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Teboul L, Amos-Landgraf J, Benavides FJ, Birling MC, Brown SDM, Bryda E, Bunton-Stasyshyn R, Chin HJ, Crispo M, Delerue F, Dobbie M, Franklin CL, Fuchtbauer EM, Gao X, Golzio C, Haffner R, Hérault Y, Hrabe de Angelis M, Lloyd KCK, Magnuson TR, Montoliu L, Murray SA, Nam KH, Nutter LMJ, Pailhoux E, Pardo Manuel de Villena F, Peterson K, Reinholdt L, Sedlacek R, Seong JK, Shiroishi T, Smith C, Takeo T, Tinsley L, Vilotte JL, Warming S, Wells S, Whitelaw CB, Yoshiki A, Pavlovic G. Improving laboratory animal genetic reporting: LAG-R guidelines. Nat Commun 2024; 15:5574. [PMID: 38956430 PMCID: PMC11220107 DOI: 10.1038/s41467-024-49439-y] [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: 02/12/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals' genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.
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Affiliation(s)
- Lydia Teboul
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK.
| | - James Amos-Landgraf
- University of Missouri School of Medicine, Columbia, MO, USA
- University of Missouri College of Veterinary Medicine, Columbia, MO, USA
- Rat Resource and Research Center, University of Missouri, Columbia, MO, USA
| | - Fernando J Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
| | - Steve D M Brown
- Visiting Scientist, Institut Clinique de la Souris, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
| | - Elizabeth Bryda
- Rat Resource and Research Center, University of Missouri, Columbia, MO, 65201, USA
| | | | - Hsian-Jean Chin
- National Laboratory Animal Center (NLAC), NARLabs, Taipei, Taiwan
| | - Martina Crispo
- Laboratory Animal Biotechnology Unit, Institut Pasteur de Montevideo, Mataojo 2020, CP 1400, Montevideo, Uruguay
| | - Fabien Delerue
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Dobbie
- Phenomics Australia, Australian National University, 131 Garran Road, Canberra, ACT 2601, Australia
| | - Craig L Franklin
- University of Missouri Mutant Mouse Resource and Research Center (MU MMRRC), University of Missouri, Columbia, MO, 65201, USA
| | | | - Xiang Gao
- National Resource Center of Mutant Mice (NRCMM), Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Christelle Golzio
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, F-67400, Illkirch, France
| | - Rebecca Haffner
- Department Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yann Hérault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, F-67400, Illkirch, France
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
| | | | - Terry R Magnuson
- Department of Genetics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7264, USA
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), 28029, Madrid, Spain
| | | | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Lauryl M J Nutter
- Genetics and Genome Biology, The Hospital for Sick Children and The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
| | - Eric Pailhoux
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | | | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, and Korea Mouse Phenotyping Center, Seoul, 08826, Republic of Korea
| | | | - Cynthia Smith
- Mouse Genome Informatics (MGI), Jackson Laboratory, Bar Harbor, ME, USA
| | - Toru Takeo
- Center for Animal Resources and Development (CARD), Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Louise Tinsley
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
| | - Jean-Luc Vilotte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Søren Warming
- Genentech, Inc., a member of the Roche group, South San Francisco, CA, USA
| | - Sara Wells
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
- Francis Crick Institute, London, NW1 1AT, UK
| | - C Bruce Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France.
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2
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Hermantara R, Richmond L, Taqi AF, Chilaka S, Jeantet V, Guerrini I, West K, West A. Improving CRISPR-Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration. J Biomed Sci 2024; 31:32. [PMID: 38532479 DOI: 10.1186/s12929-024-01020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR-Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for genome editing purposes by causing DNA double strand breaks at off-target locations and causing unwanted editing outcomes. Furthermore, for gene integration applications, which introduce transgene sequences, integration of transgenes to off-target sites could be harmful, hard to detect, and reduce faithful genome editing efficiency. METHOD Here we report the development of a multicolour fluorescence assay for studying CRISPR-Cas9-directed gene integration at an endogenous locus in human cell lines. We examine genetic integration of reporter genes in transiently transfected cells as well as puromycin-selected stable cell lines to determine the fidelity of multiple CRISPR-Cas9 strategies. RESULT We found that there is a high occurrence of unwanted DNA integration which tarnished faithful knock-in efficiency. Integration outcomes are influenced by the type of DNA DSBs, donor design, the use of enhanced specificity Cas9 variants, with S-phase regulated Cas9 activity. Moreover, restricting Cas9 expression with a self-cleaving system greatly improves knock-in outcomes by substantially reducing the percentage of cells with unwanted DNA integration. CONCLUSION Our results highlight the need for a more stringent assessment of CRISPR-Cas9-mediated knock-in outcomes, and the importance of careful strategy design to maximise efficient and faithful transgene integration.
