1
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Kouprina N, Larionov V. Transformation-associated recombination (TAR) cloning and its applications for gene function; genome architecture and evolution; biotechnology and biomedicine. Oncotarget 2023; 14:1009-1033. [PMID: 38147065 PMCID: PMC10750837 DOI: 10.18632/oncotarget.28546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Transformation-associated recombination (TAR) cloning represents a unique tool to selectively and efficiently recover a given chromosomal segment up to several hundred kb in length from complex genomes (such as animals and plants) and simple genomes (such as bacteria and viruses). The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. In this review, we summarize multiple applications of the pioneering TAR cloning technique, developed previously for complex genomes, for functional, evolutionary, and structural studies, and extended the modified TAR versions to isolate biosynthetic gene clusters (BGCs) from microbes, which are the major source of pharmacological agents and industrial compounds, and to engineer synthetic viruses with novel properties to design a new generation of vaccines. TAR cloning was adapted as a reliable method for the assembly of synthetic microbe genomes for fundamental research. In this review, we also discuss how the TAR cloning in combination with HAC (human artificial chromosome)- and CRISPR-based technologies may contribute to the future.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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2
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Lu Z, Chen P, Xu Q, Li B, Jiang S, Jiang L, Zheng X. Constitutive and conditional gene knockout mice for the study of intervertebral disc degeneration: Current status, decision considerations, and future possibilities. JOR Spine 2023; 6:e1242. [PMID: 36994464 PMCID: PMC10041386 DOI: 10.1002/jsp2.1242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
There have been an increasing number of patients with degenerative disc diseases due to the aging population. In light of this, studies on the pathogenesis of intervertebral disc degeneration have become a hot topic, and gene knockout mice have become a valuable tool in this field of research. With the development of science and technology, constitutive gene knockout mice can be constructed using homologous recombination, zinc finger nuclease, transcription activator-like effector nuclease technology and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, and conditional gene knockout mice can be constructed using the Cre/LoxP system. The gene-edited mice using these techniques have been widely used in the studies on disc degeneration. This paper reviews the development process and principles of these technologies, functions of the edited genes in disc degeneration, advantages, and disadvantages of different methods and possible targets of the specific Cre recombinase in intervertebral discs. Recommendations for the choice of suitable gene-edited model mice are presented. At the same time, possible technological improvements in the future are also discussed.
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Affiliation(s)
- Ze‐Yu Lu
- Spine CenterXinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Peng‐Bo Chen
- Spine CenterXinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Qing‐Yin Xu
- Spine CenterXinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Bo Li
- Spine CenterXinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Sheng‐Dan Jiang
- Spine CenterXinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lei‐Sheng Jiang
- Spine CenterXinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xin‐Feng Zheng
- Spine CenterXinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Soldatov VO, Kubekina MV, Skorkina MY, Belykh AE, Egorova TV, Korokin MV, Pokrovskiy MV, Deykin AV, Angelova PR. Current advances in gene therapy of mitochondrial diseases. J Transl Med 2022; 20:562. [PMID: 36471396 PMCID: PMC9724384 DOI: 10.1186/s12967-022-03685-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/04/2022] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial diseases (MD) are a heterogeneous group of multisystem disorders involving metabolic errors. MD are characterized by extremely heterogeneous symptoms, ranging from organ-specific to multisystem dysfunction with different clinical courses. Most primary MD are autosomal recessive but maternal inheritance (from mtDNA), autosomal dominant, and X-linked inheritance is also known. Mitochondria are unique energy-generating cellular organelles designed to survive and contain their own unique genetic coding material, a circular mtDNA fragment of approximately 16,000 base pairs. The mitochondrial genetic system incorporates closely interacting bi-genomic factors encoded by the nuclear and mitochondrial genomes. Understanding the dynamics of mitochondrial genetics supporting mitochondrial biogenesis is especially important for the development of strategies for the treatment of rare and difficult-to-diagnose diseases. Gene therapy is one of the methods for correcting mitochondrial disorders.
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Affiliation(s)
- Vladislav O Soldatov
- Core Facility Centre, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia.
- Laboratory of Genome Editing for Biomedicine and Animal Health, Belgorod State National Research University, Belgorod, Russia.
| | - Marina V Kubekina
- Core Facility Centre, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina Yu Skorkina
- Department of Biochemistry, Belgorod State National Research University, Belgorod, Russia
- Laboratory of Genome Editing for Biomedicine and Animal Health, Belgorod State National Research University, Belgorod, Russia
| | - Andrei E Belykh
- Dioscuri Centre for Metabolic Diseases, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Tatiana V Egorova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail V Korokin
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia
| | - Mikhail V Pokrovskiy
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia
| | - Alexey V Deykin
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia
- Laboratory of Genome Editing for Biomedicine and Animal Health, Belgorod State National Research University, Belgorod, Russia
| | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
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4
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Pakalniškytė D, Schönberger T, Strobel B, Stierstorfer B, Lamla T, Schuler M, Lenter M. Rosa26-LSL-dCas9-VPR: a versatile mouse model for tissue specific and simultaneous activation of multiple genes for drug discovery. Sci Rep 2022; 12:19268. [PMID: 36357523 PMCID: PMC9649745 DOI: 10.1038/s41598-022-23127-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
Transgenic animals with increased or abrogated target gene expression are powerful tools for drug discovery research. Here, we developed a CRISPR-based Rosa26-LSL-dCas9-VPR mouse model for targeted induction of endogenous gene expression using different Adeno-associated virus (AAV) capsid variants for tissue-specific gRNAs delivery. To show applicability of the model, we targeted low-density lipoprotein receptor (LDLR) and proprotein convertase subtilisin/kexin type 9 (PCSK9), either individually or together. We induced up to ninefold higher expression of hepatocellular proteins. In consequence of LDLR upregulation, plasma LDL levels almost abolished, whereas upregulation of PCSK9 led to increased plasma LDL and cholesterol levels. Strikingly, simultaneous upregulation of both LDLR and PCSK9 resulted in almost unaltered LDL levels. Additionally, we used our model to achieve expression of all α1-Antitrypsin (AAT) gene paralogues simultaneously. These results show the potential of our model as a versatile tool for optimized targeted gene expression, alone or in combination.
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Affiliation(s)
- Dalia Pakalniškytė
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Tanja Schönberger
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Benjamin Strobel
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Birgit Stierstorfer
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Nonclinical Drug Safety Germany, 88400 Biberach an der Riß, Germany
| | - Thorsten Lamla
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Discovery Research Coordination, 88400 Biberach an der Riß, Germany
| | - Michael Schuler
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Martin Lenter
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
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5
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Kouprina N, Kim J, Larionov V. Highly Selective, CRISPR/Cas9-Mediated Isolation of Genes and Genomic Loci from Complex Genomes by TAR Cloning in Yeast. Curr Protoc 2021; 1:e207. [PMID: 34370406 PMCID: PMC8363120 DOI: 10.1002/cpz1.207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Here we describe an updated TAR cloning protocol for the selective and efficient isolation of any genomic fragment or gene of interest up to 280 kb in size from genomic DNA. The method exploits the special recombination machinery of the yeast Saccharomyces cerevisiae. TAR cloning is based on the high level of in vivo recombination that occurs between a specific genomic DNA fragment of interest and targeting sequences (hooks) in a TAR vector that are homologous to the 5' and 3' ends of the targeted region. Upon co-transformation into yeast, this results in the isolation of the chromosomal region of interest as a circular YAC molecule, which then propagates and segregates in yeast cells and can be selected for. In the updated TAR cloning protocol described here, the fraction of region-positive clones typically obtained is increased from 1% up to 35% by pre-treatment of the genomic DNA with specifically designed CRISPR/Cas9 endonucleases that create double-strand breaks (DSBs) bracketing the target genomic DNA sequence, thereby making the ends of the chromosomal region of interest highly recombinogenic. In addition, a new TAR vector was constructed that contains YAC and BAC cassettes, permitting direct transfer of a TAR-cloned DNA from yeast to bacterial cells. Once the TAR vector with the hooks is constructed and genomic DNA is prepared, the entire procedure takes 3 weeks to complete. The updated TAR protocol does not require significant yeast experience or extensively time-consuming yeast work because screening only about a dozen yeast transformants is typically enough to find a clone with the region of interest. TAR cloning of chromosomal fragments, individual genes, or gene families can be used for functional, structural, and population studies, for comparative genomics, and for long-range haplotyping, and has potential for gene therapy. Published 2021. This article is a U.S. Government work and is in the public domain in the USA. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of CRISPR/Cas9-treated genomic DNA for TAR cloning Basic Protocol 2: Isolation of a gene or genomic locus by TAR cloning Basic Protocol 3: Transfer of TAR/YAC/BAC isolates from yeast to E. coli.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer InstituteNIHBethesdaMaryland
| | - Jung‐Hyun Kim
- Developmental Therapeutics Branch, National Cancer InstituteNIHBethesdaMaryland
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer InstituteNIHBethesdaMaryland
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6
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Zou G, Zhou Z. CRISPR/Cas9-Mediated Genome Editing of Trichoderma reesei. Methods Mol Biol 2021; 2234:87-98. [PMID: 33165782 DOI: 10.1007/978-1-0716-1048-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
In this protocol, we describe the establishment of a CRISPR/Cas9 system in Trichoderma reesei by generating a specific, codon-optimized Cas9-expressing strain and by in vitro transcription of a gRNA. This system induces mutagenesis or introduces a gene in a targeted way based on PEG-mediated protoplast transformation. Up to three targets, multiplexed genome editing can be obtained in one transformation.
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Affiliation(s)
- Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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7
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Gendoping und molekulares Doping. Rechtsmedizin (Berl) 2020. [DOI: 10.1007/s00194-020-00431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Lundin A, Porritt MJ, Jaiswal H, Seeliger F, Johansson C, Bidar AW, Badertscher L, Wimberger S, Davies EJ, Hardaker E, Martins CP, James E, Admyre T, Taheri-Ghahfarokhi A, Bradley J, Schantz A, Alaeimahabadi B, Clausen M, Xu X, Mayr LM, Nitsch R, Bohlooly-Y M, Barry ST, Maresca M. Development of an ObLiGaRe Doxycycline Inducible Cas9 system for pre-clinical cancer drug discovery. Nat Commun 2020; 11:4903. [PMID: 32994412 PMCID: PMC7525522 DOI: 10.1038/s41467-020-18548-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/26/2020] [Indexed: 12/28/2022] Open
Abstract
The CRISPR-Cas9 system has increased the speed and precision of genetic editing in cells and animals. However, model generation for drug development is still expensive and time-consuming, demanding more target flexibility and faster turnaround times with high reproducibility. The generation of a tightly controlled ObLiGaRe doxycycline inducible SpCas9 (ODInCas9) transgene and its use in targeted ObLiGaRe results in functional integration into both human and mouse cells culminating in the generation of the ODInCas9 mouse. Genomic editing can be performed in cells of various tissue origins without any detectable gene editing in the absence of doxycycline. Somatic in vivo editing can model non-small cell lung cancer (NSCLC) adenocarcinomas, enabling treatment studies to validate the efficacy of candidate drugs. The ODInCas9 mouse allows robust and tunable genome editing granting flexibility, speed and uniformity at less cost, leading to high throughput and practical preclinical in vivo therapeutic testing.
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Affiliation(s)
- Anders Lundin
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Michelle J Porritt
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Himjyot Jaiswal
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Cellink AB, Gothenburg, Sweden
| | - Frank Seeliger
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Camilla Johansson
- Clinical Pharmacology and Safety Sciences, Sweden Imaging Hub, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Abdel Wahad Bidar
- Clinical Pharmacology and Safety Sciences, Sweden Imaging Hub, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lukas Badertscher
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Emma J Davies
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
- Healx, Cambridge, UK
| | - Elizabeth Hardaker
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Carla P Martins
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Emily James
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Therese Admyre
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Amir Taheri-Ghahfarokhi
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jenna Bradley
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge Science Park, Cambridge, UK
| | - Anna Schantz
- Pharmaceutical Sciences, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Babak Alaeimahabadi
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Maryam Clausen
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Xiufeng Xu
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lorenz M Mayr
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Roberto Nitsch
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Simon T Barry
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Marcello Maresca
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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9
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Estêvão D, Rios Costa N, da Costa RG, Medeiros R. CRISPR-Cas9 therapies in experimental mouse models of cancer. Future Oncol 2018; 14:2083-2095. [PMID: 30027767 DOI: 10.2217/fon-2018-0028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The CRISPR-Cas9, a part of the defence mechanism from bacteria, has rapidly become the simplest, fastest and the most precise genome-editing tool available. The therapeutic applications of CRISPR are boundless: correction of mutations in several disorders, inactivation of oncogenes and viral oncoproteins, and activation of tumor suppressor genes. In this review, we expose recent advances concerning animal models of cancer that use CRISPR-Cas9, addressing also the current efforts to develop CRISPR-Cas9-based therapies, focusing on proof-of-concept studies. Finally, the review exposes some of the main challenges that this genome-editing tool faces. The key issue remains: does CRISPR-Cas9 have real potential for therapeutic application or will it just remain a wonderful research tool?
