1
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Moncaut N. Streamlining mouse genome editing by integrating AAV repair template delivery and CRISPR-Cas electroporation. Lab Anim (NY) 2024; 53:115-116. [PMID: 38600182 PMCID: PMC11068566 DOI: 10.1038/s41684-024-01363-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Affiliation(s)
- Natalia Moncaut
- Genome Editing and Mouse Models, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK.
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2
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McCabe CV, Price PD, Codner GF, Allan AJ, Caulder A, Christou S, Loeffler J, Mackenzie M, Malzer E, Mianné J, Nowicki KJ, O’Neill EJ, Pike FJ, Hutchison M, Petit-Demoulière B, Stewart ME, Gates H, Wells S, Sanderson ND, Teboul L. Long-read sequencing for fast and robust identification of correct genome-edited alleles: PCR-based and Cas9 capture methods. PLoS Genet 2024; 20:e1011187. [PMID: 38457464 PMCID: PMC10954187 DOI: 10.1371/journal.pgen.1011187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/20/2024] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Recent developments in CRISPR/Cas9 genome-editing tools have facilitated the introduction of precise alleles, including genetic intervals spanning several kilobases, directly into the embryo. However, the introduction of donor templates, via homology directed repair, can be erroneous or incomplete and these techniques often produce mosaic founder animals. Thus, newly generated alleles must be verified at the sequence level across the targeted locus. Screening for the presence of the desired mutant allele using traditional sequencing methods can be challenging due to the size of the interval to be sequenced, together with the mosaic nature of founders. METHODOLOGY/PRINCIPAL FINDINGS In order to help disentangle the genetic complexity of these animals, we tested the application of Oxford Nanopore Technologies long-read sequencing at the targeted locus and found that the achievable depth of sequencing is sufficient to offset the sequencing error rate associated with the technology used to validate targeted regions of interest. We have assembled an analysis workflow that facilitates interrogating the entire length of a targeted segment in a single read, to confirm that the intended mutant sequence is present in both heterozygous animals and mosaic founders. We used this workflow to compare the output of PCR-based and Cas9 capture-based targeted sequencing for validation of edited alleles. CONCLUSION Targeted long-read sequencing supports in-depth characterisation of all experimental models that aim to produce knock-in or conditional alleles, including those that contain a mix of genome-edited alleles. PCR- or Cas9 capture-based modalities bring different advantages to the analysis.
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Affiliation(s)
| | - Peter D. Price
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Gemma F. Codner
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Jorik Loeffler
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Elke Malzer
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | | | - Fran J. Pike
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Benoit Petit-Demoulière
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, Illkirch, France
| | | | - Hilary Gates
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Nicholas D. Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
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3
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Kim-Yip RP, McNulty R, Joyce B, Mollica A, Chen PJ, Ravisankar P, Law BK, Liu DR, Toettcher JE, Ivakine EA, Posfai E, Adamson B. Efficient prime editing in two-cell mouse embryos using PEmbryo. Nat Biotechnol 2024:10.1038/s41587-023-02106-x. [PMID: 38321114 DOI: 10.1038/s41587-023-02106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/14/2023] [Indexed: 02/08/2024]
Abstract
Using transient inhibition of DNA mismatch repair during a permissive stage of development, we demonstrate highly efficient prime editing of mouse embryos with few unwanted, local byproducts (average 58% precise edit frequency, 0.5% on-target error frequency across 13 substitution edits at 8 sites), enabling same-generation phenotyping of founders. Whole-genome sequencing reveals that mismatch repair inhibition increases off-target indels at low-complexity regions in the genome without any obvious phenotype in mice.
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Affiliation(s)
- Rebecca P Kim-Yip
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ryan McNulty
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Bradley Joyce
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Antonio Mollica
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Prime Medicine, Inc., Cambridge, MA, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Benjamin K Law
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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4
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Clark B, Kuwalekar M, Fischer B, Woltering J, Biran J, Juntti S, Kratochwil CF, Santos ME, Almeida MV. Genome editing in East African cichlids and tilapias: state-of-the-art and future directions. Open Biol 2023; 13:230257. [PMID: 38018094 PMCID: PMC10685126 DOI: 10.1098/rsob.230257] [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: 08/02/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.
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Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Muktai Kuwalekar
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Joost Woltering
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg 78457, Germany
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Scott Juntti
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Claudius F. Kratochwil
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | | | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
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5
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Bai Y, Bentley L, Ma C, Naveenan N, Cleak J, Wu Y, Simon MM, Westerberg H, Cañas RC, Horner N, Pandey R, Paphiti K, Schulze U, Mianné J, Hough T, Teboul L, de Baaij JH, Cox RD. Cleft palate and minor metabolic disturbances in a mouse global Arl15 gene knockout. FASEB J 2023; 37:e23211. [PMID: 37773757 PMCID: PMC10631251 DOI: 10.1096/fj.202201918r] [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: 11/21/2022] [Revised: 07/27/2023] [Accepted: 09/08/2023] [Indexed: 10/01/2023]
Abstract
ARL15, a small GTPase protein, was linked to metabolic traits in association studies. We aimed to test the Arl15 gene as a functional candidate for metabolic traits in the mouse. CRISPR/Cas9 germline knockout (KO) of Arl15 showed that homozygotes were postnatal lethal and exhibited a complete cleft palate (CP). Also, decreased cell migration was observed from Arl15 KO mouse embryonic fibroblasts (MEFs). Metabolic phenotyping of heterozygotes showed that females had reduced fat mass on a chow diet from 14 weeks of age. Mild body composition phenotypes were also observed in heterozygous mice on a high-fat diet (HFD)/low-fat diet (LFD). Females on a HFD showed reduced body weight, gonadal fat depot weight and brown adipose tissue (BAT) weight. In contrast, in the LFD group, females showed increased bone mineral density (BMD), while males showed a trend toward reduced BMD. Clinical biochemistry analysis of plasma on HFD showed transient lower adiponectin at 20 weeks of age in females. Urinary and plasma Mg2+ concentrations were not significantly different. Our phenotyping data showed that Arl15 is essential for craniofacial development. Adult metabolic phenotyping revealed potential roles in brown adipose tissue and bone development.
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Affiliation(s)
- Ying Bai
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Liz Bentley
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Chao Ma
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - James Cleak
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Yixing Wu
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Michelle M Simon
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Henrik Westerberg
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Ramón Casero Cañas
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Neil Horner
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Rajesh Pandey
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Keanu Paphiti
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | | | - Joffrey Mianné
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Tertius Hough
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Lydia Teboul
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Jeroen H.F. de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Roger D. Cox
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
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6
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Zhang P, Abel L, Casanova JL, Yang R. Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE): An Experimental and Computational Approach for Analyzing CRISPR-Edited Cells. CRISPR J 2023; 6:462-472. [PMID: 37824834 PMCID: PMC10611965 DOI: 10.1089/crispr.2023.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/10/2023] [Indexed: 10/14/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) creates double-stranded breaks, the repair of which generates indels around the target sites. These repairs can be mono-/multi-allelic, and the editing is often random and sometimes prolonged, resulting in considerable intercellular heterogeneity. The genotyping of CRISPR-Cas9-edited cells is challenging and the traditional genotyping methods are laborious. We introduce here a streamlined experimental and computational protocol for genotyping CRISPR-Cas9 genome-edited cells including cost-effective multiplexed sequencing and the software Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE). In this approach, CRISPR-Cas9-edited products are sequenced in great depth, then GMUSCLE quantitatively and qualitatively identifies the genotypes, which enable the selection and investigation of cell clones with genotypes of interest. We validate the protocol and software by performing CRISPR-Cas9-mediated disruption on interferon-α/β receptor alpha, multiplexed sequencing, and identifying the genotypes simultaneously for 20 cell clones. Besides the multiplexed sequencing ability of this protocol, GMUSCLE is also applicable for the sequencing data from bulk cell populations. GMUSCLE is publicly available at our HGIDSOFT server and GitHub.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France; Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France; Necker Hospital for Sick Children, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France; Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France; Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA; and Necker Hospital for Sick Children, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
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7
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Abstract
How might a liberal democratic community best regulate human genetic engineering? Relevant debates widely deploy the usually undefined term "human dignity." Its indeterminacy in meaning and use renders it useless as a guiding principle. In this article, I reject the human genome as somehow invested with a moral status, a position I call "genetic essentialism." I explain why a critique of genetic essentialism is not a strawman and argue against defining human rights in terms of genetic essentialism. As an alternative, I propose dignity as the decisional autonomy of future persons, held in trust by the current generation. I show why a future person could be expected to have an interest in decisional autonomy and how popular deliberation, combined with expert medical and bioethical opinion, could generate principled agreement on how the decisional autonomy of future persons might be configured at the point of genetic engineering.
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8
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Mackenzie M, Fower A, Allan AJ, Codner GF, Bunton-Stasyshyn RK, Teboul L. Genotyping Genome-Edited Founders and Subsequent Generation. Methods Mol Biol 2023; 2631:103-134. [PMID: 36995665 DOI: 10.1007/978-1-0716-2990-1_4] [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] [Indexed: 03/31/2023]
Abstract
Targeted nucleases allow the production of many types of genetic mutations directly in the early embryo. However, the outcome of their activity is a repair event of unpredictable nature, and the founder animals that are produced are generally of a mosaic nature. Here, we present the molecular assays and genotyping strategies that will support the screening of the first generation for potential founders and the validation of positive animals in the subsequent generation, according to the type of mutation generated.
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Affiliation(s)
| | - Alex Fower
- The Mary Lyon Centre, MRC Harwell, Didcot, Oxon, UK
| | | | | | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell, Didcot, Oxon, UK.
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9
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One-Step Genotyping Method in loxP-Based Conditional Knockout Mice Generated by CRISPR-Cas9 Technology. Mol Biotechnol 2022; 64:1227-1233. [PMID: 35503156 PMCID: PMC9515137 DOI: 10.1007/s12033-022-00500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 04/04/2022] [Indexed: 11/21/2022]
Abstract
With the development of CRISPR-Cas9 gene editing and in vitro fertilization (IVF) technology, we can now easily construct genetically modified mouse strains with indels, especially for loxP-based strategy. However, the general genotyping methods are time-consuming and unreliable given the loxP site is only 34 bp long. Here, based on the tetra primer-paired PCR amplification, we describe an efficient genotyping method which can simultaneously generate the internal control band, wild type (wt)-genotype band, and/or loxP-genotype band through one single PCR amplification. It is easy to interpret the mouse genotypes from the pattern of the bands. Further, the results could also help to exclude the possibility of minor cross-contamination, since the ratio between the bands’ quantity in wt/wt, wt/loxP, and loxP/loxP mice are relatively constant, which makes the genotyping more reliable when it is performed in a large amount.