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Affiliation(s)
- Rio Hermantara
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
| | - Laura Richmond
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Aqeel Faisal Taqi
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sabari Chilaka
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Valentine Jeantet
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ileana Guerrini
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katherine West
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Adam West
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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3
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Zhao JJ, Sun XY, Tian SN, Zhao ZZ, Yin MD, Zhao M, Zhang F, Li SA, Yang ZX, Wen W, Cheng T, Gong A, Zhang JP, Zhang XB. Decoding the complexity of on-target integration: characterizing DNA insertions at the CRISPR-Cas9 targeted locus using nanopore sequencing. BMC Genomics 2024; 25:189. [PMID: 38368357 PMCID: PMC10874558 DOI: 10.1186/s12864-024-10050-6] [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: 06/05/2023] [Accepted: 01/24/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND CRISPR-Cas9 technology has advanced in vivo gene therapy for disorders like hemophilia A, notably through the successful targeted incorporation of the F8 gene into the Alb locus in hepatocytes, effectively curing this disorder in mice. However, thoroughly evaluating the safety and specificity of this therapy is essential. Our study introduces a novel methodology to analyze complex insertion sequences at the on-target edited locus, utilizing barcoded long-range PCR, CRISPR RNP-mediated deletion of unedited alleles, magnetic bead-based long amplicon enrichment, and nanopore sequencing. RESULTS We identified the expected F8 insertions and various fragment combinations resulting from the in vivo linearization of the double-cut plasmid donor. Notably, our research is the first to document insertions exceeding ten kbp. We also found that a small proportion of these insertions were derived from sources other than donor plasmids, including Cas9-sgRNA plasmids, genomic DNA fragments, and LINE-1 elements. CONCLUSIONS Our study presents a robust method for analyzing the complexity of on-target editing, particularly for in vivo long insertions, where donor template integration can be challenging. This work offers a new tool for quality control in gene editing outcomes and underscores the importance of detailed characterization of edited genomic sequences. Our findings have significant implications for enhancing the safety and effectiveness of CRISPR-Cas9 gene therapy in treating various disorders, including hemophilia A.
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Affiliation(s)
- Juan-Juan Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xin-Yu Sun
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | | | - Zong-Ze Zhao
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266000, China
| | - Meng-Di Yin
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - An Gong
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266000, China.
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
- Tianjin Medical University, Tianjin, China.
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4
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Shumega AR, Pavlov YI, Chirinskaite AV, Rubel AA, Inge-Vechtomov SG, Stepchenkova EI. CRISPR/Cas9 as a Mutagenic Factor. Int J Mol Sci 2024; 25:823. [PMID: 38255897 PMCID: PMC10815272 DOI: 10.3390/ijms25020823] [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: 11/15/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The discovery of the CRISPR/Cas9 microbial adaptive immune system has revolutionized the field of genetics, by greatly enhancing the capacity for genome editing. CRISPR/Cas9-based editing starts with DNA breaks (or other lesions) predominantly at target sites and, unfortunately, at off-target genome sites. DNA repair systems differing in accuracy participate in establishing desired genetic changes but also introduce unwanted mutations, that may lead to hereditary, oncological, and other diseases. New approaches to alleviate the risks associated with genome editing include attenuating the off-target activity of editing complex through the use of modified forms of Cas9 nuclease and single guide RNA (sgRNA), improving delivery methods for sgRNA/Cas9 complex, and directing DNA lesions caused by the sgRNA/Cas9 to non-mutagenic repair pathways. Here, we have described CRISPR/Cas9 as a new powerful mutagenic factor, discussed its mutagenic properties, and reviewed factors influencing the mutagenic activity of CRISPR/Cas9.
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Affiliation(s)
- Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Sergey G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
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5
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Baik R, Cromer MK, Glenn SE, Vakulskas CA, Chmielewski KO, Dudek AM, Feist WN, Klermund J, Shipp S, Cathomen T, Dever DP, Porteus MH. Transient inhibition of 53BP1 increases the frequency of targeted integration in human hematopoietic stem and progenitor cells. Nat Commun 2024; 15:111. [PMID: 38169468 PMCID: PMC10762240 DOI: 10.1038/s41467-023-43413-w] [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: 02/23/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named "i53") as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.
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Affiliation(s)
- Ron Baik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steve E Glenn
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Amanda M Dudek
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - William N Feist
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Suzette Shipp
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel P Dever
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Quan ZJ, Li SA, Yang ZX, Zhao JJ, Li GH, Zhang F, Wen W, Cheng T, Zhang XB. GREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1221-1236. [PMID: 35752289 PMCID: PMC11082256 DOI: 10.1016/j.gpb.2022.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 05/19/2022] [Accepted: 06/13/2022] [Indexed: 05/09/2023]
Abstract
To achieve the enormous potential of gene-editing technology in clinical therapies, one needs to evaluate both the on-target efficiency and unintended editing consequences comprehensively. However, there is a lack of a pipelined, large-scale, and economical workflow for detecting genome editing outcomes, in particular insertion or deletion of a large fragment. Here, we describe an approach for efficient and accurate detection of multiple genetic changes after CRISPR/Cas9 editing by pooled nanopore sequencing of barcoded long-range PCR products. Recognizing the high error rates of Oxford nanopore sequencing, we developed a novel pipeline to capture the barcoded sequences by grepping reads of nanopore amplicon sequencing (GREPore-seq). GREPore-seq can assess nonhomologous end-joining (NHEJ)-mediated double-stranded oligodeoxynucleotide (dsODN) insertions with comparable accuracy to Illumina next-generation sequencing (NGS). GREPore-seq also reveals a full spectrum of homology-directed repair (HDR)-mediated large gene knock-in, correlating well with the fluorescence-activated cell sorting (FACS) analysis results. Of note, we discovered low-level fragmented and full-length plasmid backbone insertion at the CRISPR cutting site. Therefore, we have established a practical workflow to evaluate various genetic changes, including quantifying insertions of short dsODNs, knock-ins of long pieces, plasmid insertions, and large fragment deletions after CRISPR/Cas9-mediated editing. GREPore-seq is freely available at GitHub (https://github.com/lisiang/GREPore-seq) and the National Genomics Data Center (NGDC) BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007293).
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Affiliation(s)
- Zi-Jun Quan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Juan-Juan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Guo-Hua Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
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7
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Wei J, Brophy B, Cole SA, Leath S, Oback B, Boch J, Wells DN, Laible G. Production of light-coloured, low heat-absorbing Holstein Friesian cattle by precise embryo-mediated genome editing. Reprod Fertil Dev 2023; 36:112-123. [PMID: 38064192 DOI: 10.1071/rd23163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
CONTEXT Genome editing enables the introduction of beneficial sequence variants into the genomes of animals with high genetic merit in a single generation. This can be achieved by introducing variants into primary cells followed by producing a live animal from these cells by somatic cell nuclear transfer cloning. The latter step is associated with low efficiencies and developmental problems due to incorrect reprogramming of the donor cells, causing animal welfare concerns. Direct editing of fertilised one-cell embryos could circumvent this issue and might better integrate with genetic improvement strategies implemented by the industry. METHODS In vitro fertilised zygotes were injected with TALEN editors and repair template to introduce a known coat colour dilution mutation in the PMEL gene. Embryo biopsies of injected embryos were screened by polymerase chain reaction and sequencing for intended biallelic edits before transferring verified embryos into recipients for development to term. Calves were genotyped and their coats scanned with visible and hyperspectral cameras to assess thermal energy absorption. KEY RESULTS Multiple non-mosaic calves with precision edited genotypes were produced, including calves from high genetic merit parents. Compared to controls, the edited calves showed a strong coat colour dilution which was associated with lower thermal energy absorbance. CONCLUSIONS Although biopsy screening was not absolutely accurate, non-mosaic, precisely edited calves can be readily produced by embryo-mediated editing. The lighter coat colouring caused by the PMEL mutation can lower radiative heat gain which might help to reduce heat stress. IMPLICATIONS The study validates putative causative sequence variants to rapidly adapt grazing cattle to changing environmental conditions.
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Affiliation(s)
- Jingwei Wei
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Brigid Brophy
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Sally-Ann Cole
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Shane Leath
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Björn Oback
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand; and School of Sciences, University of Waikato, Hamilton, New Zealand; and Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - David N Wells
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Götz Laible
- Animal Biotechnology, Ruakura Research Centre, AgResearch, Hamilton, New Zealand; and Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
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8
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Koller F, Cieslak M. A perspective from the EU: unintended genetic changes in plants caused by NGT-their relevance for a comprehensive molecular characterisation and risk assessment. Front Bioeng Biotechnol 2023; 11:1276226. [PMID: 37965049 PMCID: PMC10641861 DOI: 10.3389/fbioe.2023.1276226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Several regions in the world are currently holding discussions in regard to the regulation of new genomic techniques (NGTs) and their application in agriculture. The European Commission, for instance, is proposing the introduction of specific regulation for NGT plants. Various questions need to be answered including e.g., the extent to which NGT-induced intended and unintended genetic modifications must be subjected to a mandatory risk assessment as part of an approval procedure. This review mostly focuses on findings in regard to unintended genetic changes that can be caused by the application of NGTs. More specifically, the review deals with the application of the nuclease CRISPR/Cas, which is currently the most important tool for developing NGT plants, and its potential to introduce double strand breaks (DSBs) at a targeted DNA sequence. For this purpose, we identified the differences in comparison to non-targeted mutagenesis methods used in conventional breeding. The review concludes that unintended genetic changes caused by NGT processes are relevant to risk assessment. Due to the technical characteristics of NGTs, the sites of the unintended changes, their genomic context and their frequency (in regard to specific sites) mean that the resulting gene combinations (intended or unintended) may be unlikely to occur with conventional methods. This, in turn, implies that the biological effects (phenotypes) can also be different and may cause risks to health and the environment. Therefore, we conclude that the assessment of intended as well as unintended genetic changes should be part of a mandatory comprehensive molecular characterisation and risk assessment of NGT plants that are meant for environmental releases or for market authorisation.
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Affiliation(s)
- Franziska Koller
- Fachstelle Gentechnik und Umwelt (FGU), Munich, Bavaria, Germany
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9
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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10
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Heinemann JA, Clark K, Hiscox TC, McCabe AW, Agapito-Tenfen SZ. Are null segregants new combinations of heritable material and should they be regulated? Front Genome Ed 2023; 4:1064103. [PMID: 36704579 PMCID: PMC9871356 DOI: 10.3389/fgeed.2022.1064103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Through genome editing and other techniques of gene technology, it is possible to create a class of organism called null segregants. These genetically modified organisms (GMOs) are products of gene technology but are argued to have no lingering vestige of the technology after the segregation of chromosomes or deletion of insertions. From that viewpoint regulations are redundant because any unique potential for the use of gene technology to cause harm has also been removed. We tackle this question of international interest by reviewing the early history of the purpose of gene technology regulation. The active ingredients of techniques used for guided mutagenesis, e.g., site-directed nucleases, such as CRISPR/Cas, are promoted for having a lower potential per reaction to create a hazard. However, others see this as a desirable industrial property of the reagents that will lead to genome editing being used more and nullifying the promised hazard mitigation. The contest between views revolves around whether regulations could alter the risks in the responsible use of gene technology. We conclude that gene technology, even when used to make null segregants, has characteristics that make regulation a reasonable option for mitigating potential harm. Those characteristics are that it allows people to create more harm faster, even if it creates benefits as well; the potential for harm increases with increased use of the technique, but safety does not; and regulations can control harm scaling.
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Affiliation(s)
- Jack A. Heinemann
- Centre for Integrated Research in Biosafety and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Katrin Clark
- Centre for Integrated Research in Biosafety and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Tessa C. Hiscox
- Centre for Integrated Research in Biosafety and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andrew W. McCabe
- Centre for Integrated Research in Biosafety and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sarah Z. Agapito-Tenfen
- Climate and Environment Division, NORCE Norwegian Research Centre AS, Tromsø, Norway,*Correspondence: Sarah Z. Agapito-Tenfen,
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11
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Japanese Regulatory Framework and Approach for Genome-edited Foods Based on Latest Scientific Findings. FOOD SAFETY (TOKYO, JAPAN) 2022; 10:113-128. [PMID: 36619008 PMCID: PMC9789915 DOI: 10.14252/foodsafetyfscj.d-21-00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
The food supply system is facing important challenges and its sustainability has to be considered. Genome-editing technology, which accelerates the development of new variety, could be used to achieve sustainable development goals, thereby protecting the environment and ensuring the stable production of food for an increasing global population. The most widely used genome-editing tool, CRISPR/Cas9, is easy to use, affordable, and versatile. Foods produced by genome-editing technologies have been developed worldwide to create novel traits. In the first half of the review, the latest scientific findings on genome-editing technologies are summarized, and the technical challenge in genome sequence analysis are clarified. CRISPR/Cas9 has versatile alternative techniques, such as base editor and prime editor. Genome sequencing technology has developed rapidly in recent years. However, it is still difficult to detect large deletions and structural variations. Long-read sequencing technology would solve this challenge. In the second part, regulatory framework and approach for genome-edited foods is introduced. The four government ministries, including the Ministry of Environment, the Ministry of Agriculture, Forestry and Fisheries, and the Ministry of Health, Labour and Welfare (MHLW), started to discuss how the regulation should be implemented in 2019. The SDN-1 technique is excluded from the current genetically modified organism (GMO) regulation. The Japanese regulatory framework includes pre-submission consultation and submission of notification form. In the last part of this review, transparency of regulatory framework and consumer confidence were described. Since maintaining consumer trust is vital, transparency of regulatory framework is a key to consumers. The information of notification process on approved genome-edited foods is made public immediately. This review will help regulators build regulatory frameworks, and lead to harmonization of the framework between the countries.
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12
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Safeguarding genome integrity during gene-editing therapy in a mouse model of age-related macular degeneration. Nat Commun 2022; 13:7867. [PMID: 36550137 PMCID: PMC9780342 DOI: 10.1038/s41467-022-35640-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Ensuring genome safety during gene editing is crucial for clinical translation of the high-efficient CRISPR-Cas9 toolbox. Therefore, the undesired events including chromosomal translocations, vector integrations, and large deletions arising during therapeutic gene editing remain to be adequately addressed or tackled in vivo. Here, we apply CRISPR-Cas9TX in comparison to CRISPR-Cas9 to target Vegfa for the treatment of age-related macular degeneration (AMD) disease in a mouse model. AAV delivery of both CRISPR-Cas9 and CRISPR-Cas9TX can efficiently inhibit laser-induced neovascularization. Importantly, Cas9TX almost eliminates chromosomal translocations that occur at a frequency of approximately 1% in Cas9-edited mouse retinal cells. Strikingly, the widely observed AAV integration at the target Vegfa site is also greatly reduced from nearly 50% of edited events to the background level during Cas9TX editing. Our findings reveal that chromosomal structural variations routinely occur during in vivo genome editing and highlight Cas9TX as a superior form of Cas9 for in vivo gene disruption.
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13
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Jones HE, Wilson PB. Progress and opportunities through use of genomics in animal production. Trends Genet 2022; 38:1228-1252. [PMID: 35945076 DOI: 10.1016/j.tig.2022.06.014] [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: 01/10/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/24/2023]
Abstract
The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.
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Affiliation(s)
- Huw E Jones
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK.
| | - Philippe B Wilson
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK
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14
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Singh J, Sharma D, Brar GS, