into clinical trials. In this review, we will discuss the major classes of experimental mouse models of cancer commonly used for immunotherapy assessment and provide examples to guide the selection of appropriate models. We present some new data concerning the utility of a carcinogen-induced tumor model for comparing immunotherapies and combining immunotherapy with chemotherapy. We will also highlight some recent advances in experimental modeling of human malignancies in mice that are leading towards personalized therapy in patients.
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Affiliation(s)
- Shin Foong Ngiow
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia; University of Queensland, Herston, QLD, Australia
| | - Sherene Loi
- Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; University of Melbourne, Parkville, VIC, Australia
| | - David Thomas
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mark J Smyth
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia; University of Queensland, Herston, QLD, Australia; Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; University of Melbourne, Parkville, VIC, Australia.
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1222
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Chu VT, Weber T, Graf R, Sommermann T, Petsch K, Sack U, Volchkov P, Rajewsky K, Kühn R. Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnol 2016; 16:4. [PMID: 26772810 PMCID: PMC4715285 DOI: 10.1186/s12896-016-0234-4] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/07/2016] [Indexed: 01/03/2023] Open
Abstract
Background The CRISPR/Cas9 system is increasingly used for gene inactivation in mouse zygotes, but homology-directed mutagenesis and use of inbred embryos are less established. In particular, Rosa26 knock-in alleles for the insertion of transgenes in a genomic ‘safe harbor’ site, have not been produced. Here we applied CRISPR/Cas9 for the knock-in of 8–11 kb inserts into Rosa26 of C57BL/6 zygotes. Results We found that 10–20 % of live pups derived from microinjected zygotes were founder mutants, without apparent off-target effects, and up to 50 % knock-in embryos were recovered upon coinjection of Cas9 mRNA and protein. Using this approach, we established a new mouse line for the Cre/loxP-dependent expression of Cas9. Conclusions Altogether, our protocols and resources support the fast and direct generation of new Rosa26 knock-in alleles and of Cas9-mediated in vivo gene editing in the widely used C57BL/6 inbred strain. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0234-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Van Trung Chu
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Timm Weber
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Robin Graf
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | | | - Kerstin Petsch
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Ulrike Sack
- Present Address: Bayer Pharma AG Building S107, 13353, Berlin, Germany.
| | | | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany. .,Berlin Institute of Health, Kapelle-Ufer 2, 10117, Berlin, Germany.
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1223
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Lai S, Wei S, Zhao B, Ouyang Z, Zhang Q, Fan N, Liu Z, Zhao Y, Yan Q, Zhou X, Li L, Xin J, Zeng Y, Lai L, Zou Q. Generation of Knock-In Pigs Carrying Oct4-tdTomato Reporter through CRISPR/Cas9-Mediated Genome Engineering. PLoS One 2016; 11:e0146562. [PMID: 26756580 PMCID: PMC4710570 DOI: 10.1371/journal.pone.0146562] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/18/2015] [Indexed: 01/30/2023] Open
Abstract
The porcine pluripotent cells that can generate germline chimeras have not been developed. The Oct4 promoter-based fluorescent reporter system, which can be used to monitor pluripotency, is an important tool to generate authentic porcine pluripotent cells. In this study, we established a porcine Oct4 reporter system, wherein the endogenous Oct4 promoter directly controls red fluorescent protein (RFP). 2A-tdTomato sequence was inserted to replace the stop codon of the porcine Oct4 gene by homogenous recombination (HR). Thus, the fluorescence can accurately show the activation of endogenous Oct4. Porcine fetal fibroblast (PFF) lines with knock-in (KI) of the tdTomato gene in the downstream of endogenous Oct4 promoter were achieved using the CRISPR/CAS9 system. Transgenic PFFs were used as donor cells for somatic cell nuclear transfer (SCNT). Strong RFP expression was detected in the blastocysts and genital ridges of SCNT fetuses but not in other tissues. Two viable transgenic piglets were also produced by SCNT. Reprogramming of fibroblasts from the fetuses and piglets by another round of SCNT resulted in tdTomato reactivation in reconstructed blastocysts. Result indicated that a KI porcine reporter system to monitor the pluripotent status of cells was successfully developed.