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10
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Hu Y, Lauffer P, Stewart M, Codner G, Mayerl S, Heuer H, Ng L, Forrest D, Trotsenburg P, Jongejan A, Fliers E, Hennekam R, Boelen A. An animal model for Pierpont syndrome; a mouse bearing the Tbl1xr1Y446C/Y446C mutation. Hum Mol Genet 2022; 31:2951-2963. [PMID: 35416977 PMCID: PMC9433735 DOI: 10.1093/hmg/ddac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/23/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
Pierpont syndrome is a rare disorder characterized mainly by global developmental delay, unusual facial features, altered fat distribution in the limbs and hearing loss. A specific mutation (p.Tyr446Cys) in TBL1XR1, encoding a WD40 repeat-containing protein, which is a component of the SMRT/NCoR (silencing mediator retinoid and thyroid hormone receptors/nuclear receptor corepressors), has been reported as the genetic cause of Pierpont syndrome. Here, we used CRISPR-cas9 technology to generate a mutant mouse with the Y446C mutation in Tbl1xr1, which is also present in Pierpont syndrome. Several aspects of the phenotype were studied in the mutant mice: growth, body composition, hearing, motor behavior, thyroid hormone state and lipid and glucose metabolism. The mutant mice (Tbl1xr1Y446C/Y446C) displayed delayed growth, altered body composition with increased relative lean mass and impaired hearing. Expression of several genes involved in fatty acid metabolism differed in white adipose tissue, but not in liver or muscle of mutant mice compared to wild-type mice (Tbl1xr1+/+). No difference in thyroid hormone plasma concentrations was observed. Tbl1xr1Y446C/Y446C mice can be used as a model for distinct features of Pierpont syndrome, which will enable future studies on the pathogenic mechanisms underlying the various phenotypic characteristics.
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Affiliation(s)
- Yalan Hu
- Endocrine Laboratory, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Lauffer
- Department of Pediatric Endocrinology, Emma Children's Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Michelle Stewart
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Gemma Codner
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Steffen Mayerl
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Heike Heuer
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lily Ng
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Douglas Forrest
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Paul Trotsenburg
- Department of Pediatric Endocrinology, Emma Children's Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health, Methodology Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric Fliers
- Department of Endocrinology, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Raoul Hennekam
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anita Boelen
- Endocrine Laboratory, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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11
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Maniego J, Pesko B, Habershon-Butcher J, Hincks P, Taylor P, Tozaki T, Ohnuma A, Stewart G, Proudman C, Ryder E. Use of mitochondrial sequencing to detect gene doping in horses via gene editing and somatic cell nuclear transfer. Drug Test Anal 2022; 14:1429-1437. [PMID: 35362263 DOI: 10.1002/dta.3267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 11/09/2022]
Abstract
Gene editing and subsequent cloning techniques offer great potential not only in genetic disease correction in domestic animals, but also in livestock production by enhancement of desirable traits. The existence of the technology, however, leaves it open to potential misuse in performance-led sports such as horseracing and other equestrian events. Recent advances in equine gene editing, regarding the generation of gene-edited embryos using CRISPR/Cas9 technology and somatic cell nuclear transfer, has highlighted the need to develop tools to detect potential prohibited use of the technology. One possible method involves the characterisation of the mitochondrial genome (which is not routinely preserved during cloning) and comparing it to the sequence of the registered dam. We present here our approach to whole-mitochondrial sequencing using tiled long-range PCR and next-generation sequencing. To determine whether the background mutation rate in the mitochondrial genome could potentially confound results, we sequenced ten sets of dam and foal duos. We found variation between duos but none within duos, indicating that this method is feasible for future screening systems. Analysis of WGS data from over one hundred Thoroughbred horses revealed wide variation in the mitochondria sequence within the breed, further displaying the utility of this approach.
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Affiliation(s)
- Jillian Maniego
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, UK
| | - Bogusia Pesko
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, UK
| | | | - Pamela Hincks
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, UK
| | - Polly Taylor
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, UK
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan
| | - Aoi Ohnuma
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan
| | - Graham Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Christopher Proudman
- School of Veterinary Medicine, Daphne Jackson Road, University of Surrey, Guildford, UK
| | - Edward Ryder
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, UK
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12
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Okada K, Aoki K, Tabei T, Sugio K, Imai K, Bonkohara Y, Kamachi Y. Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9. Nucleic Acids Res 2022; 50:2854-2871. [PMID: 35166844 PMCID: PMC8934663 DOI: 10.1093/nar/gkac100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/22/2022] Open
Abstract
Specific sequence features of the protospacer and protospacer-adjacent motif (PAM) are critical for efficient cleavage by CRISPR-Cas9, but current knowledge is largely derived from single-guide RNA (sgRNA) systems assessed in cultured cells. In this study, we sought to determine gRNA sequence features of a more native CRISPR-Cas9 ribonucleoprotein (RNP) complex with dual-guide RNAs (dgRNAs) composed of crRNA and tracrRNA, which has been used increasingly in recent CRISPR-Cas9 applications, particularly in zebrafish. Using both wild-type and HiFi SpCas9, we determined on-target cleavage efficiencies of 51 crRNAs in zebrafish embryos by assessing indel occurrence. Statistical analysis of these data identified novel position-specific mononucleotide features relevant to cleavage efficiencies throughout the protospacer sequence that may be unique to CRISPR-Cas9 RNPs pre-assembled with perfectly matched gRNAs. Overall features for wild-type Cas9 resembled those for HiFi Cas9, but specific differences were also observed. Mutational analysis of mononucleotide features confirmed their relevance to cleavage efficiencies. Moreover, the mononucleotide feature-based score, CRISPR-kp, correlated well with efficiencies of gRNAs reported in previous zebrafish RNP injection experiments, as well as independently tested crRNAs only in RNP format, but not with Cas9 mRNA co-injection. These findings will facilitate design of gRNA/crRNAs in genome editing applications, especially when using pre-assembled RNPs.
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Affiliation(s)
- Keita Okada
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Kanae Aoki
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Teruyuki Tabei
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Kota Sugio
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Katsunori Imai
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Yuki Bonkohara
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
| | - Yusuke Kamachi
- School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan
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13
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Rajan DS, Kour S, Fortuna TR, Cousin MA, Barnett SS, Niu Z, Babovic-Vuksanovic D, Klee EW, Kirmse B, Innes M, Rydning SL, Selmer KK, Vigeland MD, Erichsen AK, Nemeth AH, Millan F, DeVile C, Fawcett K, Legendre A, Sims D, Schnekenberg RP, Burglen L, Mercier S, Bakhtiari S, Francisco-Velilla R, Embarc-Buh A, Martinez-Salas E, Wigby K, Lenberg J, Friedman JR, Kruer MC, Pandey UB. Autosomal Recessive Cerebellar Atrophy and Spastic Ataxia in Patients With Pathogenic Biallelic Variants in GEMIN5. Front Cell Dev Biol 2022; 10:783762. [PMID: 35295849 PMCID: PMC8918504 DOI: 10.3389/fcell.2022.783762] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/17/2022] [Indexed: 01/01/2023] Open
Abstract
The hereditary ataxias are a heterogenous group of disorders with an increasing number of causative genes being described. Due to the clinical and genetic heterogeneity seen in these conditions, the majority of such individuals endure a diagnostic odyssey or remain undiagnosed. Defining the molecular etiology can bring insights into the responsible molecular pathways and eventually the identification of therapeutic targets. Here, we describe the identification of biallelic variants in the GEMIN5 gene among seven unrelated families with nine affected individuals presenting with spastic ataxia and cerebellar atrophy. GEMIN5, an RNA-binding protein, has been shown to regulate transcription and translation machinery. GEMIN5 is a component of small nuclear ribonucleoprotein (snRNP) complexes and helps in the assembly of the spliceosome complexes. We found that biallelic GEMIN5 variants cause structural abnormalities in the encoded protein and reduce expression of snRNP complex proteins in patient cells compared with unaffected controls. Finally, knocking out endogenous Gemin5 in mice caused early embryonic lethality, suggesting that Gemin5 expression is crucial for normal development. Our work further expands on the phenotypic spectrum associated with GEMIN5-related disease and implicates the role of GEMIN5 among patients with spastic ataxia, cerebellar atrophy, and motor predominant developmental delay.
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Affiliation(s)
- Deepa S. Rajan
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Sukhleen Kour
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Tyler R. Fortuna
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Margot A. Cousin
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Sarah S. Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Zhiyv Niu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Dusica Babovic-Vuksanovic
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Eric W. Klee
- Department of Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Brian Kirmse
- Division of Genetics, University of Mississippi Medical Center, Jackson, MS, United States
| | - Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Kaja K. Selmer
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Magnus Dehli Vigeland
- Department of Medical Genetics, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Andrea H. Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Katherine Fawcett
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Adrien Legendre
- Laboratoire de biologie médicale multisites Seqoia—FMG2025, Paris, France
| | - David Sims
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet et Laboratoire de Neurogénétique Moléculaire, Département de Génétique, AP-HP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Sandra Mercier
- CHU Nantes, Service de génétique médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Nantes, France
- Nantes Université, CNRS, INSERM, l’institut du thorax, Nantes, France
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, United States
- Departments of Child Health, Neurology, Cellular and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, United States
| | | | - Azman Embarc-Buh
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | | | - Kristen Wigby
- Department of Pediatrics, University of California San Diego, San Diego, CA, United States
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Jerica Lenberg
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Jennifer R. Friedman
- Department of Neurosciences, University of California San Diego, San Diego, CA, United States
- Department of Pediatrics, University of California San Diego, San Diego, CA, United States
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States
| | - Michael C. Kruer
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, United States
- Departments of Child Health, Neurology, Cellular and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine—Phoenix, Phoenix, AZ, United States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
- *Correspondence: Udai Bhan Pandey,
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14
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Owens DDG, Anselmi G, Oudelaar AM, Downes DJ, Cavallo A, Harman JR, Schwessinger R, Bucakci A, Greder L, de Ornellas S, Jeziorska D, Telenius J, Hughes JR, de Bruijn MFTR. Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nat Commun 2022; 13:773. [PMID: 35140205 PMCID: PMC8828719 DOI: 10.1038/s41467-022-28376-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/12/2022] [Indexed: 01/22/2023] Open
Abstract
The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.
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Affiliation(s)
- Dominic D G Owens
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Giorgio Anselmi
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Damien J Downes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Alessandro Cavallo
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joe R Harman
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Akin Bucakci
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lucas Greder
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sara de Ornellas
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Physical and Theoretical Chemistry Building, Department of Chemistry, University of Oxford, Oxford, UK
| | - Danuta Jeziorska
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Marella F T R de Bruijn
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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15
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Kuno A, Ikeda Y, Ayabe S, Kato K, Sakamoto K, Suzuki SR, Morimoto K, Wakimoto A, Mikami N, Ishida M, Iki N, Hamada Y, Takemura M, Daitoku Y, Tanimoto Y, Dinh TTH, Murata K, Hamada M, Muratani M, Yoshiki A, Sugiyama F, Takahashi S, Mizuno S. DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. PLoS Biol 2022; 20:e3001507. [PMID: 35041655 PMCID: PMC8765641 DOI: 10.1371/journal.pbio.3001507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.
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Affiliation(s)
- Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Ikeda
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kotaro Sakamoto
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Sayaka R. Suzuki
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Arata Wakimoto
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Natsuki Mikami
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Miyuki Ishida
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Natsumi Iki
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuko Hamada
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Megumi Takemura
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tra Thi Huong Dinh
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuya Murata
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Michito Hamada
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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16
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Birling MC, Fray MD, Kasparek P, Kopkanova J, Massimi M, Matteoni R, Montoliu L, Nutter LMJ, Raspa M, Rozman J, Ryder EJ, Scavizzi F, Voikar V, Wells S, Pavlovic G, Teboul L. Importing genetically altered animals: ensuring quality. Mamm Genome 2021; 33:100-107. [PMID: 34536110 PMCID: PMC8913481 DOI: 10.1007/s00335-021-09908-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022]
Abstract
The reproducibility of research using laboratory animals requires reliable management of their quality, in particular of their genetics, health and environment, all of which contribute to their phenotypes. The point at which these biological materials are transferred between researchers is particularly sensitive, as it may result in a loss of integrity of the animals and/or their documentation. Here, we describe the various aspects of laboratory animal quality that should be confirmed when sharing rodent research models. We also discuss how repositories of biological materials support the scientific community to ensure the continuity of the quality of laboratory animals. Both the concept of quality and the role of repositories themselves extend to all exchanges of biological materials and all networks that support the sharing of these reagents.
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Affiliation(s)
- M-C Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, 67404, Strasbourg, France.
| | - M D Fray
- The Mary Lyon Centre, Medical Research Council Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
| | - P Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - J Kopkanova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - M Massimi
- Institute of Biochemistry and Cell Biology, Italian National Research Council (CNR), Monterotondo Scalo, Rome, Italy
| | - R Matteoni
- Institute of Biochemistry and Cell Biology, Italian National Research Council (CNR), Monterotondo Scalo, Rome, Italy
| | - L Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC) Madrid and CIBERER-ISCIII, Madrid, Spain
| | - L M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Raspa
- Institute of Biochemistry and Cell Biology, Italian National Research Council (CNR), Monterotondo Scalo, Rome, Italy
| | - J Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - E J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,LGC, Sport and Specialised Analytical Services, Fordham, UK
| | - F Scavizzi
- Institute of Biochemistry and Cell Biology, Italian National Research Council (CNR), Monterotondo Scalo, Rome, Italy
| | - V Voikar
- Neuroscience Center and Laboratory Animal Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - S Wells
- The Mary Lyon Centre, Medical Research Council Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
| | - G Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, 67404, Strasbourg, France.
| | - L Teboul
- The Mary Lyon Centre, Medical Research Council Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK.
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17
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Abstract
The emergence of an array of genome-editing tools in recent years has facilitated the introduction of genetic modifications directly into the embryo, increasing the ease, efficiency and catalogue of alleles accessible to researchers across a range of species. Bypassing the requirement for a selection cassette and resulting in a broad range of outcomes besides the desired allele, genome editing has altered the allele validation process both temporally and technically. Whereas traditional gene targeting relies upon selection and allows allele validation at the embryonic stem cell modification stage, screening for the presence of the intended allele now occurs in the (frequently mosaic) founder animals. Final confirmation of the edited allele can only take place at the subsequent G1 generation and the validation strategy must differentiate the desired allele from a range of unintended outcomes. Here we present some of the challenges posed by gene editing, strategies for validation and considerations for animal colony management.
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Affiliation(s)
| | - Gemma F Codner
- The Mary Lyon Centre, Medical Research Council Harwell Institute, UK
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, UK
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18
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Gertsenstein M, Nutter LMJ. Production of knockout mouse lines with Cas9. Methods 2021; 191:32-43. [PMID: 33524495 DOI: 10.1016/j.ymeth.2021.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/05/2020] [Accepted: 01/13/2021] [Indexed: 12/26/2022] Open
Abstract
Knockout mice are used extensively to explore the phenotypic effects of mammalian gene dysfunction. With the application of RNA-guided Cas9 nuclease technology for the production of knockout mouse lines, the time, as well as the resources needed, to progress from identification of a gene of interest to production of a knockout line is significantly reduced. Here we present our standard methodology to produce knockout mouse lines by the electroporation of Cas9 ribonucleoprotein (RNP) into mouse zygotes. Using this protocol, we have obtained an 80% success rate in the generation of founders for null alleles with a subsequent 93% germline transmission rate. These methods rely on equipment already present in the majority of transgenic facilities and should be straightforward to implement where appropriate embryo handling expertise exists.
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Affiliation(s)
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto M5T 3H7, Canada; The Hospital for Sick Children, Toronto M5G 1X8, Canada
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19
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Laber S, Forcisi S, Bentley L, Petzold J, Moritz F, Smirnov KS, Al Sadat L, Williamson I, Strobel S, Agnew T, Sengupta S, Nicol T, Grallert H, Heier M, Honecker J, Mianne J, Teboul L, Dumbell R, Long H, Simon M, Lindgren C, Bickmore WA, Hauner H, Schmitt-Kopplin P, Claussnitzer M, Cox RD. Linking the FTO obesity rs1421085 variant circuitry to cellular, metabolic, and organismal phenotypes in vivo. SCIENCE ADVANCES 2021; 7:eabg0108. [PMID: 34290091 PMCID: PMC8294759 DOI: 10.1126/sciadv.abg0108] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/04/2021] [Indexed: 05/09/2023]
Abstract
Variants in FTO have the strongest association with obesity; however, it is still unclear how those noncoding variants mechanistically affect whole-body physiology. We engineered a deletion of the rs1421085 conserved cis-regulatory module (CRM) in mice and confirmed in vivo that the CRM modulates Irx3 and Irx5 gene expression and mitochondrial function in adipocytes. The CRM affects molecular and cellular phenotypes in an adipose depot-dependent manner and affects organismal phenotypes that are relevant for obesity, including decreased high-fat diet-induced weight gain, decreased whole-body fat mass, and decreased skin fat thickness. Last, we connected the CRM to a genetically determined effect on steroid patterns in males that was dependent on nutritional challenge and conserved across mice and humans. Together, our data establish cross-species conservation of the rs1421085 regulatory circuitry at the molecular, cellular, metabolic, and organismal level, revealing previously unknown contextual dependence of the variant's action.
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Affiliation(s)
- Samantha Laber
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sara Forcisi
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Liz Bentley
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Julia Petzold
- Institute of Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Franco Moritz
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kirill S Smirnov
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Loubna Al Sadat
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Else Kröner-Fresenius-Centre for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Sophie Strobel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute of Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Thomas Agnew
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Shahana Sengupta
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Tom Nicol
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Center Munich, Germany
| | - Margit Heier
- KORA Study Center Augsburg, University Hospital of Augsburg, Augsburg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Munich, Germany
| | - Julius Honecker
- Else Kröner-Fresenius-Centre for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Joffrey Mianne
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, UK
| | - Lydia Teboul
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, UK
| | - Rebecca Dumbell
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Helen Long
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
- Nuffield Department of Medicine, University of Oxford, Henry Wellcome Building for Molecular Physiology, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Michelle Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Cecilia Lindgren
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Hans Hauner
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Else Kröner-Fresenius-Centre for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Analytical Food Chemistry, Technical University of Munich, Freising, Germany
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA, USA
| | - Roger D Cox
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK.
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20
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Sachse G, Haythorne E, Hill T, Proks P, Joynson R, Terrón-Expósito R, Bentley L, Tucker SJ, Cox RD, Ashcroft FM. The KCNJ11-E23K Gene Variant Hastens Diabetes Progression by Impairing Glucose-Induced Insulin Secretion. Diabetes 2021; 70:1145-1156. [PMID: 33568422 DOI: 10.2337/db20-0691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022]
Abstract
The ATP-sensitive K+ (KATP) channel controls blood glucose levels by coupling glucose metabolism to insulin secretion in pancreatic β-cells. E23K, a common polymorphism in the pore-forming KATP channel subunit (KCNJ11) gene, has been linked to increased risk of type 2 diabetes. Understanding the risk-allele-specific pathogenesis has the potential to improve personalized diabetes treatment, but the underlying mechanism has remained elusive. Using a genetically engineered mouse model, we now show that the K23 variant impairs glucose-induced insulin secretion and increases diabetes risk when combined with a high-fat diet (HFD) and obesity. KATP-channels in β-cells with two K23 risk alleles (KK) showed decreased ATP inhibition, and the threshold for glucose-stimulated insulin secretion from KK islets was increased. Consequently, the insulin response to glucose and glycemic control was impaired in KK mice fed a standard diet. On an HFD, the effects of the KK genotype were exacerbated, accelerating diet-induced diabetes progression and causing β-cell failure. We conclude that the K23 variant increases diabetes risk by impairing insulin secretion at threshold glucose levels, thus accelerating loss of β-cell function in the early stages of diabetes progression.
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Affiliation(s)
- Gregor Sachse
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, U.K.
| | - Elizabeth Haythorne
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, U.K
| | - Thomas Hill
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, U.K
| | - Peter Proks
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, U.K
- Department of Physics, University of Oxford, Oxford, U.K
| | - Russell Joynson
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, U.K
| | - Raul Terrón-Expósito
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, U.K
| | - Liz Bentley
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, U.K
| | | | - Roger D Cox
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, U.K
| | - Frances M Ashcroft
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, U.K
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21
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Lindner L, Cayrou P, Rosahl TW, Zhou HH, Birling MC, Herault Y, Pavlovic G. Droplet digital PCR or quantitative PCR for in-depth genomic and functional validation of genetically altered rodents. Methods 2021; 191:107-119. [PMID: 33838271 DOI: 10.1016/j.ymeth.2021.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Gene targeting and additive (random) transgenesis have proven to be powerful technologies with which to decipher the mammalian genome. With the advent of CRISPR/Cas9 genome editing, the ability to inactivate or modify the function of a gene has become even more accessible. However, the impact of each generated modification may be different from what was initially desired. Minimal validation of mutant alleles from genetically altered (GA) rodents remains essential to guarantee the interpretation of experimental results. The protocol described here combines design strategies for genomic and functional validation of genetically modified alleles with droplet digital PCR (ddPCR) or quantitative PCR (qPCR) for target DNA or mRNA quantification. In-depth analysis of the results obtained with GA models through the analysis of target DNA and mRNA quantification is also provided, to evaluate which pitfalls can be detected using these two methods, and we propose recommendations for the characterization of different type of mutant allele (knock-out, knock-in, conditional knock-out, FLEx, IKMC model or transgenic). Our results also highlight the possibility that mRNA expression of any mutated allele can be different from what might be expected in theory or according to common assumptions. For example, mRNA analyses on knock-out lines showed that nonsense-mediated mRNA decay is generally not achieved with a critical-exon approach. Likewise, comparison of multiple conditional lines crossed with the same CreERT2 deleter showed that the inactivation outcome was very different for each conditional model. DNA quantification by ddPCR of G0 to G2 generations of transgenic rodents generated by pronuclear injection showed an unexpected variability, demonstrating that G1 generation rodents cannot be considered as established lines.
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Affiliation(s)
- Loic Lindner
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Pauline Cayrou
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Thomas W Rosahl
- Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Heather H Zhou
- Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Yann Herault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France.
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22
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Gurumurthy CB, Saunders TL, Ohtsuka M. Designing and generating a mouse model: frequently asked questions. J Biomed Res 2021; 35:76-90. [PMID: 33797414 PMCID: PMC8038528 DOI: 10.7555/jbr.35.20200197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetically engineered mouse (GEM) models are commonly used in biomedical research. Generating GEMs involve complex set of experimental procedures requiring sophisticated equipment and highly skilled technical staff. Because of these reasons, most research institutes set up centralized core facilities where custom GEMs are created for research groups. Researchers, on the other hand, when they begin thinking about generating GEMs for their research, several questions arise in their minds. For example, what type of model(s) would be best useful for my research, how do I design them, what are the latest technologies and tools available for developing my model(s), and finally how to breed GEMs in my research. As there are several considerations and options in mouse designs, and as it is an expensive and time-consuming endeavor, careful planning upfront can ensure the highest chance of success. In this article, we provide brief answers to several frequently asked questions that arise when researchers begin thinking about generating mouse model(s) for their work.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
| | - Thomas L Saunders
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.,The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan
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23
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Horner NR, Venkataraman S, Armit C, Casero R, Brown JM, Wong MD, van Eede MC, Henkelman RM, Johnson S, Teboul L, Wells S, Brown SD, Westerberg H, Mallon AM. LAMA: automated image analysis for the developmental phenotyping of mouse embryos. Development 2021; 148:dev192955. [PMID: 33574040 PMCID: PMC8015254 DOI: 10.1242/dev.192955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022]
Abstract
Advanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines.
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Affiliation(s)
- Neil R Horner
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Shanmugasundaram Venkataraman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Chris Armit
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
- BGI Hong Kong, 26/F, Kings Wing Plaza 2, 1 On Kwan Street, Shek Mun, New Territories, Hong Kong
| | - Ramón Casero
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - James M Brown
- School of Computer Science, University of Lincoln, Lincoln LN6 7TS
| | - Michael D Wong
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Matthijs C van Eede
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Sara Johnson
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Sara Wells
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Steve D Brown
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
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24
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van der Weyden L, Harle V, Turner G, Offord V, Iyer V, Droop A, Swiatkowska A, Rabbie R, Campbell AD, Sansom OJ, Pardo M, Choudhary JS, Ferreira I, Tullett M, Arends MJ, Speak AO, Adams DJ. CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation. Commun Biol 2021; 4:395. [PMID: 33758365 PMCID: PMC7987976 DOI: 10.1038/s42003-021-01912-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 02/25/2021] [Indexed: 02/08/2023] Open
Abstract
Melanoma represents ~5% of all cutaneous malignancies, yet accounts for the majority of skin cancer deaths due to its propensity to metastasise. To develop new therapies, novel target molecules must to be identified and the accessibility of cell surface proteins makes them attractive targets. Using CRISPR activation technology, we screened a library of guide RNAs targeting membrane protein-encoding genes to identify cell surface molecules whose upregulation enhances the metastatic pulmonary colonisation capabilities of tumour cells in vivo. We show that upregulated expression of the cell surface protein LRRN4CL led to increased pulmonary metastases in mice. Critically, LRRN4CL expression was elevated in melanoma patient samples, with high expression levels correlating with decreased survival. Collectively, our findings uncover an unappreciated role for LRRN4CL in the outcome of melanoma patients and identifies a potential therapeutic target and biomarker.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- CRISPR-Cas Systems
- Cell Line, Tumor
- Cell Movement
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/secondary
- Male
- Melanoma, Experimental/genetics
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/secondary
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Knockout
- Neoplasm Invasiveness
- Skin Neoplasms/genetics
- Skin Neoplasms/metabolism
- Skin Neoplasms/pathology
- Up-Regulation
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Affiliation(s)
| | - Victoria Harle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gemma Turner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alastair Droop
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Roy Rabbie
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ingrid Ferreira
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mark Tullett
- Western Sussex NHS Foundation Trust, Chichester, West Sussex, UK
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Edinburgh Cancer Research UK Cancer Centre, Institute of Genetics & Molecular Medicine, Edinburgh, UK
| | - Anneliese O Speak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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25
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Hannan FM, Stevenson M, Bayliss AL, Stokes VJ, Stewart M, Kooblall KG, Gorvin CM, Codner G, Teboul L, Wells S, Thakker RV. Ap2s1 mutation causes hypercalcaemia in mice and impairs interaction between calcium-sensing receptor and adaptor protein-2. Hum Mol Genet 2021; 30:880-892. [PMID: 33729479 PMCID: PMC8165646 DOI: 10.1093/hmg/ddab076] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/09/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Adaptor protein 2 (AP2), a heterotetrameric complex comprising AP2α, AP2β2, AP2μ2 and AP2σ2 subunits, is ubiquitously expressed and involved in endocytosis and trafficking of membrane proteins, such as the calcium-sensing receptor (CaSR), a G-protein coupled receptor that signals via Gα11. Mutations of CaSR, Gα11 and AP2σ2, encoded by AP2S1, cause familial hypocalciuric hypercalcaemia types 1–3 (FHH1–3), respectively. FHH3 patients have heterozygous AP2S1 missense Arg15 mutations (p.Arg15Cys, p.Arg15His or p.Arg15Leu) with hypercalcaemia, which may be marked and symptomatic, and occasional hypophosphataemia and osteomalacia. To further characterize the phenotypic spectrum and calcitropic pathophysiology of FHH3, we used CRISPR/Cas9 genome editing to generate mice harboring the AP2S1 p.Arg15Leu mutation, which causes the most severe FHH3 phenotype. Heterozygous (Ap2s1+/L15) mice were viable, and had marked hypercalcaemia, hypermagnesaemia, hypophosphataemia, and increases in alkaline phosphatase activity and fibroblast growth factor-23. Plasma 1,25-dihydroxyvitamin D was normal, and no alterations in bone mineral density or bone turnover were noted. Homozygous (Ap2s1L15/L15) mice invariably died perinatally. Co-immunoprecipitation studies showed that the AP2S1 p.Arg15Leu mutation impaired protein–protein interactions between AP2σ2 and the other AP2 subunits, and also with the CaSR. Cinacalcet, a CaSR positive allosteric modulator, decreased plasma calcium and parathyroid hormone concentrations in Ap2s1+/L15 mice, but had no effect on the diminished AP2σ2-CaSR interaction in vitro. Thus, our studies have established a mouse model that is representative for FHH3 in humans, and demonstrated that the AP2S1 p.Arg15Leu mutation causes a predominantly calcitropic phenotype, which can be ameliorated by treatment with cinacalcet.
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Affiliation(s)
- Fadil M Hannan
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK.,Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Asha L Bayliss
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Victoria J Stokes
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Michelle Stewart
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Kreepa G Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Caroline M Gorvin
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Gemma Codner
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Lydia Teboul
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Sara Wells
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
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26
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Ratner LD, La Motta GE, Briski O, Salamone DF, Fernandez-Martin R. Practical Approaches for Knock-Out Gene Editing in Pigs. Front Genet 2021; 11:617850. [PMID: 33747029 PMCID: PMC7973260 DOI: 10.3389/fgene.2020.617850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022] Open
Abstract
Pigs are an important resource for meat production and serve as a model for human diseases. Due to their physiological and anatomical similarities to humans, these animals can recapitulate symptoms of human diseases, becoming an effective model for biomedical research. Although, in the past pig have not been widely used partially because of the difficulty in genetic modification; nowadays, with the new revolutionary technology of programmable nucleases, and fundamentally of the CRISPR-Cas9 systems, it is possible for the first time to precisely modify the porcine genome as never before. To this purpose, it is necessary to introduce the system into early stage zygotes or to edit cells followed by somatic cell nuclear transfer. In this review, several strategies for pig knock-out gene editing, using the CRISPR-Cas9 system, will be summarized, as well as genotyping methods and different delivery techniques to introduce these tools into the embryos. Finally, the best approaches to produce homogeneous, biallelic edited animals will be discussed.
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Affiliation(s)
- Laura Daniela Ratner
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gaston Emilio La Motta
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Olinda Briski
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Felipe Salamone
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Fernandez-Martin
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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27
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One-Step Generation of Multiple Gene-Edited Pigs by Electroporation of the CRISPR/Cas9 System into Zygotes to Reduce Xenoantigen Biosynthesis. Int J Mol Sci 2021; 22:ijms22052249. [PMID: 33668187 PMCID: PMC7956194 DOI: 10.3390/ijms22052249] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 02/08/2023] Open
Abstract
Xenoantigens cause hyperacute rejection and limit the success of interspecific xenografts. Therefore, genes involved in xenoantigen biosynthesis, such as GGTA1, CMAH, and B4GALNT2, are key targets to improve the outcomes of xenotransplantation. In this study, we introduced a CRISPR/Cas9 system simultaneously targeting GGTA1, CMAH, and B4GALNT2 into in vitro-fertilized zygotes using electroporation for the one-step generation of multiple gene-edited pigs without xenoantigens. First, we optimized the combination of guide RNAs (gRNAs) targeting GGTA1 and CMAH with respect to gene editing efficiency in zygotes, and transferred electroporated embryos with the optimized gRNAs and Cas9 into recipient gilts. Next, we optimized the Cas9 protein concentration with respect to the gene editing efficiency when GGTA1, CMAH, and B4GALNT2 were targeted simultaneously, and generated gene-edited pigs using the optimized conditions. We achieved the one-step generation of GGTA1/CMAH double-edited pigs and GGTA1/CMAH/B4GALNT2 triple-edited pigs. Immunohistological analyses demonstrated the downregulation of xenoantigens; however, these multiple gene-edited pigs were genetic mosaics that failed to knock out some xenoantigens. Although mosaicism should be resolved, the electroporation technique could become a primary method for the one-step generation of multiple gene modifications in pigs aimed at improving pig-to-human xenotransplantation.
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28
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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29
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Lee NE, Ha DI, Ko JH, Kim YS. One-step genotyping method in CRISPR based on short inner primer-assisted, tetra primer-paired amplifications. Mol Cell Probes 2021; 55:101675. [PMID: 33245992 DOI: 10.1016/j.mcp.2020.101675] [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] [Received: 10/26/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 11/26/2022]
Abstract
Base editors and prime editors induce precise DNA modifications over one or several nucleotides in eukaryotic cells. The T7E1 assay has been widely adopted for the assessment of genome editing, but it has several limitations in the applications for prime editing and base editing due to low sensitivity, inaccuracy and additional disadvantages. Here, we propose a short inner primer-assisted, tetra primer-paired amplification (SIPATA) method as an alternative to T7E1 analysis. SIPATA is a PCR-based method in which two long outer and two short (15 nt) inner primers are used for the amplification of a specific genotype in the presence of Hot start-Taq. One of the inner primers carries a 3'-terminally wild-type nucleotide sequence, and the other carries a post-editing sequence. Under optimized conditions, SIPATA enabled sensitive and accurate genotyping of single-nucleotide conversions by base editors and prime editors. Furthermore, SIPATA could be applied to trace low levels of DNA modifications achieved by HDR-mediated gene correction or chimerism during the generation of model animals. Multiplexed genotyping was also possible without compromising those multifaceted analytical advantages of SIPATA. Our findings demonstrate that SIPATA offers a robust, fast and sensitive genotyping platform for single-nucleotide variations in a variety of CRISPR applications.
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Affiliation(s)
- Nan-Ee Lee
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea
| | - Dae-In Ha
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea
| | - Jeong-Heon Ko
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea; GenKOre, Daejeon (34141), Republic of Korea.
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30
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Leung KY, De Castro SCP, Galea GL, Copp AJ, Greene NDE. Glycine Cleavage System H Protein Is Essential for Embryonic Viability, Implying Additional Function Beyond the Glycine Cleavage System. Front Genet 2021; 12:625120. [PMID: 33569080 PMCID: PMC7868403 DOI: 10.3389/fgene.2021.625120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/04/2021] [Indexed: 12/03/2022] Open
Abstract
Glycine cleavage system H protein (GCSH) is a component of the glycine cleavage system (GCS), a conserved protein complex that acts to decarboxylate glycine. Mutation of AMT or GLDC, encoding the GCS components aminomethyltransferase and glycine decarboxylase, can cause malformations of the developing CNS (neural tube defects (NTDs) and ventriculomegaly) as well as a post-natal life-limiting neurometabolic disorder, Non-Ketotic Hyperglycinemia. In contrast, it is unclear whether mutation of GCSH contributes to these conditions and we therefore investigated GCSH loss of function in mice. Mice that were heterozygous for a Gcsh null allele were viable and did not exhibit elevated plasma glycine. Moreover, heterozygous mutation of Gcsh did not increase the frequency of NTDs in Gldc mutant embryos. Homozygous Gcsh null mice were not recovered at post-natal stages. Analysis of litters at E8.5-10.5, revealed the presence of homozygous null embryos which were much smaller than littermates and had failed to develop beyond early post-implantation stages with no visible somites or head-folds. Hence, unlike null mutations of Gldc or Amt, which are compatible with embryonic survival despite the presence of NTDs, loss of Gcsh causes embryonic death prior to mid-gestation. Maternal supplementation with formate did not restore embryonic development beyond E7.5, suggesting that the primary cause of lethality was not loss of glycine cleavage activity or suppression of folate one-carbon metabolism. These findings suggest that GCSH has additional roles beyond function in the glycine cleavage system. We hypothesize that GCSH potentially acts in lipoylation of 2-oxoacid dehydrogenase proteins, as reported in bacteria.
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Affiliation(s)
- Kit-Yi Leung
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sandra C P De Castro
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Gabriel L Galea
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Andrew J Copp
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Nicholas D E Greene
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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31
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Burgio G, Teboul L. Anticipating and Identifying Collateral Damage in Genome Editing. Trends Genet 2020; 36:905-914. [PMID: 33039248 PMCID: PMC7658041 DOI: 10.1016/j.tig.2020.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023]
Abstract
Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion article discusses how to anticipate and detect those editing events by a combination of assays to capture all possible genomic changes. It also discusses strategies for preventing unwanted effects, critical to appraise the benefit or risk associated with the use of the technology. Anticipating and verifying the result of genome editing are essential for the success for all applications.
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Affiliation(s)
- Gaëtan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, ACT 2603, Australia.
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK.
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Chang J, Chen X, Zhang T, Wang R, Wang A, Lan X, Zhou Y, Ma S, Xia Q. The novel insight into the outcomes of CRISPR/Cas9 editing intra- and inter-species. Int J Biol Macromol 2020; 163:711-717. [PMID: 32652159 DOI: 10.1016/j.ijbiomac.2020.07.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
The CRISPR/Cas (clustered regularly interspaced short palindromic repeat technology/CRISPR-associated protein) is a widely used and powerful research tool in biosciences and a promising therapeutic agent for treating genetic diseases. Mutations induced by Cas9 are generally considered stochastic and unpredictable, thus hindering its applications where precise genetic alternations are required. Here, through deep sequencing and analysis of genome editing outcomes of multiple sites in four distinct species, we found that Cas9-induced mutations are coincident in mutation types but are significantly different in indel patterns among species. In human and mouse cells, indels were almost evenly distributed at both ends of the cleavage sites. However, the indels mainly appeared at the upstream of cleavage sites in Bombyx mori, while they predominantly occurred downstream of the cleavage sites in the zebrafish Danio rerio. We also found that within a species, indel patterns are sequence dependent, wherein deletions between two adjacent micro-homology sequences were the most frequently observed mutations in the repair spectrum. These results suggested the species differences in DNA repair processes during Cas9-induced gene editing, and the important role of sequence structure at the target site in predicting the gene editing outcome.
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Affiliation(s)
- Jiasong Chang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xiaoxu Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ruolin Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Aoming Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xinhui Lan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Yuyu Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
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Gleeson D, Sethi D, Platte R, Burvill J, Barrett D, Akhtar S, Bruntraeger M, Bottomley J, Mouse Genetics Project S, Bussell J, Ryder E. High-throughput genotyping of high-homology mutant mouse strains by next-generation sequencing. Methods 2020; 191:78-86. [PMID: 33096238 PMCID: PMC8205115 DOI: 10.1016/j.ymeth.2020.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/25/2020] [Accepted: 10/18/2020] [Indexed: 11/05/2022] Open
Abstract
Next generation sequencing is a scalable solution to genotyping mutant mice. Ratios of wild type and mutant sequence counts are used to call the genotype. Hundreds of samples can be multiplexed into one sequencing experiment. Amplification of high-homology genes can be easily filtered out during analysis.
Genotyping of knockout alleles in mice is commonly performed by end-point PCR or gene-specific/universal cassette qPCR. Both have advantages and limitations in terms of assay design and interpretation of results. As an alternative method for high-throughput genotyping, we investigated next generation sequencing (NGS) of PCR amplicons, with a focus on CRISPR-mediated exon deletions where antibiotic selection markers are not present. By multiplexing the wild type and mutant-specific PCR reactions, the genotype can be called by the relative sequence counts of each product. The system is highly scalable and can be applied to a variety of different allele types, including those produced by the International Mouse Phenotyping Consortium and associated projects. One potential challenge with any assay design is locating unique areas of the genome, especially when working with gene families or regions of high homology. These can result in misleading or ambiguous genotypes for either qPCR or end-point assays. Here, we show that genotyping by NGS can negate these issues by simple, automated filtering of undesired sequences. Analysis and genotype calls can also be fully automated, using FASTQ or FASTA input files and an in-house Perl script and SQL database.
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Affiliation(s)
- Diane Gleeson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Debarati Sethi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Radka Platte
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jonathan Burvill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Shaheen Akhtar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Michaela Bruntraeger
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Joanna Bottomley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - James Bussell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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34
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Camargo LSA, Owen JR, Van Eenennaam AL, Ross PJ. Efficient One-Step Knockout by Electroporation of Ribonucleoproteins Into Zona-Intact Bovine Embryos. Front Genet 2020; 11:570069. [PMID: 33133156 PMCID: PMC7504904 DOI: 10.3389/fgene.2020.570069] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
Somatic cell nuclear transfer or cytoplasm microinjection have been used to generate genome-edited farm animals; however, these methods have several drawbacks that reduce their efficiency. This study aimed to develop electroporation conditions that allow delivery of CRISPR/Cas9 system to bovine zygotes for efficient gene knock-out. We optimized electroporation conditions to deliver Cas9:sgRNA ribonucleoproteins to bovine zygotes without compromising embryo development. Higher electroporation pulse voltage resulted in increased membrane permeability; however, voltages above 15 V/mm decreased embryo developmental potential. The zona pellucida of bovine embryos was not a barrier to efficient RNP electroporation. Using parameters optimized for maximal membrane permeability while maintaining developmental competence we achieved high rates of gene editing when targeting bovine OCT4, which resulted in absence of OCT4 protein in 100% of the evaluated embryos and the expected arrest of embryonic development at the morula stage. In conclusion, Cas9:sgRNA ribonucleoproteins can be delivered efficiently by electroporation to zona-intact bovine zygotes, resulting in efficient gene knockouts.
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Affiliation(s)
| | - Joseph R Owen
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | | | - Pablo Juan Ross
- Department of Animal Science, University of California, Davis, Davis, CA, United States
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35
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Diverse species-specific phenotypic consequences of loss of function sorting nexin 14 mutations. Sci Rep 2020; 10:13763. [PMID: 32792680 PMCID: PMC7427099 DOI: 10.1038/s41598-020-70797-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 08/05/2020] [Indexed: 11/08/2022] Open
Abstract
Mutations in the SNX14 gene cause spinocerebellar ataxia, autosomal recessive 20 (SCAR20) in both humans and dogs. Studies implicating the phenotypic consequences of SNX14 mutations to be consequences of subcellular disruption to autophagy and lipid metabolism have been limited to in vitro investigation of patient-derived dermal fibroblasts, laboratory engineered cell lines and developmental analysis of zebrafish morphants. SNX14 homologues Snz (Drosophila) and Mdm1 (yeast) have also been conducted, demonstrated an important biochemical role during lipid biogenesis. In this study we report the effect of loss of SNX14 in mice, which resulted in embryonic lethality around mid-gestation due to placental pathology that involves severe disruption to syncytiotrophoblast cell differentiation. In contrast to other vertebrates, zebrafish carrying a homozygous, maternal zygotic snx14 genetic loss-of-function mutation were both viable and anatomically normal. Whilst no obvious behavioural effects were observed, elevated levels of neutral lipids and phospholipids resemble previously reported effects on lipid homeostasis in other species. The biochemical role of SNX14 therefore appears largely conserved through evolution while the consequences of loss of function varies between species. Mouse and zebrafish models therefore provide valuable insights into the functional importance of SNX14 with distinct opportunities for investigating its cellular and metabolic function in vivo.
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36
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Mianné J, Bourguignon C, Nguyen Van C, Fieldès M, Nasri A, Assou S, De Vos J. Pipeline for the Generation and Characterization of Transgenic Human Pluripotent Stem Cells Using the CRISPR/Cas9 Technology. Cells 2020; 9:cells9051312. [PMID: 32466123 PMCID: PMC7290981 DOI: 10.3390/cells9051312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
Recent advances in genome engineering based on the CRISPR/Cas9 technology have revolutionized our ability to manipulate genomic DNA. Its use in human pluripotent stem cells (hPSCs) has allowed a wide range of mutant cell lines to be obtained at an unprecedented rate. The combination of these two groundbreaking technologies has tremendous potential, from disease modeling to stem cell-based therapies. However, the generation, screening and molecular characterization of these cell lines remain a cumbersome and multi-step endeavor. Here, we propose a pipeline of strategies to efficiently generate, sub-clone, and characterize CRISPR/Cas9-edited hPSC lines in the function of the introduced mutation (indels, point mutations, insertion of large constructs, deletions).
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Affiliation(s)
- Joffrey Mianné
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Chloé Bourguignon
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Chloé Nguyen Van
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Mathieu Fieldès
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Amel Nasri
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
| | - Said Assou
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
- Correspondence: (S.A.); (J.D.V.)
| | - John De Vos
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, 34000 Montpellier, France; (J.M.); (C.B.); (C.N.V.); (M.F.); (A.N.)
- Department of Cell and Tissue Engineering, Univ Montpellier, CHU Montpellier, 34000 Montpellier, France
- Correspondence: (S.A.); (J.D.V.)
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Mizuno-Iijima S, Ayabe S, Kato K, Matoba S, Ikeda Y, Dinh TTH, Le HT, Suzuki H, Nakashima K, Hasegawa Y, Hamada Y, Tanimoto Y, Daitoku Y, Iki N, Ishida M, Ibrahim EAE, Nakashiba T, Hamada M, Murata K, Miwa Y, Okada-Iwabu M, Iwabu M, Yagami KI, Ogura A, Obata Y, Takahashi S, Mizuno S, Yoshiki A, Sugiyama F. Efficient production of large deletion and gene fragment knock-in mice mediated by genome editing with Cas9-mouse Cdt1 in mouse zygotes. Methods 2020; 191:23-31. [PMID: 32334080 DOI: 10.1016/j.ymeth.2020.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Genetically modified mouse models are essential for in vivo investigation of gene function and human disease research. Targeted mutations can be introduced into mouse embryos using genome editing technology such as CRISPR-Cas. Although mice with small indel mutations can be produced, the production of mice carrying large deletions or gene fragment knock-in alleles remains inefficient. We introduced the nuclear localisation property of Cdt1 protein into the CRISPR-Cas system for efficient production of genetically engineered mice. Mouse Cdt1-connected Cas9 (Cas9-mC) was present in the nucleus of HEK293T cells and mouse embryos. Cas9-mC induced a bi-allelic full deletion of Dmd, GC-rich fragment knock-in, and floxed allele knock-in with high efficiency compared to standard Cas9. These results indicate that Cas9-mC is a useful tool for producing mouse models carrying targeted mutations.
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Affiliation(s)
- Saori Mizuno-Iijima
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
| | - Kanako Kato
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshihisa Ikeda
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Charles River Laboratories Japan, Inc., 955 Kamibayashi, Ishioka 315-0138, Japan
| | - Tra Thi Huong Dinh
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hoai Thu Le
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hayate Suzuki
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenichi Nakashima
- Gene Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshikazu Hasegawa
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuko Hamada
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Tanimoto
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Daitoku
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Natsumi Iki
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miyuki Ishida
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Elzeftawy Abdelaziz Elsayed Ibrahim
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Toshiaki Nakashiba
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Michito Hamada
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazuya Murata
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshihiro Miwa
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miki Okada-Iwabu
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Advanced Research on Pathophysiology of Metabolic Diseases, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masato Iwabu
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Advanced Research on Pathophysiology of Metabolic Diseases, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ken-Ichi Yagami
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yuichi Obata
- Gene Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Satoru Takahashi
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Fumihiro Sugiyama
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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Jacquot S, Chartoire N, Piguet F, Hérault Y, Pavlovic G. Optimizing PCR for Mouse Genotyping: Recommendations for Reliable, Rapid, Cost Effective, Robust and Adaptable to High-Throughput Genotyping Protocol for Any Type of Mutation. ACTA ACUST UNITED AC 2020; 9:e65. [PMID: 31756054 DOI: 10.1002/cpmo.65] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genotyping consists of searching for a DNA sequence variation localized at a well-defined locus in the genome. It is an essential step in animal research because it allows the identification of animals that will be bred to generate and maintain a colony, euthanized to control the available space in the animal facility, or used in experiment protocols. Here we describe polymerase chain reaction (PCR) genotyping protocols for fast, sensitive, easy, and cost-effective characterization of mouse genotype. We discuss optimization of parameters to improve the reliability of each assay and propose recommendations for enhancing reproducibility and reducing the occurrence of inconclusive genotyping. All steps required for efficient genotyping are presented: tissue collection; sample verification and direct DNA lysis; establishment of a robust genotyping strategy with reliable, rapid, and cost-effective assays; and finally, transition to high-throughput automatized PCR, including mix miniaturization and automation. © 2019 The Authors. Basic Protocol 1: Tissue sampling methods and procedure Basic Protocol 2: Sample verification and DNA lysis Basic Protocol 3: Design of a genotyping strategy Basic Protocol 4: Moving to high-throughput genotyping.
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Affiliation(s)
- Sylvie Jacquot
- Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | | | - Françoise Piguet
- NeuroGenCell Thérapie Génique et Cellulaire des Maladies Neurodégénératives de l'Adulte et de l'Enfant, INSERM U1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Yann Hérault
- Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France.,Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Illkirch, France
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Yang J, Schleicher TR, Dong Y, Park HB, Lan J, Cresswell P, Crawford J, Dimopoulos G, Fikrig E. Disruption of mosGILT in Anopheles gambiae impairs ovarian development and Plasmodium infection. J Exp Med 2020; 217:e20190682. [PMID: 31658986 PMCID: PMC7037243 DOI: 10.1084/jem.20190682] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/06/2019] [Accepted: 10/25/2019] [Indexed: 11/04/2022] Open
Abstract
Plasmodium infection in Anopheles is influenced by mosquito-derived factors. We previously showed that a protein in saliva from infected Anopheles, mosquito gamma-interferon-inducible lysosomal thiol reductase (mosGILT), inhibits the ability of sporozoites to traverse cells and readily establish infection of the vertebrate host. To determine whether mosGILT influences Plasmodium within the mosquito, we generated Anopheles gambiae mosquitoes carrying mosaic mutations in the mosGILT gene using CRISPR/CRISPR associated protein 9 (Cas9). Here, we show that female mosaic mosGILT mutant mosquitoes display defects in ovarian development and refractoriness to Plasmodium. Following infection by either Plasmodium berghei or Plasmodium falciparum, mutant mosquitoes have significantly reduced oocyst numbers as a result of increased thioester-containing protein 1 (TEP1)-dependent parasite killing. Expression of vitellogenin (Vg), the major yolk protein that can reduce the parasite-killing efficiency of TEP1, is severely impaired in mutant mosquitoes. MosGILT is a mosquito factor that is essential for ovarian development and indirectly protects both human and rodent Plasmodium species from mosquito immunity.
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Affiliation(s)
- Jing Yang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Tyler R. Schleicher
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Yuemei Dong
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Hyun Bong Park
- Department of Chemistry, Yale University, New Haven, CT
- Chemical Biology Institute, Yale University, West Haven, CT
| | - Jiangfeng Lan
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Jason Crawford
- Department of Chemistry, Yale University, New Haven, CT
- Chemical Biology Institute, Yale University, West Haven, CT
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT
| | - George Dimopoulos
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
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40
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Kuure S, Sariola H. Mouse Models of Congenital Kidney Anomalies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:109-136. [PMID: 32304071 DOI: 10.1007/978-981-15-2389-2_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are common birth defects, which cause the majority of chronic kidney diseases in children. CAKUT covers a wide range of malformations that derive from deficiencies in embryonic kidney and lower urinary tract development, including renal aplasia, hypodysplasia, hypoplasia, ectopia, and different forms of ureter abnormalities. The majority of the genetic causes of CAKUT remain unknown. Research on mutant mice has identified multiple genes that critically regulate renal differentiation. The data generated from this research have served as an excellent resource to identify the genetic bases of human kidney defects and have led to significantly improved diagnostics. Furthermore, genetic data from human CAKUT studies have also revealed novel genes regulating kidney differentiation.
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Affiliation(s)
- Satu Kuure
- GM-Unit, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland. .,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Hannu Sariola
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Paediatric Pathology, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
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41
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Perretta-Tejedor N, Freke G, Seda M, Long DA, Jenkins D. Generating Mutant Renal Cell Lines Using CRISPR Technologies. Methods Mol Biol 2020; 2067:323-340. [PMID: 31701460 PMCID: PMC9703199 DOI: 10.1007/978-1-4939-9841-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Gene editing using the CRISPR/Cas9 system is an extremely efficient approach for generating mutations within the genomic DNA of immortalized cell lines. This procedure begins with a straightforward cloning step to generate a single plasmid encoding the Cas9 enzyme as well as a synthetic guide RNA (sgRNA) which is selected to target specific sites within the genome. This plasmid is transfected into cells either alone, in order to generate random insertion-deletion alleles ("indels") at the desired locus via the nonhomologous end-joining pathway, or in conjunction with a homology-directed repair template oligonucleotide to generate a specific point mutation. Here we describe a procedure to perform gene editing in IMCD3 and HEK293 cells and to subsequently isolate clonal cell lines carrying mutations of interest.
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Affiliation(s)
- Nuria Perretta-Tejedor
- Developmental Biology and Cancer, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Grace Freke
- Genetics and Genomic Medicine Programmes, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Marian Seda
- Genetics and Genomic Medicine Programmes, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - David A Long
- Developmental Biology and Cancer, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Dagan Jenkins
- Genetics and Genomic Medicine Programmes, Great Ormond Street Institute of Child Health, University College London, London, UK.
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42
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Livermore C, Warr N, Chalon N, Siggers P, Mianné J, Codner G, Teboul L, Wells S, Greenfield A. Male mice lacking ADAMTS-16 are fertile but exhibit testes of reduced weight. Sci Rep 2019; 9:17195. [PMID: 31748609 PMCID: PMC6868159 DOI: 10.1038/s41598-019-53900-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 11/06/2019] [Indexed: 01/04/2023] Open
Abstract
Adamts16 encodes a disintegrin-like and metalloproteinase with thrombospondin motifs, 16, a member of a family of multi-domain, zinc-binding proteinases. ADAMTS-16 is implicated in a number of pathological conditions, including hypertension, cancer and osteoarthritis. A large number of observations, including a recent report of human ADAMTS16 variants in cases of 46,XY disorders/differences of sex development (DSD), also implicate this gene in human testis determination. We used CRISPR/Cas9 genome editing to generate a loss-of-function allele in the mouse in order to examine whether ADAMTS-16 functions in mouse testis determination or testicular function. Male mice lacking Adamts16 on the C57BL/6N background undergo normal testis determination in the fetal period. However, adult homozygotes have an average testis weight that is around 10% lower than age-matched controls. Cohorts of mutant males tested at 3-months and 6-months of age were fertile. We conclude that ADAMTS-16 is not required for testis determination or male fertility in mice. We discuss these phenotypic data and their significance for our understanding of ADAMTS-16 function.
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Affiliation(s)
- Catherine Livermore
- Mammalian Genetics Unit, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Nick Warr
- Mammalian Genetics Unit, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Nicolas Chalon
- Mammalian Genetics Unit, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Pam Siggers
- Mammalian Genetics Unit, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Joffrey Mianné
- Mary Lyon Centre, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK.,Institute for Regenerative Medicine and Biotherapy, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | - Gemma Codner
- Mary Lyon Centre, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Lydia Teboul
- Mary Lyon Centre, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Sara Wells
- Mary Lyon Centre, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Andy Greenfield
- Mammalian Genetics Unit, Medical Research Council, Harwell Institute, Oxfordshire, OX11 0RD, UK.
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43
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Owens DDG, Caulder A, Frontera V, Harman JR, Allan AJ, Bucakci A, Greder L, Codner GF, Hublitz P, McHugh PJ, Teboul L, de Bruijn MFTR. Microhomologies are prevalent at Cas9-induced larger deletions. Nucleic Acids Res 2019; 47:7402-7417. [PMID: 31127293 PMCID: PMC6698657 DOI: 10.1093/nar/gkz459] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 11/18/2022] Open
Abstract
The CRISPR system is widely used in genome editing for biomedical research. Here, using either dual paired Cas9D10A nickases or paired Cas9 nuclease we characterize unintended larger deletions at on-target sites that frequently evade common genotyping practices. We found that unintended larger deletions are prevalent at multiple distinct loci on different chromosomes, in cultured cells and mouse embryos alike. We observed a high frequency of microhomologies at larger deletion breakpoint junctions, suggesting the involvement of microhomology-mediated end joining in their generation. In populations of edited cells, the distribution of larger deletion sizes is dependent on proximity to sgRNAs and cannot be predicted by microhomology sequences alone.
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Affiliation(s)
- Dominic D G Owens
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Vincent Frontera
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Joe R Harman
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alasdair J Allan
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Akin Bucakci
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lucas Greder
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Gemma F Codner
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Philip Hublitz
- WIMM Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Marella F T R de Bruijn
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
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44
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Guth BD, Grobler AF, Frazier KS, Greiter-Wilke A, Herzyk D, Hough TA, Khan AA, Markert M, Smith JD, Svenson KL, Wells S, Pugsley MK. Drug safety Africa: An overview of safety pharmacology & toxicology in South Africa. J Pharmacol Toxicol Methods 2019; 98:106579. [PMID: 31085319 DOI: 10.1016/j.vascn.2019.106579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/25/2019] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
Abstract
This meeting report is based on presentations given at the first Drug Safety Africa Meeting in Potchefstroom, South Africa from November 20-22, 2018 at the North-West University campus. There were 134 attendees (including 26 speakers and 34 students) from the pharmaceutical industry, academia, regulatory agencies as well as 6 exhibitors. These meeting proceedings are designed to inform the content that was presented in terms of Safety Pharmacology (SP) and Toxicology methods and models that are used by the pharmaceutical industry to characterize the safety profile of novel small chemical or biological molecules. The first part of this report includes an overview of the core battery studies defined by cardiovascular, central nervous system (CNS) and respiratory studies. Approaches to evaluating drug effects on the renal and gastrointestinal systems and murine phenotyping were also discussed. Subsequently, toxicological approaches were presented including standard strategies and options for early identification and characterization of risks associated with a novel therapeutic, the types of toxicology studies conducted and relevance to risk assessment supporting first-in-human (FIH) clinical trials and target organ toxicity. Biopharmaceutical development and principles of immunotoxicology were discussed as well as emerging technologies. An additional poster session was held that included 18 posters on advanced studies and topics by South African researchers, postgraduate students and postdoctoral fellows.
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Affiliation(s)
- Brian D Guth
- Boehringer Ingelheim GmbH & Co KG, Biberach an der Riss, Germany; North-West University, Potchefstroom, South Africa.
| | | | | | | | - Danuta Herzyk
- Merck Sharp & Dohme Corp., A subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Tertius A Hough
- Mary Lyon Centre and Mammalian Genetics Unit, Medical Research Council, Harwell, UK
| | | | - Michael Markert
- Boehringer Ingelheim GmbH & Co KG, Biberach an der Riss, Germany
| | - James D Smith
- Boehringer-Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | | | - Sara Wells
- Mary Lyon Centre and Mammalian Genetics Unit, Medical Research Council, Harwell, UK
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45
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Bhattacharya D, Van Meir EG. A simple genotyping method to detect small CRISPR-Cas9 induced indels by agarose gel electrophoresis. Sci Rep 2019; 9:4437. [PMID: 30872606 PMCID: PMC6418129 DOI: 10.1038/s41598-019-39950-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/25/2019] [Indexed: 01/22/2023] Open
Abstract
CRISPR gene editing creates indels in targeted genes that are detected by genotyping. Separating PCR products generated from wild-type versus mutant alleles with small indels based on size is beyond the resolution capacity of regular agarose gel electrophoresis. To overcome this limitation, we developed a simple genotyping method that exploits the differential electrophoretic mobility of homoduplex versus heteroduplex DNA hybrids in high concentration agarose gels. First, the CRISPR target region is PCR amplified and homo- and hetero-duplexed amplicons formed during the last annealing cycle are separated by 4–6% agarose gel electrophoresis. WT/mutant heteroduplexes migrate more slowly and are distinguished from WT or mutant homoduplexes. Heterozygous alleles are immediately identified as they produce two distinct bands, while homozygous wild-type or mutant alleles yield a single band. To discriminate the latter, equal amounts of PCR products of homozygous samples are mixed with wild-type control samples, subjected to one denaturation/renaturation cycle and products are electrophoresed again. Samples from homozygous mutant alleles now produce two bands, while those from wild-type alleles yield single bands. This method is simple, fast and inexpensive and can identify indels >2 bp. in size in founder pups and genotype offspring in established transgenic mice colonies.
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Affiliation(s)
- Debanjan Bhattacharya
- Laboratory of Molecular Neuro-Oncology, Departments of Neurosurgery and Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Erwin G Van Meir
- Laboratory of Molecular Neuro-Oncology, Departments of Neurosurgery and Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.
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46
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Homanics GE. Gene-edited CRISPy Critters for alcohol research. Alcohol 2019; 74:11-19. [PMID: 30621855 PMCID: PMC6334660 DOI: 10.1016/j.alcohol.2018.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 12/26/2022]
Abstract
Genetically engineered animals are powerful tools that have provided invaluable insights into mechanisms of alcohol action and alcohol-use disorder. Traditionally, production of gene-targeted animals was a tremendously expensive, time consuming, and technically demanding undertaking. However, the recent advent of facile methods for editing the genome at very high efficiency is revolutionizing how these animals are made. While pioneering approaches to create gene-edited animals first used zinc finger nucleases and subsequently used transcription activator-like effector nucleases, these approaches have been largely supplanted in an extremely short period of time with the recent discovery and precocious maturation of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system. CRISPR uses a short RNA sequence to guide a non-specific CRISPR-associated nuclease (Cas) to a precise, single location in the genome. Because the CRISPR/Cas system can be cheaply, rapidly, and easily reprogrammed to target nearly any genomic locus of interest simply by recoding the sequence of the guide RNA, this gene-editing system has been rapidly adopted by numerous labs around the world. With CRISPR/Cas, it is now possible to perform gene editing directly in early embryos from every species of animals that is of interest to the alcohol field. Techniques have been developed that enable the rapid production of animals in which a gene has been inactivated (knockout) or modified to harbor specific nucleotide changes (knockins). This system has also been used to insert specific DNA sequences such as reporter or recombinase genes into specific loci of interest. Genetically engineered animals created with the CRISPR/Cas system (CRISPy Critters) are being produced at an astounding pace. Animal production is no longer a significant bottleneck to new discoveries. CRISPy animal studies are just beginning to appear in the alcohol literature, but their use is expected to explode in the near future. CRISPy mice, rats, and other model organisms are sure to facilitate advances in our understanding of alcohol-use disorder.
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Affiliation(s)
- Gregg E Homanics
- Department of Anesthesiology, University of Pittsburgh School of Medicine, 6060 Biomedical Science Tower-3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States; Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, 6060 Biomedical Science Tower-3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States; Department of Neurobiology, University of Pittsburgh School of Medicine, 6060 Biomedical Science Tower-3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States.
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47
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas-based genome editing technology has enabled manipulation of the embryonic genome. Unbiased whole genome sequencing comparing parents to progeny has revealed that the rate of Cas9-induced mutagenesis in mouse embryos is indistinguishable from the background rate of de novo mutation. However, establishing the best practice to confirm on-target alleles of interest remains a challenge. We believe that improvement in editing strategies and screening methods for founder mice will contribute to the generation of quality-controlled animals, thereby ensuring reproducibility of results in animal studies and advancing the 3Rs (replacement, reduction, and refinement).
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Affiliation(s)
- Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
| | - Kenichi Nakashima
- Gene Engineering Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
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48
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Codner GF, Mianné J, Caulder A, Loeffler J, Fell R, King R, Allan AJ, Mackenzie M, Pike FJ, McCabe CV, Christou S, Joynson S, Hutchison M, Stewart ME, Kumar S, Simon MM, Agius L, Anstee QM, Volynski KE, Kullmann DM, Wells S, Teboul L. Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants. BMC Biol 2018; 16:70. [PMID: 29925374 PMCID: PMC6011369 DOI: 10.1186/s12915-018-0530-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 01/22/2023] Open
Abstract
Background Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing have led to the use of long single-stranded DNA (lssDNA) molecules for generating conditional mutations. However, there is still limited available data on the efficiency and reliability of this method. Results We generated conditional mouse alleles using lssDNA donor templates and performed extensive characterization of the resulting mutations. We observed that the use of lssDNA molecules as donors efficiently yielded founders bearing the conditional allele, with seven out of nine projects giving rise to modified alleles. However, rearranged alleles including nucleotide changes, indels, local rearrangements and additional integrations were also frequently generated by this method. Specifically, we found that alleles containing unexpected point mutations were found in three of the nine projects analyzed. Alleles originating from illegitimate repairs or partial integration of the donor were detected in eight projects. Furthermore, additional integrations of donor molecules were identified in four out of the seven projects analyzed by copy counting. This highlighted the requirement for a thorough allele validation by polymerase chain reaction, sequencing and copy counting of the mice generated through this method. We also demonstrated the feasibility of using lssDNA donors to generate thus far problematic point mutations distant from active CRISPR cutting sites by targeting two distinct genes (Gckr and Rims1). We propose a strategy to perform extensive quality control and validation of both types of mouse models generated using lssDNA donors. Conclusion lssDNA donors reproducibly generate conditional alleles and can be used to introduce point mutations away from CRISPR/Cas9 cutting sites in mice. However, our work demonstrates that thorough quality control of new models is essential prior to reliably experimenting with mice generated by this method. These advances in genome editing techniques shift the challenge of mutagenesis from generation to the validation of new mutant models. Electronic supplementary material The online version of this article (10.1186/s12915-018-0530-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma F Codner
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Jorik Loeffler
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Rachel Fell
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Ruairidh King
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Alasdair J Allan
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Matthew Mackenzie
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Fran J Pike
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | | | | | - Sam Joynson
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | | | - Saumya Kumar
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Michelle M Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Loranne Agius
- Institute of Cellular Medicine and Ageing and Health, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Quentin M Anstee
- Institute of Cellular Medicine and Ageing and Health, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Kirill E Volynski
- UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Dimitri M Kullmann
- UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK.
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49
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Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. CONSERV GENET 2018; 19:995-1005. [PMID: 30100824 PMCID: PMC6061128 DOI: 10.1007/s10592-018-1072-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/03/2018] [Indexed: 01/08/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
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Affiliation(s)
- Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Juan Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Steve D. M. Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - K. C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA 95618 USA
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Lauryl M. J. Nutter
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Patrick T. Reilly
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
| | - Michelle Simon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - the IMPC consortium
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
- Mouse Biology Program, University of California, Davis, CA 95618 USA
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
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50
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Fratta P, Sivakumar P, Humphrey J, Lo K, Ricketts T, Oliveira H, Brito-Armas JM, Kalmar B, Ule A, Yu Y, Birsa N, Bodo C, Collins T, Conicella AE, Mejia Maza A, Marrero-Gagliardi A, Stewart M, Mianne J, Corrochano S, Emmett W, Codner G, Groves M, Fukumura R, Gondo Y, Lythgoe M, Pauws E, Peskett E, Stanier P, Teboul L, Hallegger M, Calvo A, Chiò A, Isaacs AM, Fawzi NL, Wang E, Housman DE, Baralle F, Greensmith L, Buratti E, Plagnol V, Fisher EM, Acevedo-Arozena A. Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis. EMBO J 2018; 37:embj.201798684. [PMID: 29764981 PMCID: PMC5983119 DOI: 10.15252/embj.201798684] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/15/2018] [Accepted: 03/22/2018] [Indexed: 12/11/2022] Open
Abstract
TDP‐43 (encoded by the gene TARDBP) is an RNA binding protein central to the pathogenesis of amyotrophic lateral sclerosis (ALS). However, how TARDBP mutations trigger pathogenesis remains unknown. Here, we use novel mouse mutants carrying point mutations in endogenous Tardbp to dissect TDP‐43 function at physiological levels both in vitro and in vivo. Interestingly, we find that mutations within the C‐terminal domain of TDP‐43 lead to a gain of splicing function. Using two different strains, we are able to separate TDP‐43 loss‐ and gain‐of‐function effects. TDP‐43 gain‐of‐function effects in these mice reveal a novel category of splicing events controlled by TDP‐43, referred to as “skiptic” exons, in which skipping of constitutive exons causes changes in gene expression. In vivo, this gain‐of‐function mutation in endogenous Tardbp causes an adult‐onset neuromuscular phenotype accompanied by motor neuron loss and neurodegenerative changes. Furthermore, we have validated the splicing gain‐of‐function and skiptic exons in ALS patient‐derived cells. Our findings provide a novel pathogenic mechanism and highlight how TDP‐43 gain of function and loss of function affect RNA processing differently, suggesting they may act at different disease stages.
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Affiliation(s)
- Pietro Fratta
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Prasanth Sivakumar
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Jack Humphrey
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK.,UCL Genetics Institute, London, UK
| | - Kitty Lo
- UCL Genetics Institute, London, UK
| | | | | | - Jose M Brito-Armas
- Unidad de Investigación, Hospital Universitario de Canarias, Fundación Canaria de Investigación Sanitaria and Instituto de Tecnologías Biomédicas (CIBICAN), La Laguna, Spain
| | - Bernadett Kalmar
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Agnieszka Ule
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Yichao Yu
- UCL Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - Nicol Birsa
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Cristian Bodo
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Toby Collins
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Alexander E Conicella
- Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Alan Mejia Maza
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Alessandro Marrero-Gagliardi
- Unidad de Investigación, Hospital Universitario de Canarias, Fundación Canaria de Investigación Sanitaria and Instituto de Tecnologías Biomédicas (CIBICAN), La Laguna, Spain
| | | | | | | | | | | | - Michael Groves
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Ryutaro Fukumura
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yoichi Gondo
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Mark Lythgoe
- UCL Centre for Advanced Biomedical Imaging, University College London, London, UK
| | | | | | | | | | | | - Andrea Calvo
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
| | - Adrian M Isaacs
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK.,UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, UK
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology & Biotechnology, Brown University, Providence, RI, USA
| | - Eric Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David E Housman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Francisco Baralle
- International Center for Genomic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Linda Greensmith
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Emanuele Buratti
- International Center for Genomic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | | | - Elizabeth Mc Fisher
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Abraham Acevedo-Arozena
- MRC Mammalian Genetics Unit, Harwell, UK .,Unidad de Investigación, Hospital Universitario de Canarias, Fundación Canaria de Investigación Sanitaria and Instituto de Tecnologías Biomédicas (CIBICAN), La Laguna, Spain
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