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Affiliation(s)
- Diogo Estêvão
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal Porto, Portugal
| | - Natália Rios Costa
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal
| | - Rui Gil da Costa
- Laboratory for Process Engineering, Environment, Biotechnology & Energy (LEPABE), Faculty of Engineering of the University of Porto (FEUP), 4200-465 Porto, Portugal.,Center for the Research & Technology of Agro-Environmental & Biological Sciences (CITAB), University of Trás-os-Montes & Alto Douro (UTAD), 5001-911 Vila Real, Portugal
| | - Rui Medeiros
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal Porto, Portugal.,Research Department of the Portuguese League Against Cancer (Liga Portuguesa Contra o Cancro - Núcleo Regional do Norte), 4200-177 Porto, Portugal Porto, Portugal.,Biomedical Research Center (CEBIMED), Faculty of Health Sciences of the Fernando Pessoa University, 4249-004 Porto, Portugal Porto, Portugal
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10
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Cytogenetic Analysis of the Results of Genome Editing on the Cell Model of Parkinson’s Disease. Bull Exp Biol Med 2018; 165:378-381. [DOI: 10.1007/s10517-018-4174-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Indexed: 12/13/2022]
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11
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Liu T, Hu Y, Guo S, Tan L, Zhan Y, Yang L, Liu W, Wang N, Li Y, Zhang Y, Liu C, Yang Y, Adelstein RS, Wang A. Identification and characterization of MYH9 locus for high efficient gene knock-in and stable expression in mouse embryonic stem cells. PLoS One 2018; 13:e0192641. [PMID: 29438440 PMCID: PMC5811019 DOI: 10.1371/journal.pone.0192641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/26/2018] [Indexed: 01/22/2023] Open
Abstract
Targeted integration of exogenous genes into so-called safe harbors/friend sites, offers the advantages of expressing normal levels of target genes and preventing potentially adverse effects on endogenous genes. However, the ideal genomic loci for this purpose remain limited. Additionally, due to the inherent and unresolved issues with the current genome editing tools, traditional embryonic stem (ES) cell-based targeted transgenesis technology is still preferred in practical applications. Here, we report that a high and repeatable homologous recombination (HR) frequency (>95%) is achieved when an approximate 6kb DNA sequence flanking the MYH9 gene exon 2 site is used to create the homology arms for the knockout/knock-in of diverse nonmuscle myosin II (NM II) isoforms in mouse ES cells. The easily obtained ES clones greatly facilitated the generation of multiple NM II genetic replacement mouse models, as characterized previously. Further investigation demonstrated that though the targeted integration site for exogenous genes is shifted to MYH9 intron 2 (about 500bp downstream exon 2), the high HR efficiency and the endogenous MYH9 gene integrity are not only preserved, but the expected expression of the inserted gene(s) is observed in a pre-designed set of experiments conducted in mouse ES cells. Importantly, we confirmed that the expression and normal function of the endogenous MYH9 gene is not affected by the insertion of the exogenous gene in these cases. Therefore, these findings suggest that like the commonly used ROSA26 site, the MYH9 gene locus may be considered a new safe harbor for high-efficiency targeted transgenesis and for biomedical applications.
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Affiliation(s)
- Tanbin Liu
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yi Hu
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Shiyin Guo
- College of Food Science and Technology, HUNAU, Changsha, Hunan, China
| | - Lei Tan
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yang Zhan
- Lab of Functional Proteomics (LFP), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, HUNAU, Changsha, Hunan, China
| | - Lingchen Yang
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Wei Liu
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Naidong Wang
- Lab of Functional Proteomics (LFP), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, HUNAU, Changsha, Hunan, China
| | - Yalan Li
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yingfan Zhang
- Lab of Molecular Cardiology (LMC), National Heart, Lung, and Blood Institute (NHLBI)/National Institutes of Health (NIH), Bethesda, MD, United States of America
| | - Chengyu Liu
- Transgenic Core, NHLBI/ NIH, Bethesda, MD, United States of America
| | - Yi Yang
- Lab of Functional Proteomics (LFP), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, HUNAU, Changsha, Hunan, China
| | - Robert S. Adelstein
- Lab of Molecular Cardiology (LMC), National Heart, Lung, and Blood Institute (NHLBI)/National Institutes of Health (NIH), Bethesda, MD, United States of America
| | - Aibing Wang
- Lab of Animal Models and Functional Genomics (LAMFG), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
- Lab of Molecular Cardiology (LMC), National Heart, Lung, and Blood Institute (NHLBI)/National Institutes of Health (NIH), Bethesda, MD, United States of America
- * E-mail:
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12
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Gervasi MG, Visconti PE. Chang's meaning of capacitation: A molecular perspective. Mol Reprod Dev 2018; 83:860-874. [PMID: 27256723 DOI: 10.1002/mrd.22663] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 05/31/2016] [Indexed: 02/04/2023]
Abstract
Dr. Min Chue Chang's contributions to the field of reproductive biology set the stage for the development of the contraceptive pill and in vitro fertilization. Throughout his publications, Dr. Chang was also able to transmit his view of the fertilization process in ways that organized research for newer generations of reproductive biologists. Particularly relevant for the achievement of in vitro fertilization in mammals was the discovery that the sperm required a period of residence in the female tract to become fertilization-competent; Dr. Chang and Dr. Austin, in Australia, independently reported this process, now known as sperm capacitation. This review discusses Dr. Chang's views on capacitation, and puts them in the context of recent advances in the understanding of the molecular basis of this process. Mol. Reprod. Dev. 83: 860-874, 2016 © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Maria Gracia Gervasi
- Department of Veterinary and Animal Sciences, ISB, University of Massachusetts, Amherst, Massachusetts
| | - Pablo E Visconti
- Department of Veterinary and Animal Sciences, ISB, University of Massachusetts, Amherst, Massachusetts.
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13
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Gervasi MG, Visconti PE. Molecular changes and signaling events occurring in spermatozoa during epididymal maturation. Andrology 2017; 5:204-218. [PMID: 28297559 DOI: 10.1111/andr.12320] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/01/2016] [Accepted: 11/30/2016] [Indexed: 12/11/2022]
Abstract
After leaving the testis, spermatozoa have not yet acquired the ability to move progressively and are unable to fertilize oocytes. To become fertilization competent, they must go through an epididymal maturation process in the male, and capacitation in the female tract. Epididymal maturation can be defined as those changes occurring to spermatozoa in the epididymis that render the spermatozoa the ability to capacitate in the female tract. As part of this process, sperm cells undergo a series of biochemical and physiological changes that require incorporation of new molecules derived from the epididymal epithelium, as well as post-translational modifications of endogenous proteins synthesized during spermiogenesis in the testis. This review will focus on epididymal maturation events, with emphasis in recent advances in the understanding of the molecular basis of this process.
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Affiliation(s)
- M G Gervasi
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - P E Visconti
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
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14
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Jeon S, Lim JM, Lee HG, Shin SE, Kang NK, Park YI, Oh HM, Jeong WJ, Jeong BR, Chang YK. Current status and perspectives of genome editing technology for microalgae. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:267. [PMID: 29163669 PMCID: PMC5686953 DOI: 10.1186/s13068-017-0957-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/04/2017] [Indexed: 05/25/2023]
Abstract
Genome editing techniques are critical for manipulating genes not only to investigate their functions in biology but also to improve traits for genetic engineering in biotechnology. Genome editing has been greatly facilitated by engineered nucleases, dubbed molecular scissors, including zinc-finger nuclease (ZFN), TAL effector endonuclease (TALEN) and clustered regularly interspaced palindromic sequences (CRISPR)/Cas9. In particular, CRISPR/Cas9 has revolutionized genome editing fields with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in numerous organisms including microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feedstocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.
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Affiliation(s)
- Seungjib Jeon
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Sung-Eun Shin
- LG Chem, 188 Munji-ro, Yuseong-gu, Daejeon, 34122 Republic of Korea
| | - Nam Kyu Kang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Byeong-ryool Jeong
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Yong Keun Chang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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15
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Hanusova Z, Mosko T, Matej R, Holada K. Precision in the design of an experimental study deflects the significance of proteinase-activated receptor 2 expression in scrapie-inoculated mice. J Gen Virol 2017; 98:1563-1569. [DOI: 10.1099/jgv.0.000803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Zdenka Hanusova
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Studnickova 7, Prague 2, 128 00, Czech Republic
| | - Tibor Mosko
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Studnickova 7, Prague 2, 128 00, Czech Republic
| | - Radoslav Matej
- Department of Pathology and Molecular Medicine, Thomayer Teaching Hospital, Videnska 800, Prague 4, 14059, Czech Republic
- Department of Pathology, First Faculty of Medicine, Charles University, Studnickova 2, Prague 2, 12800, Czech Republic
| | - Karel Holada
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Studnickova 7, Prague 2, 128 00, Czech Republic
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Klinghammer K, Walther W, Hoffmann J. Choosing wisely - Preclinical test models in the era of precision medicine. Cancer Treat Rev 2017; 55:36-45. [PMID: 28314175 DOI: 10.1016/j.ctrv.2017.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/03/2023]
Abstract
Through the introduction of a steadily growing variety of preclinical test models drug development and biomarker research has advanced. Next to classical used 2D cell line cultures, tissue-slice cultures, 3D organoid cell cultures, genetically engineered mouse models, cell line derived mouse models and patient derived xenografts may be selected for a specific question. All models harbor advantages and disadvantages. This review focuses on the available preclinical test models, novel developments such as humanized mice and discusses for which question a particular model should be employed.
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Affiliation(s)
| | - Wolfgang Walther
- Experimental and Clinical Research Center, Charité and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Jens Hoffmann
- Experimental Pharmacology & Oncology GmbH, Berlin, Germany
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17
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Rutkowski TP, Schroeder JP, Gafford GM, Warren ST, Weinshenker D, Caspary T, Mulle JG. Unraveling the genetic architecture of copy number variants associated with schizophrenia and other neuropsychiatric disorders. J Neurosci Res 2016; 95:1144-1160. [PMID: 27859486 DOI: 10.1002/jnr.23970] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
Abstract
Recent studies show that the complex genetic architecture of schizophrenia (SZ) is driven in part by polygenic components, or the cumulative effect of variants of small effect in many genes, as well as rare single-locus variants with large effect sizes. Here we discuss genetic aberrations known as copy number variants (CNVs), which fall in the latter category and are associated with a high risk for SZ and other neuropsychiatric disorders. We briefly review recurrent CNVs associated with SZ, and then highlight one CNV in particular, a recurrent 1.6-Mb deletion on chromosome 3q29, which is estimated to confer a 40-fold increased risk for SZ. Additionally, we describe the use of genetic mouse models, behavioral tools, and patient-derived induced pluripotent stem cells as a means to study CNVs in the hope of gaining mechanistic insight into their respective disorders. Taken together, the genomic data connecting CNVs with a multitude of human neuropsychiatric disease, our current technical ability to model such chromosomal anomalies in mouse, and the existence of precise behavioral measures of endophenotypes argue that the time is ripe for systematic dissection of the genetic mechanisms underlying such disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Timothy P Rutkowski
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jason P Schroeder
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Georgette M Gafford
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - David Weinshenker
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
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18
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Wensel TG, Zhang Z, Anastassov IA, Gilliam JC, He F, Schmid MF, Robichaux MA. Structural and molecular bases of rod photoreceptor morphogenesis and disease. Prog Retin Eye Res 2016; 55:32-51. [PMID: 27352937 PMCID: PMC5112133 DOI: 10.1016/j.preteyeres.2016.06.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022]
Abstract
The rod cell has an extraordinarily specialized structure that allows it to carry out its unique function of detecting individual photons of light. Both the structural features of the rod and the metabolic processes required for highly amplified light detection seem to have rendered the rod especially sensitive to structural and metabolic defects, so that a large number of gene defects are primarily associated with rod cell death and give rise to blinding retinal dystrophies. The structures of the rod, especially those of the sensory cilium known as the outer segment, have been the subject of structural, biochemical, and genetic analysis for many years, but the molecular bases for rod morphogenesis and for cell death in rod dystrophies are still poorly understood. Recent developments in imaging technology, such as cryo-electron tomography and super-resolution fluorescence microscopy, in gene sequencing technology, and in gene editing technology are rapidly leading to new breakthroughs in our understanding of these questions. A summary is presented of our current understanding of selected aspects of these questions, highlighting areas of uncertainty and contention as well as recent discoveries that provide new insights. Examples of structural data from emerging imaging technologies are presented.
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Affiliation(s)
- Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Zhixian Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan A Anastassov
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jared C Gilliam
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng He
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F Schmid
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael A Robichaux
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Fujita T, Yuno M, Fujii H. Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus. Sci Rep 2016; 6:30485. [PMID: 27465215 PMCID: PMC4964623 DOI: 10.1038/srep30485] [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: 02/02/2016] [Accepted: 07/06/2016] [Indexed: 01/08/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system has been adopted for a wide range of biological applications including genome editing. In some cases, dissection of genome functions requires allele-specific genome editing, but the use of CRISPR for this purpose has not been studied in detail. In this study, using the p16INK4a gene in HCT116 as a model locus, we investigated whether chromatin states, such as CpG methylation, or a single-nucleotide gap form in a target site can be exploited for allele-specific locus binding and genome editing by CRISPR in vivo. First, we showed that allele-specific locus binding and genome editing could be achieved by targeting allele-specific CpG-methylated regions, which was successful for one, but not all guide RNAs. In this regard, molecular basis underlying the success remains elusive at this stage. Next, we demonstrated that an allele-specific single-nucleotide gap form could be employed for allele-specific locus binding and genome editing by CRISPR, although it was important to avoid CRISPR tolerance of a single nucleotide mismatch brought about by mismatched base skipping. Our results provide information that might be useful for applications of CRISPR in studies of allele-specific functions in the genomes.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan
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20
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Kusano H, Onodera H, Kihira M, Aoki H, Matsuzaki H, Shimada H. A simple Gateway-assisted construction system of TALEN genes for plant genome editing. Sci Rep 2016; 6:30234. [PMID: 27452606 PMCID: PMC4958979 DOI: 10.1038/srep30234] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/01/2016] [Indexed: 11/17/2022] Open
Abstract
TALEN is an artificial nuclease being applied for sequence-specific genome editing. For the plant genome editing, a pair of TALEN genes is expressed in the cells, and a binary plasmid for Agrobacterium-mediated transformation should be assembled. We developed a novel procedure using the Gateway-assisted plasmids, named Emerald–Gateway TALEN system. We constructed entry vectors, pPlat plasmids, for construction of a desired TALEN gene using Platinum Gate TALEN kit. We also created destination plasmid, pDual35SGw1301, which allowed two TALEN genes to both DNA strands to recruit using Gateway technology. Resultant TALEN genes were evaluated by the single-strand annealing (SSA) assay in E. coli cells. By this assay, the TALENs recognized the corresponding targets in the divided luciferase gene, and induced a specific recombination to generate an active luciferase gene. Using the TALEN genes constructed, we created a transformant potato cells in which a site-specific mutation occurred at the target site of the GBSS gene. This suggested that our system worked effectively and was applicable as a convenient tool for the plant genome editing.
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Affiliation(s)
- Hiroaki Kusano
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Hitomi Onodera
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Miho Kihira
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Hiromi Aoki
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Hikaru Matsuzaki
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
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21
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Tschaharganeh DF, Lowe SW, Garippa RJ, Livshits G. Using CRISPR/Cas to study gene function and model disease in vivo. FEBS J 2016; 283:3194-203. [PMID: 27149548 DOI: 10.1111/febs.13750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 12/23/2022]
Abstract
The recent discovery of the CRISPR/Cas system and repurposing of this technology to edit a variety of different genomes have revolutionized an array of scientific fields, from genetics and translational research, to agriculture and bioproduction. In particular, the prospect of rapid and precise genome editing in laboratory animals by CRISPR/Cas has generated an immense interest in the scientific community. Here we review current in vivo applications of CRISPR/Cas and how this technology can improve our knowledge of gene function and our understanding of biological processes in animal models.
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Affiliation(s)
- Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA
| | - Ralph J Garippa
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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22
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Sirokmány G, Donkó Á, Geiszt M. Nox/Duox Family of NADPH Oxidases: Lessons from Knockout Mouse Models. Trends Pharmacol Sci 2016; 37:318-327. [DOI: 10.1016/j.tips.2016.01.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 11/21/2015] [Accepted: 01/11/2016] [Indexed: 02/07/2023]
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23
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Stanley P. What Have We Learned from Glycosyltransferase Knockouts in Mice? J Mol Biol 2016; 428:3166-3182. [PMID: 27040397 DOI: 10.1016/j.jmb.2016.03.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 11/16/2022]
Abstract
There are five major classes of glycan including N- and O-glycans, glycosaminoglycans, glycosphingolipids, and glycophosphatidylinositol anchors, all expressed at the molecular frontier of each mammalian cell. Numerous biological consequences of altering the expression of mammalian glycans are understood at a mechanistic level, but many more remain to be characterized. Mouse mutants with deleted, defective, or misexpressed genes that encode activities necessary for glycosylation have led the way to identifying key functions of glycans in biology. However, with the advent of exome sequencing, humans with mutations in genes involved in glycosylation are also revealing specific requirements for glycans in mammalian development. The aim of this review is to summarize glycosylation genes that are necessary for mouse embryonic development, pathway-specific glycosylation genes whose deletion leads to postnatal morbidity, and glycosylation genes for which effects are mild, but perturbation of the organism may reveal functional consequences. General strategies for generating and interpreting the phenotype of mice with glycosylation defects are discussed in relation to human congenital disorders of glycosylation (CDG).
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Affiliation(s)
- Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, USA.
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24
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Increased Understanding of Stem Cell Behavior in Neurodegenerative and Neuromuscular Disorders by Use of Noninvasive Cell Imaging. Stem Cells Int 2016; 2016:6235687. [PMID: 26997958 PMCID: PMC4779824 DOI: 10.1155/2016/6235687] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/07/2016] [Accepted: 01/11/2016] [Indexed: 12/13/2022] Open
Abstract
Numerous neurodegenerative and neuromuscular disorders are associated with cell-specific depletion in the human body. This imbalance in tissue homeostasis is in healthy individuals repaired by the presence of endogenous stem cells that can replace the lost cell type. However, in most disorders, a genetic origin or limited presence or exhaustion of stem cells impairs correct cell replacement. During the last 30 years, methods to readily isolate and expand stem cells have been developed and this resulted in a major change in the regenerative medicine field as it generates sufficient amount of cells for human transplantation applications. Furthermore, stem cells have been shown to release cytokines with beneficial effects for several diseases. At present however, clinical stem cell transplantations studies are struggling to demonstrate clinical efficacy despite promising preclinical results. Therefore, to allow stem cell therapy to achieve its full potential, more insight in their in vivo behavior has to be achieved. Different methods to noninvasively monitor these cells have been developed and are discussed. In some cases, stem cell monitoring even reached the clinical setting. We anticipate that by further exploring these imaging possibilities and unraveling their in vivo behavior further improvement in stem cell transplantations will be achieved.
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25
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Latorre A, Latorre A, Somoza Á. Modifizierte RNAs in CRISPR/Cas9: ein bewährter Trick, der immer noch funktioniert. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201512002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alfonso Latorre
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia); Unidad Asociada al Centro Nacional de Biotecnología (CSIC); Faraday 9 28049 Madrid Spanien
| | - Ana Latorre
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia); Unidad Asociada al Centro Nacional de Biotecnología (CSIC); Faraday 9 28049 Madrid Spanien
| | - Álvaro Somoza
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia); Unidad Asociada al Centro Nacional de Biotecnología (CSIC); Faraday 9 28049 Madrid Spanien
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26
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Latorre A, Latorre A, Somoza Á. Modified RNAs in CRISPR/Cas9: An Old Trick Works Again. Angew Chem Int Ed Engl 2016; 55:3548-50. [PMID: 26880106 DOI: 10.1002/anie.201512002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Indexed: 12/20/2022]
Abstract
Old tricks, new dog: CRISPR/Cas9 is a powerful tool for gene editing that requires an endonuclease (Cas9) and RNA strands. It has been shown that chemical modification of the RNA structures, an approach that has been used to improve the efficiency of RNA interference, can also be applied to enhance the activity of CRISPR/Cas9 and reduce its off-target effects.
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Affiliation(s)
- Alfonso Latorre
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC), Faraday 9, 28049, Madrid, Spain
| | - Ana Latorre
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC), Faraday 9, 28049, Madrid, Spain
| | - Álvaro Somoza
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC), Faraday 9, 28049, Madrid, Spain.
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27
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Fujita T, Yuno M, Fujii H. Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins. Genes Cells 2016; 21:370-7. [PMID: 26848818 DOI: 10.1111/gtc.12341] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 12/18/2015] [Indexed: 01/08/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for various biological applications, including genome editing. We developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR to isolate target genomic regions from cells for their biochemical characterization. In this study, we developed 'in vitro enChIP' using recombinant CRISPR ribonucleoproteins (RNPs) to isolate target genomic regions. in vitro enChIP has the great advantage over conventional enChIP of not requiring expression of CRISPR complexes in cells. We first showed that in vitro enChIP using recombinant CRISPR RNPs can be used to isolate target DNA from mixtures of purified DNA in a sequence-specific manner. In addition, we showed that this technology can be used to efficiently isolate target genomic regions, while retaining their intracellular molecular interactions, with negligible contamination from irrelevant genomic regions. Thus, in vitro enChIP technology is of potential use for sequence-specific isolation of DNA, as well as for identification of molecules interacting with genomic regions of interest in vivo in combination with downstream analysis.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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28
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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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29
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Landek-Salgado MA, Faust TE, Sawa A. Molecular substrates of schizophrenia: homeostatic signaling to connectivity. Mol Psychiatry 2016; 21:10-28. [PMID: 26390828 PMCID: PMC4684728 DOI: 10.1038/mp.2015.141] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 02/06/2023]
Abstract
Schizophrenia (SZ) is a devastating psychiatric condition affecting numerous brain systems. Recent studies have identified genetic factors that confer an increased risk of SZ and participate in the disease etiopathogenesis. In parallel to such bottom-up approaches, other studies have extensively reported biological changes in patients by brain imaging, neurochemical and pharmacological approaches. This review highlights the molecular substrates identified through studies with SZ patients, namely those using top-down approaches, while also referring to the fruitful outcomes of recent genetic studies. We have subclassified the molecular substrates by system, focusing on elements of neurotransmission, targets in white matter-associated connectivity, immune/inflammatory and oxidative stress-related substrates, and molecules in endocrine and metabolic cascades. We further touch on cross-talk among these systems and comment on the utility of animal models in charting the developmental progression and interaction of these substrates. Based on this comprehensive information, we propose a framework for SZ research based on the hypothesis of an imbalance in homeostatic signaling from immune/inflammatory, oxidative stress, endocrine and metabolic cascades that, at least in part, underlies deficits in neural connectivity relevant to SZ. Thus, this review aims to provide information that is translationally useful and complementary to pathogenic hypotheses that have emerged from genetic studies. Based on such advances in SZ research, it is highly expected that we will discover biomarkers that may help in the early intervention, diagnosis or treatment of SZ.
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Affiliation(s)
- M A Landek-Salgado
- Department of Psychiatry, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - T E Faust
- Department of Psychiatry, John Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Sawa
- Department of Psychiatry, John Hopkins University School of Medicine, Baltimore, MD, USA
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Jo YI, Kim H, Ramakrishna S. Recent developments and clinical studies utilizing engineered zinc finger nuclease technology. Cell Mol Life Sci 2015; 72:3819-30. [PMID: 26089249 PMCID: PMC11113831 DOI: 10.1007/s00018-015-1956-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 12/27/2022]
Abstract
Efficient methods for creating targeted genetic modifications have long been sought for the investigation of gene function and the development of therapeutic modalities for various diseases, including genetic disorders. Although such modifications are possible using homologous recombination, the efficiency is extremely low. Zinc finger nucleases (ZFNs) are custom-designed artificial nucleases that make double-strand breaks at specific sequences, enabling efficient targeted genetic modifications such as corrections, additions, gene knockouts and structural variations. ZFNs are composed of two domains: (i) a DNA-binding domain comprised of zinc finger modules and (ii) the FokI nuclease domain that cleaves the DNA strand. Over 17 years after ZFNs were initially developed, a number of improvements have been made. Here, we will review the developments and future perspectives of ZFN technology. For example, ZFN activity and specificity have been significantly enhanced by modifying the DNA-binding domain and FokI cleavage domain. Advances in culture methods, such as the application of a cold shock and the use of small molecules that affect ZFN stability, have also increased ZFN activity. Furthermore, ZFN-induced mutant cells can be enriched using episomal surrogate reporters. Additionally, we discuss several ongoing clinical studies that are based on ZFN-mediated genome editing in humans. These breakthroughs have substantially facilitated the use of ZFNs in research, medicine and biotechnology.
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Affiliation(s)
| | - Hyongbum Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
- Graduate Program of Nano Science and Technology, Yonsei University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Sungdong-gu, Seoul, South Korea.
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Korge S, Grudziecki A, Kramer A. Highly Efficient Genome Editing via CRISPR/Cas9 to Create Clock Gene Knockout Cells. J Biol Rhythms 2015; 30:389-95. [PMID: 26243628 DOI: 10.1177/0748730415597519] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Targeted genome editing using CRISPR/Cas9 is a relatively new, revolutionary technology allowing for efficient and directed alterations of the genome. It has been widely used for loss-of-function studies in animals and cell lines but has not yet been used to study circadian rhythms. Here, we describe the application of CRISPR/Cas9 genome editing for the generation of an F-box and leucine-rich repeat protein 3 (Fbxl3) knockout in a human cell line. Genomic alterations at the Fbxl3 locus occurred with very high efficiency (70%-100%) and specificity at both alleles, resulting in insertions and deletions that led to premature stop codons and hence FBXL3 knockout. Fbxl3 knockout cells displayed low amplitude and long period oscillations of Bmal1-luciferase reporter activity as well as increased CRY1 protein stability in line with previously published phenotypes for Fbxl3 knockout in mice. Thus, CRISPR/Cas9 genome editing should be highly valuable for studying circadian rhythms not only in human cells but also in classic model systems as well as nonmodel organisms.
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Affiliation(s)
- Sandra Korge
- Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Astrid Grudziecki
- Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Berlin, Germany
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Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research. Int J Mol Sci 2015; 16:23143-64. [PMID: 26404236 PMCID: PMC4632690 DOI: 10.3390/ijms161023143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 08/31/2015] [Accepted: 09/14/2015] [Indexed: 11/16/2022] Open
Abstract
Engineered DNA-binding molecules such as transcription activator-like effector (TAL or TALE) proteins and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) (CRISPR/Cas) system have been used extensively for genome editing in cells of various types and species. The sequence-specific DNA-binding activities of these engineered DNA-binding molecules can also be utilized for other purposes, such as transcriptional activation, transcriptional repression, chromatin modification, visualization of genomic regions, and isolation of chromatin in a locus-specific manner. In this review, we describe applications of these engineered DNA-binding molecules for biological purposes other than genome editing.
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Uy N, Reidy K. Developmental Genetics and Congenital Anomalies of the Kidney and Urinary Tract. J Pediatr Genet 2015; 5:51-60. [PMID: 27617142 DOI: 10.1055/s-0035-1558423] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/10/2015] [Indexed: 02/06/2023]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are common birth defects and the leading cause of end-stage renal disease in children. There is a wide spectrum of renal abnormalities, from mild hydronephrosis to more severe cases, such as bilateral renal dysplasia. The etiology of the majority of cases of CAKUT remains unknown, but there is increasing evidence that genomic imbalance contributes to the pathogenesis of CAKUT. Advances in human and mouse genetics have contributed to increased understanding of the pathophysiology of CAKUT. Mutations in genes involved in both transcription factors and signal transduction pathways involved in renal development are associated with CAKUT. Large cohort studies suggest that copy number variants, genomic, or de novo mutations may explain up to one-third of all cases of CAKUT. One of the major challenges to the use of genetic information in the clinical setting remains the lack of strict genotype-phenotype correlation. However, identifying genetic causes of CAKUT may lead to improved diagnosis of extrarenal complications. With the advent of decreasing costs for whole genome and exome sequencing, future studies focused on genotype-phenotype correlations, gene modifiers, and animal models of gene mutations will be needed to translate genetic advances into improved clinical care.
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Affiliation(s)
- Natalie Uy
- Department of Pediatrics/Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York, United States
| | - Kimberly Reidy
- Department of Pediatrics/Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York, United States
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Villalobos X, Rodríguez L, Solé A, Lliberós C, Mencia N, Ciudad CJ, Noé V. Effect of Polypurine Reverse Hoogsteen Hairpins on Relevant Cancer Target Genes in Different Human Cell Lines. Nucleic Acid Ther 2015; 25:198-208. [PMID: 26042602 DOI: 10.1089/nat.2015.0531] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We studied the ability of polypurine reverse Hoogsteen hairpins (PPRHs) to silence a variety of relevant cancer-related genes in several human cell lines. PPRHs are hairpins formed by two antiparallel polypurine strands bound by intramolecular Hoogsteen bonds linked by a pentathymidine loop. These hairpins are able to bind to their target DNA sequence through Watson-Crick bonds producing specific silencing of gene expression. We designed PPRHs against the following genes: BCL2, TOP1, mTOR, MDM2, and MYC and tested them for mRNA levels, cytotoxicity, and apoptosis in prostate, pancreas, colon, and breast cancer cell lines. Even though all PPRHs were effective, the most remarkable results were obtained with those against BCL2 and mammalian target of rapamycin (mTOR) in decreasing cell survival and mRNA levels and increasing apoptosis in prostate, colon, and pancreatic cancer cells. In the case of TOP1, MDM2, and MYC, their corresponding PPRHs produced a strong effect in decreasing cell viability and mRNA levels and increasing apoptosis in breast cancer cells. Thus, we confirm that the PPRH technology is broadly useful to silence the expression of cancer-related genes as demonstrated using target genes involved in metabolism (DHFR), proliferation (mTOR), DNA topology (TOP1), lifespan and senescence (telomerase), apoptosis (survivin, BCL2), transcription factors (MYC), and proto-oncogenes (MDM2).
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Affiliation(s)
- Xenia Villalobos
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Barcelona, Spain
| | - Laura Rodríguez
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Barcelona, Spain
| | - Anna Solé
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Barcelona, Spain
| | - Carolina Lliberós
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Barcelona, Spain
| | - Núria Mencia
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Barcelona, Spain
| | - Carlos J Ciudad
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Barcelona, Spain
| | - Véronique Noé
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Barcelona, Spain
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Lee NCO, Larionov V, Kouprina N. Highly efficient CRISPR/Cas9-mediated TAR cloning of genes and chromosomal loci from complex genomes in yeast. Nucleic Acids Res 2015; 43:e55. [PMID: 25690893 PMCID: PMC4417148 DOI: 10.1093/nar/gkv112] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 12/14/2022] Open
Abstract
Transformation-associated recombination (TAR) protocol allowing the selective isolation of full-length genes complete with their distal enhancer regions and entire genomic loci with sizes up to 250 kb from complex genomes in yeast S. cerevisiae has been developed more than a decade ago. However, its wide spread usage has been impeded by a low efficiency (0.5–2%) of chromosomal region capture during yeast transformants which in turn requires a time-consuming screen of hundreds of colonies. Here, we demonstrate that pre-treatment of genomic DNA with CRISPR-Cas9 nucleases to generate double-strand breaks near the targeted genomic region results in a dramatic increase in the fraction of gene-positive colonies (up to 32%). As only a dozen or less yeast transformants need to be screened to obtain a clone with the desired chromosomal region, extensive experience with yeast is no longer required. A TAR-CRISPR protocol may help to create a bank of human genes, each represented by a genomic copy containing its native regulatory elements, that would lead to a significant advance in functional, structural and comparative genomics, in diagnostics, gene replacement, generation of animal models for human diseases and has a potential for gene therapy.
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Affiliation(s)
- Nicholas C O Lee
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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Abstract
Today’s laboratory mouse, Mus musculus, has its origins as the ‘house mouse’ of North America and Europe. Beginning with mice bred by mouse fanciers, laboratory stocks (outbred) derived from M. musculus musculus from eastern Europe and M. m. domesticus from western Europe were developed into inbred strains. Since the mid-1980s, additional strains have been developed from Asian mice (M. m. castaneus from Thailand and M. m. molossinus from Japan) and from M. spretus which originated from the western Mediterranean region.
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Brandl C, Ortiz O, Röttig B, Wefers B, Wurst W, Kühn R. Creation of targeted genomic deletions using TALEN or CRISPR/Cas nuclease pairs in one-cell mouse embryos. FEBS Open Bio 2014; 5:26-35. [PMID: 25685662 PMCID: PMC4309836 DOI: 10.1016/j.fob.2014.11.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/25/2014] [Accepted: 11/27/2014] [Indexed: 12/26/2022] Open
Abstract
Targeted genomic deletions can be generated directly in one-cell mouse embryos using sequence-specific nucleases. Deletions occur by end ligation repair and are not supported by homologous recombination. TALEN as well as CRISPR/Cas nucleases can be used. Homozygous mutants exhibiting phenotypes can be obtained in a single step.
The use of TALEN and CRISPR/CAS nucleases is becoming increasingly popular as a means to edit single target sites in one-cell mouse embryos. Nevertheless, an area that has received less attention concerns the engineering of structural genome variants and the necessary religation of two distant double-strand breaks. Herein, we applied pairs of TALEN or sgRNAs and Cas9 to create deletions in the Rab38 gene. We found that the deletion of 3.2 or 9.3 kb, but not of 30 kb, occurs at a frequency of 6–37%. This is sufficient for the direct production of mutants by embryo microinjection. Therefore, deletions up to ∼10 kb can be readily achieved for modeling human disease alleles. This work represents an important step towards the establishment of new protocols that support the ligation of remote DSB ends to achieve even larger rearrangements.
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Affiliation(s)
- Christina Brandl
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Oskar Ortiz
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Bernhard Röttig
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Benedikt Wefers
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany ; Max-Planck-Institute of Psychiatry, 80804 Munich, Germany ; Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
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Hofker MH, Fu J, Wijmenga C. The genome revolution and its role in understanding complex diseases. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1889-1895. [DOI: 10.1016/j.bbadis.2014.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/30/2014] [Accepted: 05/06/2014] [Indexed: 12/26/2022]
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Zhu X, Xu Y, Yu S, Lu L, Ding M, Cheng J, Song G, Gao X, Yao L, Fan D, Meng S, Zhang X, Hu S, Tian Y. An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system. Sci Rep 2014; 4:6420. [PMID: 25236476 PMCID: PMC4168274 DOI: 10.1038/srep06420] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/20/2014] [Indexed: 01/11/2023] Open
Abstract
The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system, and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.
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Affiliation(s)
- Xiaoxiao Zhu
- 1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100080, China [3]
| | - Yajie Xu
- 1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2]
| | - Shanshan Yu
- 1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2]
| | - Lu Lu
- 1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100080, China
| | - Mingqin Ding
- 1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100080, China
| | - Jing Cheng
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoxu Song
- 1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100080, China
| | - Xing Gao
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liangming Yao
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongdong Fan
- 1] Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100080, China
| | - Shu Meng
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuewen Zhang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengdi Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Tian
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Incontro S, Asensio CS, Edwards RH, Nicoll RA. Efficient, complete deletion of synaptic proteins using CRISPR. Neuron 2014; 83:1051-7. [PMID: 25155957 PMCID: PMC4195490 DOI: 10.1016/j.neuron.2014.07.043] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2014] [Indexed: 12/26/2022]
Abstract
One of the most powerful ways to test the function of a protein is to characterize the consequences of its deletion. In the past, this has involved inactivation of the gene by homologous recombination either in the germline or later through conditional deletion. RNA interference (RNAi) provides an alternative way to knock down proteins, but both of these approaches have their limitations. Recently, the CRISPR/Cas9 system has suggested another way to selectively inactivate genes. We have now tested this system in postmitotic neurons by targeting two well-characterized synaptic proteins, the obligatory GluN1 subunit of the NMDA receptor and the GluA2 subunit of the AMPA receptor. Expression of CRISPR/Cas9 in hippocampal slice cultures completely eliminated NMDA receptor and GluA2 function. CRISPR/Cas9 thus provides a powerful tool to study the function of synaptic proteins.
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Affiliation(s)
- Salvatore Incontro
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Cedric S Asensio
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Robert H Edwards
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Roger A Nicoll
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA.
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Makzhami S, Passet B, Halliez S, Castille J, Moazami-Goudarzi K, Duchesne A, Vilotte M, Laude H, Mouillet-Richard S, Béringue V, Vaiman D, Vilotte JL. The prion protein family: a view from the placenta. Front Cell Dev Biol 2014; 2:35. [PMID: 25364742 PMCID: PMC4207016 DOI: 10.3389/fcell.2014.00035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/22/2014] [Indexed: 02/01/2023] Open
Abstract
Based on its developmental pattern of expression, early studies suggested the implication of the mammalian Prion protein PrP, a glycosylphosphatidylinositol-anchored ubiquitously expressed and evolutionary conserved glycoprotein encoded by the Prnp gene, in early embryogenesis. However, gene invalidation in several species did not result in obvious developmental abnormalities and it was only recently that it was associated in mice with intra-uterine growth retardation and placental dysfunction. A proposed explanation for this lack of easily detectable developmental-related phenotype is the existence in the genome of one or more gene (s) able to compensate for the absence of PrP. Indeed, two other members of the Prnp gene family have been recently described, Doppel and Shadoo, and the consequences of their invalidation alongside that of PrP tested in mice. No embryonic defect was observed in mice depleted for Doppel and PrP. Interestingly, the co-invalidation of PrP and Shadoo in two independent studies led to apparently conflicting observations, with no apparent consequences in one report and the observation of a developmental defect of the ectoplacental cone that leads to early embryonic lethality in the other. This short review aims at summarizing these recent, apparently conflicting data highlighting the related biological questions and associated implications in terms of animal and human health.
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Affiliation(s)
- Samira Makzhami
- INRA, UMR1313 Génétique Animale et Biologie Intégrative Jouy-en-Josas, France
| | - Bruno Passet
- INRA, UMR1313 Génétique Animale et Biologie Intégrative Jouy-en-Josas, France
| | - Sophie Halliez
- INRA, U892 Virologie et Immunologie Moléculaires Jouy-en-Josas, France
| | - Johan Castille
- INRA, UMR1313 Génétique Animale et Biologie Intégrative Jouy-en-Josas, France
| | | | - Amandine Duchesne
- INRA, UMR1313 Génétique Animale et Biologie Intégrative Jouy-en-Josas, France
| | - Marthe Vilotte
- INRA, UMR1313 Génétique Animale et Biologie Intégrative Jouy-en-Josas, France
| | - Hubert Laude
- INRA, U892 Virologie et Immunologie Moléculaires Jouy-en-Josas, France
| | - Sophie Mouillet-Richard
- INSERM, UMR-S1124 Signalisation et Physiopathologie Neurologique, Université Paris Descartes Paris, France
| | - Vincent Béringue
- INRA, U892 Virologie et Immunologie Moléculaires Jouy-en-Josas, France
| | - Daniel Vaiman
- Faculté Paris Descartes, UMR8104 CNRS, U1016 INSERM, Institut Cochin Paris, France
| | - Jean-Luc Vilotte
- INRA, UMR1313 Génétique Animale et Biologie Intégrative Jouy-en-Josas, France
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Davis EE, Frangakis S, Katsanis N. Interpreting human genetic variation with in vivo zebrafish assays. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1960-1970. [PMID: 24887202 DOI: 10.1016/j.bbadis.2014.05.024] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/14/2014] [Accepted: 05/24/2014] [Indexed: 12/15/2022]
Abstract
Rapid advances and cost erosion in exome and genome analysis of patients with both rare and common genetic disorders have accelerated gene discovery and illuminated fundamental biological mechanisms. The thrill of discovery has been accompanied, however, with the sobering appreciation that human genomes are burdened with a large number of rare and ultra rare variants, thereby posing a significant challenge in dissecting both the effect of such alleles on protein function and also the biological relevance of these events to patient pathology. In an effort to develop model systems that are able to generate surrogates of human pathologies, a powerful suite of tools have been developed in zebrafish, taking advantage of the relatively small (compared to invertebrate models) evolutionary distance of that genome to humans, the orthology of several organs and signaling processes, and the suitability of this organism for medium and high throughput phenotypic screening. Here we will review the use of this model organism in dissecting human genetic disorders; we will highlight how diverse strategies have informed disease causality and genetic architecture; and we will discuss relative strengths and limitations of these approaches in the context of medical genome sequencing. This article is part of a Special Issue entitled: From Genome to Function.
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Affiliation(s)
- Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA.
| | - Stephan Frangakis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA.
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