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Affiliation(s)
- Sisi Lai
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shu Wei
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Bentian Zhao
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhen Ouyang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Quanjun Zhang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Nana Fan
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhaoming Liu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yu Zhao
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Quanmei Yan
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoqing Zhou
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Li Li
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jige Xin
- Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Animal Science and Technology College, Yunnan Agricultural University, Kunming, China
| | - Yangzhi Zeng
- Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Animal Science and Technology College, Yunnan Agricultural University, Kunming, China
| | - Liangxue Lai
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Qingjian Zou
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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1224
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Carroll KJ, Makarewich CA, McAnally J, Anderson DM, Zentilin L, Liu N, Giacca M, Bassel-Duby R, Olson EN. A mouse model for adult cardiac-specific gene deletion with CRISPR/Cas9. Proc Natl Acad Sci U S A 2016; 113:338-43. [PMID: 26719419 PMCID: PMC4720342 DOI: 10.1073/pnas.1523918113] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas)9 genomic editing has revolutionized the generation of mutant animals by simplifying the creation of null alleles in virtually any organism. However, most current approaches with this method require zygote injection, making it difficult to assess the adult, tissue-specific functions of genes that are widely expressed or which cause embryonic lethality when mutated. Here, we describe the generation of cardiac-specific Cas9 transgenic mice, which express high levels of Cas9 in the heart, but display no overt defects. In proof-of-concept experiments, we used Adeno-Associated Virus 9 (AAV9) to deliver single-guide RNA (sgRNA) that targets the Myh6 locus exclusively in cardiomyocytes. Intraperitoneal injection of postnatal cardiac-Cas9 transgenic mice with AAV9 encoding sgRNA against Myh6 resulted in robust editing of the Myh6 locus. These mice displayed severe cardiomyopathy and loss of cardiac function, with elevation of several markers of heart failure, confirming the effectiveness of this method of adult cardiac gene deletion. Mice with cardiac-specific expression of Cas9 provide a tool that will allow rapid and accurate deletion of genes following a single injection of AAV9-sgRNAs, thereby circumventing embryonic lethality. This method will be useful for disease modeling and provides a means of rapidly editing genes of interest in the heart.
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Affiliation(s)
- Kelli J Carroll
- Department of Molecular Biology and the Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148
| | - Catherine A Makarewich
- Department of Molecular Biology and the Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148
| | - John McAnally
- Department of Molecular Biology and the Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148
| | - Douglas M Anderson
- Department of Molecular Biology and the Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148
| | - Lorena Zentilin
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy
| | - Ning Liu
- Department of Molecular Biology and the Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy
| | - Rhonda Bassel-Duby
- Department of Molecular Biology and the Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148
| | - Eric N Olson
- Department of Molecular Biology and the Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148;
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1225
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Walters BJ, Azam AB, Gillon CJ, Josselyn SA, Zovkic IB. Advanced In vivo Use of CRISPR/Cas9 and Anti-sense DNA Inhibition for Gene Manipulation in the Brain. Front Genet 2016; 6:362. [PMID: 26793235 PMCID: PMC4709581 DOI: 10.3389/fgene.2015.00362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/19/2015] [Indexed: 12/28/2022] Open
Abstract
Gene editing tools are essential for uncovering how genes mediate normal brain-behavior relationships and contribute to neurodegenerative and neuropsychiatric disorders. Recent progress in gene editing technology now allows neuroscientists unprecedented access to edit the genome efficiently. Although many important tools have been developed, here we focus on approaches that allow for rapid gene editing in the adult nervous system, particularly CRISPR/Cas9 and anti-sense nucleotide-based techniques. CRISPR/Cas9 is a flexible gene editing tool, allowing the genome to be manipulated in diverse ways. For instance, CRISPR/Cas9 has been successfully used to knockout genes, knock-in mutations, overexpress or inhibit gene activity, and provide scaffolding for recruiting specific epigenetic regulators to individual genes and gene regions. Moreover, the CRISPR/Cas9 system may be modified to target multiple genes at one time, affording simultaneous inhibition and overexpression of distinct genetic targets. Although many of the more advanced applications of CRISPR/Cas9 have not been applied to the nervous system, the toolbox is widely accessible, such that it is poised to help advance neuroscience. Anti-sense nucleotide-based technologies can be used to rapidly knockdown genes in the brain. The main advantage of anti-sense based tools is their simplicity, allowing for rapid gene delivery with minimal technical expertise. Here, we describe the main applications and functions of each of these systems with an emphasis on their many potential applications in neuroscience laboratories.
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Affiliation(s)
- Brandon J Walters
- Department of Neuroscience and Mental Health, The Hospital for Sick Children Toronto, ON, Canada
| | - Amber B Azam
- Department of Psychology, University of Toronto Mississauga Mississauga, ON, Canada
| | - Colleen J Gillon
- Department of Neuroscience and Mental Health, The Hospital for Sick ChildrenToronto, ON, Canada; Department of Physiology, University of TorontoToronto, ON, Canada
| | - Sheena A Josselyn
- Department of Neuroscience and Mental Health, The Hospital for Sick ChildrenToronto, ON, Canada; Department of Physiology, University of TorontoToronto, ON, Canada
| | - Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga Mississauga, ON, Canada
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1226
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Yeung TL, Leung CS, Li F, Wong SST, Mok SC. Targeting Stromal-Cancer Cell Crosstalk Networks in Ovarian Cancer Treatment. Biomolecules 2016; 6:3. [PMID: 26751490 PMCID: PMC4808797 DOI: 10.3390/biom6010003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/20/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Ovarian cancer is a histologically, clinically, and molecularly diverse disease with a five-year survival rate of less than 30%. It has been estimated that approximately 21,980 new cases of epithelial ovarian cancer will be diagnosed and 14,270 deaths will occur in the United States in 2015, making it the most lethal gynecologic malignancy. Ovarian tumor tissue is composed of cancer cells and a collection of different stromal cells. There is increasing evidence that demonstrates that stromal involvement is important in ovarian cancer pathogenesis. Therefore, stroma-specific signaling pathways, stroma-derived factors, and genetic changes in the tumor stroma present unique opportunities for improving the diagnosis and treatment of ovarian cancer. Cancer-associated fibroblasts (CAFs) are one of the major components of the tumor stroma that have demonstrated supportive roles in tumor progression. In this review, we highlight various types of signaling crosstalk between ovarian cancer cells and stromal cells, particularly with CAFs. In addition to evaluating the importance of signaling crosstalk in ovarian cancer progression, we discuss approaches that can be used to target tumor-promoting signaling crosstalk and how these approaches can be translated into potential ovarian cancer treatment.
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Affiliation(s)
- Tsz-Lun Yeung
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Cecilia S Leung
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Fuhai Li
- Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA.
| | - Stephen S T Wong
- Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA.
- National Cancer Institute Center for Modeling Cancer Development, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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1227
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Sim DS, Kauser K. In Vivo Target Validation Using Biological Molecules in Drug Development. Handb Exp Pharmacol 2016; 232:59-70. [PMID: 26552401 DOI: 10.1007/164_2015_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Drug development is a resource-intensive process requiring significant financial and time investment. Preclinical target validation studies and in vivo testing of the therapeutic molecules in clinically relevant disease models can accelerate and significantly de-risk later stage clinical development. In this chapter, we will focus on (1) in vivo animal models and (2) pharmacological tools for target validation.
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Affiliation(s)
- Derek S Sim
- Bayer HealthCare, 455 Mission Bay Blvd. South, Suite 493, San Francisco, CA, 94158, USA.
| | - Katalin Kauser
- Bayer HealthCare, 455 Mission Bay Blvd. South, Suite 493, San Francisco, CA, 94158, USA
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1228
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Sun L, Lutz BM, Tao YX. The CRISPR/Cas9 system for gene editing and its potential application in pain research. TRANSLATIONAL PERIOPERATIVE AND PAIN MEDICINE 2016; 1:22-33. [PMID: 27500183 PMCID: PMC4971521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The CRISPR/Cas9 system is a research hotspot in genome editing and regulation. Currently, it is used in genomic silencing and knock-in experiments as well as transcriptional activation and repression. This versatile system consists of two components: a guide RNA (gRNA) and a Cas9 nuclease. Recognition of a genomic DNA target is mediated through base pairing with a 20-base gRNA. The latter further recruits the Cas9 endonuclease protein to the target site and creates double-stranded breaks in the target DNA. Compared with traditional genome editing directed by DNA-binding protein domains, this short RNA-directed Cas9 endonuclease system is simple and easily programmable. Although this system may have off-target effects and in vivo delivery and immune challenges, researchers have employed this system in vivo to establish disease models, study specific gene functions under certain disease conditions, and correct genomic information for disease treatment. In regards to pain research, the CRISPR/Cas9 system may act as a novel tool in gene correction therapy for pain-associated hereditary diseases and may be a new approach for RNA-guided transcriptional activation or repression of pain-related genes. In addition, this system is also applied to loss-of-function mutations in pain-related genes and knockin of reporter genes or loxP tags at pain-related genomic loci. The CRISPR/Cas9 system will likely be carried out widely in both bench work and clinical settings in the pain field.
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Affiliation(s)
- Linlin Sun
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Brianna Marie Lutz
- Rutgers Graduate School of Biomedical Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Yuan-Xiang Tao
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Rutgers Graduate School of Biomedical Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Departments of Cell Biology & Molecular Medicine, Physiology, Pharmacology, & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
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1229
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Sun N, Tischfield JA, King RA, Heiman GA. Functional Evaluations of Genes Disrupted in Patients with Tourette's Disorder. Front Psychiatry 2016; 7:11. [PMID: 26903887 PMCID: PMC4746269 DOI: 10.3389/fpsyt.2016.00011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/18/2016] [Indexed: 01/04/2023] Open
Abstract
Tourette's disorder (TD) is a highly heritable neurodevelopmental disorder with complex genetic architecture and unclear neuropathology. Disruptions of particular genes have been identified in subsets of TD patients. However, none of the findings have been replicated, probably due to the complex and heterogeneous genetic architecture of TD that involves both common and rare variants. To understand the etiology of TD, functional analyses are required to characterize the molecular and cellular consequences caused by mutations in candidate genes. Such molecular and cellular alterations may converge into common biological pathways underlying the heterogeneous genetic etiology of TD patients. Herein, we review specific genes implicated in TD etiology, discuss the functions of these genes in the mammalian central nervous system and the corresponding behavioral anomalies exhibited in animal models, and importantly, review functional analyses that can be performed to evaluate the role(s) that the genetic disruptions might play in TD. Specifically, the functional assays include novel cell culture systems, genome editing techniques, bioinformatics approaches, transcriptomic analyses, and genetically modified animal models applied or developed to study genes associated with TD or with other neurodevelopmental and neuropsychiatric disorders. By describing methods used to study diseases with genetic architecture similar to TD, we hope to develop a systematic framework for investigating the etiology of TD and related disorders.
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Affiliation(s)
- Nawei Sun
- Department of Genetics, Rutgers University, Piscataway, NJ, USA; Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics, Rutgers University, Piscataway, NJ, USA; Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Robert A King
- Child Study Center, Yale School of Medicine , New Haven, CT , USA
| | - Gary A Heiman
- Department of Genetics, Rutgers University, Piscataway, NJ, USA; Human Genetics Institute of New Jersey, Piscataway, NJ, USA
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1230
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De Santis F, Di Donato V, Del Bene F. Clonal analysis of gene loss of function and tissue-specific gene deletion in zebrafish via CRISPR/Cas9 technology. Methods Cell Biol 2016; 135:171-88. [DOI: 10.1016/bs.mcb.2016.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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1231
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Parant JM, Yeh JRJ. Approaches to Inactivate Genes in Zebrafish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:61-86. [PMID: 27165349 DOI: 10.1007/978-3-319-30654-4_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Animal models of tumor initiation and tumor progression are essential components toward understanding cancer and designing/validating future therapies. Zebrafish is a powerful model for studying tumorigenesis and has been successfully exploited in drug discovery. According to the zebrafish reference genome, 82 % of disease-associated genes in the Online Mendelian Inheritance in Man (OMIM) database have clear zebrafish orthologues. Using a variety of large-scale random mutagenesis methods developed to date, zebrafish can provide a unique opportunity to identify gene mutations that may be associated with cancer predisposition. On the other hand, newer technologies enabling targeted mutagenesis can facilitate reverse cancer genetic studies and open the door for complex genetic analysis of tumorigenesis. In this chapter, we will describe the various technologies for conducting genome editing in zebrafish with special emphasis on the approaches to inactivate genes.
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Affiliation(s)
- John M Parant
- Department of Pharmacology and Toxicology, UAB Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35294, USA.
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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1232
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Castrillo JI, Oliver SG. Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks. Methods Mol Biol 2016; 1303:3-48. [PMID: 26235058 DOI: 10.1007/978-1-4939-2627-5_1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD), and many neurodegenerative disorders, are multifactorial in nature. They involve a combination of genomic, epigenomic, interactomic and environmental factors. Progress is being made, and these complex diseases are beginning to be understood as having their origin in altered states of biological networks at the cellular level. In the case of AD, genomic susceptibility and mechanisms leading to (or accompanying) the impairment of the central Amyloid Precursor Protein (APP) processing and tau networks are widely accepted as major contributors to the diseased state. The derangement of these networks may result in both the gain and loss of functions, increased generation of toxic species (e.g., toxic soluble oligomers and aggregates) and imbalances, whose effects can propagate to supra-cellular levels. Although well sustained by empirical data and widely accepted, this global perspective often overlooks the essential roles played by the main counteracting homeostatic networks (e.g., protein quality control/proteostasis, unfolded protein response, protein folding chaperone networks, disaggregases, ER-associated degradation/ubiquitin proteasome system, endolysosomal network, autophagy, and other stress-protective and clearance networks), whose relevance to AD is just beginning to be fully realized. In this chapter, an integrative perspective is presented. Alzheimer's disease is characterized to be a result of: (a) intrinsic genomic/epigenomic susceptibility and, (b) a continued dynamic interplay between the deranged networks and the central homeostatic networks of nerve cells. This interplay of networks will underlie both the onset and rate of progression of the disease in each individual. Integrative Systems Biology approaches are required to effect its elucidation. Comprehensive Systems Biology experiments at different 'omics levels in simple model organisms, engineered to recapitulate the basic features of AD may illuminate the onset and sequence of events underlying AD. Indeed, studies of models of AD in simple organisms, differentiated cells in culture and rodents are beginning to offer hope that the onset and progression of AD, if detected at an early stage, may be stopped, delayed, or even reversed, by activating or modulating networks involved in proteostasis and the clearance of toxic species. In practice, the incorporation of next-generation neuroimaging, high-throughput and computational approaches are opening the way towards early diagnosis well before irreversible cell death. Thus, the presence or co-occurrence of: (a) accumulation of toxic Aβ oligomers and tau species; (b) altered splicing and transcriptome patterns; (c) impaired redox, proteostatic, and metabolic networks together with, (d) compromised homeostatic capacities may constitute relevant 'AD hallmarks at the cellular level' towards reliable and early diagnosis. From here, preventive lifestyle changes and tailored therapies may be investigated, such as combined strategies aimed at both lowering the production of toxic species and potentiating homeostatic responses, in order to prevent or delay the onset, and arrest, alleviate, or even reverse the progression of the disease.
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Affiliation(s)
- Juan I Castrillo
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,
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1233
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Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA, Castellanos Rivera RM, Madhavan S, Pan X, Ran FA, Yan WX, Asokan A, Zhang F, Duan D, Gersbach CA. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 2015; 351:403-7. [PMID: 26721684 DOI: 10.1126/science.aad5143] [Citation(s) in RCA: 818] [Impact Index Per Article: 90.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/07/2015] [Indexed: 12/12/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a devastating disease affecting about 1 out of 5000 male births and caused by mutations in the dystrophin gene. Genome editing has the potential to restore expression of a modified dystrophin gene from the native locus to modulate disease progression. In this study, adeno-associated virus was used to deliver the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system to the mdx mouse model of DMD to remove the mutated exon 23 from the dystrophin gene. This includes local and systemic delivery to adult mice and systemic delivery to neonatal mice. Exon 23 deletion by CRISPR-Cas9 resulted in expression of the modified dystrophin gene, partial recovery of functional dystrophin protein in skeletal myofibers and cardiac muscle, improvement of muscle biochemistry, and significant enhancement of muscle force. This work establishes CRISPR-Cas9-based genome editing as a potential therapy to treat DMD.
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Affiliation(s)
- Christopher E Nelson
- Department of Biomedical Engineering, Duke University, Durham, NC, USA. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Chady H Hakim
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - David G Ousterout
- Department of Biomedical Engineering, Duke University, Durham, NC, USA. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Pratiksha I Thakore
- Department of Biomedical Engineering, Duke University, Durham, NC, USA. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, NC, USA. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Ruth M Castellanos Rivera
- Gene Therapy Center, Departments of Genetics, Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarina Madhavan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Xiufang Pan
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - F Ann Ran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Winston X Yan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Graduate Program in Biophysics, Harvard Medical School, Boston, MA, USA. Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Aravind Asokan
- Gene Therapy Center, Departments of Genetics, Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dongsheng Duan
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA. Department of Neurology, University of Missouri, Columbia, MO, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA. Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, USA.
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1234
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Day CP, Merlino G, Van Dyke T. Preclinical mouse cancer models: a maze of opportunities and challenges. Cell 2015; 163:39-53. [PMID: 26406370 DOI: 10.1016/j.cell.2015.08.068] [Citation(s) in RCA: 402] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/20/2022]
Abstract
Significant advances have been made in developing novel therapeutics for cancer treatment, and targeted therapies have revolutionized the treatment of some cancers. Despite the promise, only about five percent of new cancer drugs are approved, and most fail due to lack of efficacy. The indication is that current preclinical methods are limited in predicting successful outcomes. Such failure exacts enormous cost, both financial and in the quality of human life. This Primer explores the current status, promise, and challenges of preclinical evaluation in advanced mouse cancer models and briefly addresses emerging models for early-stage preclinical development.
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Affiliation(s)
- Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Terry Van Dyke
- Center for Advanced Preclinical Research, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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1235
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Rahdar M, McMahon MA, Prakash TP, Swayze EE, Bennett CF, Cleveland DW. Synthetic CRISPR RNA-Cas9-guided genome editing in human cells. Proc Natl Acad Sci U S A 2015; 112:E7110-7. [PMID: 26589814 PMCID: PMC4697396 DOI: 10.1073/pnas.1520883112] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genome editing with the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 nuclease system is a powerful technology for manipulating genomes, including introduction of gene disruptions or corrections. Here we develop a chemically modified, 29-nucleotide synthetic CRISPR RNA (scrRNA), which in combination with unmodified transactivating crRNA (tracrRNA) is shown to functionally replace the natural guide RNA in the CRISPR-Cas9 nuclease system and to mediate efficient genome editing in human cells. Incorporation of rational chemical modifications known to protect against nuclease digestion and stabilize RNA-RNA interactions in the tracrRNA hybridization region of CRISPR RNA (crRNA) yields a scrRNA with enhanced activity compared with the unmodified crRNA and comparable gene disruption activity to the previously published single guide RNA. Taken together, these findings provide a platform for therapeutic applications, especially for nervous system disease, using successive application of cell-permeable, synthetic CRISPR RNAs to activate and then silence Cas9 nuclease activity.
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Affiliation(s)
| | - Moira A McMahon
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093
| | | | | | | | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093
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1236
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Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol 2015; 17:5-15. [PMID: 26670017 DOI: 10.1038/nrm.2015.2] [Citation(s) in RCA: 569] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterial CRISPR-Cas9 system has emerged as a multifunctional platform for sequence-specific regulation of gene expression. This Review describes the development of technologies based on nuclease-deactivated Cas9, termed dCas9, for RNA-guided genomic transcription regulation, both by repression through CRISPR interference (CRISPRi) and by activation through CRISPR activation (CRISPRa). We highlight different uses in diverse organisms, including bacterial and eukaryotic cells, and summarize current applications of harnessing CRISPR-dCas9 for multiplexed, inducible gene regulation, genome-wide screens and cell fate engineering. We also provide a perspective on future developments of the technology and its applications in biomedical research and clinical studies.
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1237
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Kannan R, Ventura A. The CRISPR revolution and its impact on cancer research. Swiss Med Wkly 2015; 145:w14230. [PMID: 26661454 DOI: 10.4414/smw.2015.14230] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A revolution in cancer research is underway. Spurred by the advent of the CRISPR-Cas9 technology, new methods to probe the mammalian genomes are being developed. By providing simple, flexible, and cost-effective ways to edit and manipulate the genome of somatic cells of adult animals, these new methods present the opportunity to model cancer progression in vivo with an unprecedented degree of sophistication. Here we provide a brief overview of this exciting and fast-moving field.
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Affiliation(s)
- Ram Kannan
- Memorial Sloan Kettering Cancer Center, Cancer Biology and Genetics Program, New York
| | - Andrea Ventura
- Memorial Sloan Kettering Cancer Center, Cancer Biology and Genetics Program, New York, USA
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1238
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Abstract
Genome-editing tools, and in particular those based on CRISPR-Cas (clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein) systems, are accelerating the pace of biological research and enabling targeted genetic interrogation in almost any organism and cell type. These tools have opened the door to the development of new model systems for studying the complexity of the nervous system, including animal models and stem cell-derived in vitro models. Precise and efficient gene editing using CRISPR-Cas systems has the potential to advance both basic and translational neuroscience research.
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1239
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Abstract
PURPOSE OF REVIEW This review discusses the ways that rodent models of autism spectrum disorders (ASDs) have been used to gain critical information about convergent molecular pathways, the mechanisms underlying altered microcircuit structure and function, and as a screen for potential cutting edge-treatments for ASDs. RECENT FINDINGS There is convergent evidence that impaired developmental pruning of connections may be a common finding among several mouse models of ASDs. Recent studies have uncovered impaired autophagy by pathological mTOR activation as a potential contributor to microcircuit dysfunction and behavior. ASD-related disinhibition and exaggerated synaptic plasticity in multiple distinct circuits in cortex and reward circuits in striatum also contribute to social dysfunction and repetitive behaviors. New exciting molecular therapeutic techniques have reversed cognitive deficits in models of ASD, indicating that mouse models could be used for preclinical translational studies of new treatments. SUMMARY Rodent models of ASDs coupled to new emerging technologies for genome editing, cell-specific functional and structural imaging, and neuronal activity manipulation will yield critical insights into ASD pathogenesis and fuel the emergence of new treatments.
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1240
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Deshpande K, Vyas A, Balakrishnan A, Vyas D. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Genetic Engineering: Robotic Genetic Surgery. ACTA ACUST UNITED AC 2015; 2:49-52. [PMID: 27453936 DOI: 10.1166/ajrs.2015.1023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As a novel technology that utilizes the endogenous immune defense system in bacteria, CRISPR/Cas9 has transcended DNA engineering into a more pragmatic and clinically efficacious field. Using programmable sgRNA sequences and nucleases, the system effectively introduces double strand breaks in target genes within an entire organism. The applications of CRISPR range from biomedicine to drug development and epigenetic modification. Studies have demonstrated CRISPR mediated targeting of various tumorigenic genes and effector proteins known to be involved in colon carcinomas. This technology significantly expands the scope of gene manipulation and allows for an enhanced modeling of colon cancers, as well as various other malignancies.
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Affiliation(s)
- Kaivalya Deshpande
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, United States
| | - Arpita Vyas
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, United States
| | - Archana Balakrishnan
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, United States
| | - Dinesh Vyas
- Texas Tech University Health Sciences Center, Department of Surgery, 61391 ODE Surgery
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1241
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Abstract
CRISPR-based approaches have quickly become a favored method to perturb genes to uncover their functions. Here, we review the key considerations in the design of genome editing experiments, and survey the tools and resources currently available to assist users of this technology.
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Affiliation(s)
- Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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1242
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Weeden CE, Solomon B, Asselin-Labat ML. FGFR1 inhibition in lung squamous cell carcinoma: questions and controversies. Cell Death Discov 2015; 1:15049. [PMID: 27551478 PMCID: PMC4979434 DOI: 10.1038/cddiscovery.2015.49] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/17/2015] [Indexed: 12/29/2022] Open
Abstract
Although the incidence of lung cancer has decreased due to the reduction of tobacco use, lung cancer remains the leading cause of cancer-related death. Lung squamous cell carcinoma represents 30% of lung cancers and only recently have possible drug-targetable mutations been identified in this disease, including fibroblast growth factor receptor 1 (FGFR1) gene amplification and genetic alterations in the phosphoinositide-3 kinase pathway. These discoveries have generated a great interest in the clinic and the initiation of clinical trials using FGFR tyrosine kinase inhibitors to treat FGFR-altered lung cancers. However, preliminary results from these studies have shown that not all patients respond to therapy. Here we review current unresolved questions on the selection of patients for their recruitment in FGFR tyrosine kinase inhibitor trials, how FGFR inhibitors could be combined with other targeted therapies or immunotherapies to improve patient outcome, and how the current preclinical models can help address these questions.
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Affiliation(s)
- CE Weeden
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - B Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - M-L Asselin-Labat
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
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1243
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Lin WC, Tsai MC, Davenport CM, Smith CM, Veit J, Wilson NM, Adesnik H, Kramer RH. A Comprehensive Optogenetic Pharmacology Toolkit for In Vivo Control of GABA(A) Receptors and Synaptic Inhibition. Neuron 2015; 88:879-891. [PMID: 26606997 DOI: 10.1016/j.neuron.2015.10.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/21/2015] [Accepted: 10/01/2015] [Indexed: 01/27/2023]
Abstract
Exogenously expressed opsins are valuable tools for optogenetic control of neurons in circuits. A deeper understanding of neural function can be gained by bringing control to endogenous neurotransmitter receptors that mediate synaptic transmission. Here we introduce a comprehensive optogenetic toolkit for controlling GABA(A) receptor-mediated inhibition in the brain. We developed a series of photoswitch ligands and the complementary genetically modified GABA(A) receptor subunits. By conjugating the two components, we generated light-sensitive versions of the entire GABA(A) receptor family. We validated these light-sensitive receptors for applications across a broad range of spatial scales, from subcellular receptor mapping to in vivo photo-control of visual responses in the cerebral cortex. Finally, we generated a knockin mouse in which the "photoswitch-ready" version of a GABA(A) receptor subunit genomically replaces its wild-type counterpart, ensuring normal receptor expression. This optogenetic pharmacology toolkit allows scalable interrogation of endogenous GABA(A) receptor function with high spatial, temporal, and biochemical precision.
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Affiliation(s)
- Wan-Chen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ming-Chi Tsai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher M Davenport
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Caleb M Smith
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Julia Veit
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Neil M Wilson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hillel Adesnik
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Richard H Kramer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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1244
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Kaulich M, Dowdy SF. Combining CRISPR/Cas9 and rAAV Templates for Efficient Gene Editing. Nucleic Acid Ther 2015; 25:287-96. [PMID: 26540648 DOI: 10.1089/nat.2015.0545] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Altering endogenous genes in cells is an integral tool of modern cell biology. The ease-of-use of the CRISPR/Cas9 system to introduce genomic DNA breaks at specific sites in vivo has led to its rapid and wide adoption. In the absence of a DNA template, the lesion is repaired by nonhomologous end joining resolving as internal deletions. However, in the presence of a homologous DNA template, homology-directed repair occurs with variable efficiencies. Recent work has demonstrated that highly efficient gene targeting can be induced by combining CRISPR/Cas9 targeting of genomic loci with recombinant adeno-associated virus (rAAV) to provide a single-stranded homologous DNA template. Here we review the current state of CRISPR/Cas-based gene editing and provide a practical guide to applying the CRISPR/Cas and rAAV system for highly efficient, time- and cost-effective gene targeting.
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Affiliation(s)
- Manuel Kaulich
- Department of Cellular and Molecular Medicine, University of California , San Diego, La Jolla, California
| | - Steven F Dowdy
- Department of Cellular and Molecular Medicine, University of California , San Diego, La Jolla, California
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1245
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Stewart MP, Lorenz A, Dahlman J, Sahay G. Challenges in carrier-mediated intracellular delivery: moving beyond endosomal barriers. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 8:465-78. [PMID: 26542891 DOI: 10.1002/wnan.1377] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/07/2015] [Accepted: 09/15/2015] [Indexed: 01/08/2023]
Abstract
The deployment of molecular to microscale carriers for intracellular delivery has tremendous potential for biology and medicine, especially for in vivo therapies. The field remains limited, however, by a poor understanding of how carriers gain access to the cell interior. In this review, we provide an overview of the different types of carriers, their speculated modes of entry, putative pathways of vesicular transport, and sites of endosomal escape. We compare this alongside pertinent examples from the cell biology of how viruses, bacteria, and their effectors enter cells and escape endosomal confinement. We anticipate insights into the mechanisms of cellular entry and endosomal escape will benefit future research efforts on effective carrier-mediated intracellular delivery. WIREs Nanomed Nanobiotechnol 2016, 8:465-478. doi: 10.1002/wnan.1377 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Martin P Stewart
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna Lorenz
- Department of Pharmaceutical Sciences, OSU/OHSU College of Pharmacy, Portland, OR, USA
| | - James Dahlman
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gaurav Sahay
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pharmaceutical Sciences, OSU/OHSU College of Pharmacy, Portland, OR, USA
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1246
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Qi H, Li BZ, Zhang WQ, Liu D, Yuan YJ. Modularization of genetic elements promotes synthetic metabolic engineering. Biotechnol Adv 2015; 33:1412-9. [DOI: 10.1016/j.biotechadv.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/12/2015] [Accepted: 04/05/2015] [Indexed: 01/24/2023]
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1247
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Bowtell DD, Böhm S, Ahmed AA, Aspuria PJ, Bast RC, Beral V, Berek JS, Birrer MJ, Blagden S, Bookman MA, Brenton JD, Chiappinelli KB, Martins FC, Coukos G, Drapkin R, Edmondson R, Fotopoulou C, Gabra H, Galon J, Gourley C, Heong V, Huntsman DG, Iwanicki M, Karlan BY, Kaye A, Lengyel E, Levine DA, Lu KH, McNeish IA, Menon U, Narod SA, Nelson BH, Nephew KP, Pharoah P, Powell DJ, Ramos P, Romero IL, Scott CL, Sood AK, Stronach EA, Balkwill FR. Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer. Nat Rev Cancer 2015; 15:668-79. [PMID: 26493647 PMCID: PMC4892184 DOI: 10.1038/nrc4019] [Citation(s) in RCA: 788] [Impact Index Per Article: 87.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) accounts for 70-80% of ovarian cancer deaths, and overall survival has not changed significantly for several decades. In this Opinion article, we outline a set of research priorities that we believe will reduce incidence and improve outcomes for women with this disease. This 'roadmap' for HGSOC was determined after extensive discussions at an Ovarian Cancer Action meeting in January 2015.
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Affiliation(s)
- David D Bowtell
- Cancer Genomics and Genetics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 8006, Australia; and the Kinghorn Cancer Centre, Garvan Institute for Medical Research, Darlinghurst, Sydney, 2010 New South Wales, Australia
| | - Steffen Böhm
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M6BQ, UK
| | - Ahmed A Ahmed
- Nuffield Department of Obstetrics and Gynaecology and the Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Paul-Joseph Aspuria
- Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, California 90048, USA
| | - Robert C Bast
- MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, USA
| | - Valerie Beral
- University of Oxford, Headington, Oxford, OX3 7LF, UK
| | | | | | - Sarah Blagden
- Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | | | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | | | - Filipe Correia Martins
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - George Coukos
- University Hospital of Lausanne, Lausanne, Switzerland
| | - Ronny Drapkin
- University of Pennsylvania, Penn Ovarian Cancer Research Center, Philadelphia, Pennsylvania 19104, USA
| | | | - Christina Fotopoulou
- Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Jérôme Galon
- Institut National de la Santé et de la Recherche Médicale, UMRS1138, Laboratory of Integrative Cancer Immunology, Cordeliers Research Center, Université Paris Descartes, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ Paris 06, 75006 Paris, France
| | - Charlie Gourley
- Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Valerie Heong
- Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia
| | - David G Huntsman
- University of British Columbia, Departments of Pathology and Laboratory Medicine and Obstetrics and Gynecology, Faculty of Medicine, Vancouver, British Columbia V6T 2B5, Canada
| | | | - Beth Y Karlan
- Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, California 90048, USA
| | | | | | - Douglas A Levine
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Karen H Lu
- MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, USA
| | | | - Usha Menon
- Women's Cancer, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Steven A Narod
- Women's College Research Institute, Toronto, Ontario M5G 1N8, Canada
| | - Brad H Nelson
- British Columbia Cancer Agency, Victoria, British Columbia V8R 6V5, Canada
| | - Kenneth P Nephew
- Indiana University School of Medicine &Simon Cancer Center, Bloomington, IN 47405-4401, USA
| | - Paul Pharoah
- University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Daniel J Powell
- University of Pennsylvania, Philadelphia, PA 19104-5156, USA
| | - Pilar Ramos
- Translational Genomics Research Institute (Tgen), Phoenix, Arizona 85004, USA
| | | | - Clare L Scott
- Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia
| | - Anil K Sood
- MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, USA
| | - Euan A Stronach
- Ovarian Cancer Action Research Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Frances R Balkwill
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M6BQ, UK
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1248
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Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJK, Ebrahimkhani MR, Collins JJ, Weiss R, Church G. Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods 2015; 12:1051-4. [PMID: 26344044 PMCID: PMC4666719 DOI: 10.1038/nmeth.3580] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/10/2015] [Indexed: 12/18/2022]
Abstract
We demonstrate that by altering the length of Cas9-associated guide RNA (gRNA) we were able to control Cas9 nuclease activity and simultaneously perform genome editing and transcriptional regulation with a single Cas9 protein. We exploited these principles to engineer mammalian synthetic circuits with combined transcriptional regulation and kill functions governed by a single multifunctional Cas9 protein.
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Affiliation(s)
- Samira Kiani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alejandro Chavez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Marcelle Tuttle
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Richard N Hall
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Raj Chari
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Dmitry Ter-Ovanesyan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason Qian
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin W Pruitt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts, USA
| | - Suhani Vora
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joanna Buchthal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Emma J K Kowal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Mohammad R Ebrahimkhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Emergent Behaviors of Integrated Cellular Systems (EBICS), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Institute for Medical Engineering &Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Emergent Behaviors of Integrated Cellular Systems (EBICS), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - George Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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1249
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Dahlman JE, Abudayyeh OO, Joung J, Gootenberg JS, Zhang F, Konermann S. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat Biotechnol 2015; 33:1159-61. [PMID: 26436575 PMCID: PMC4747789 DOI: 10.1038/nbt.3390] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 09/28/2015] [Indexed: 11/08/2022]
Abstract
We have developed a CRISPR-based method that uses catalytically active Cas9 and distinct single guide (sgRNA) constructs to knock out and activate different genes in the same cell. These sgRNAs, with 14- to 15-bp target sequences and MS2 binding loops, can activate gene expression using an active Streptococcus pyogenes Cas9 nuclease, without inducing double-stranded breaks. We use these 'dead RNAs' to perform orthogonal gene knockout and transcriptional activation in human cells.
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1250
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CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice. Proc Natl Acad Sci U S A 2015; 112:13982-7. [PMID: 26508638 DOI: 10.1073/pnas.1512392112] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here, we show CRISPR/Cas9-based targeted somatic multiplex-mutagenesis and its application for high-throughput analysis of gene function in mice. Using hepatic single guide RNA (sgRNA) delivery, we targeted large gene sets to induce hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC). We observed Darwinian selection of target genes, which suppress tumorigenesis in the respective cellular/tissue context, such as Pten or Cdkn2a, and conversely found low frequency of Brca1/2 alterations, explaining mutational spectra in human ICC/HCC. Our studies show that multiplexed CRISPR/Cas9 can be used for recessive genetic screening or high-throughput cancer gene validation in mice. The analysis of CRISPR/Cas9-induced tumors provided support for a major role of chromatin modifiers in hepatobiliary tumorigenesis, including that of ARID family proteins, which have recently been reported to be mutated in ICC/HCC. We have also comprehensively characterized the frequency and size of chromosomal alterations induced by combinatorial sgRNA delivery and describe related limitations of CRISPR/Cas9 multiplexing, as well as opportunities for chromosome engineering in the context of hepatobiliary tumorigenesis. Our study describes novel approaches to model and study cancer in a high-throughput multiplexed format that will facilitate the functional annotation of cancer genomes.
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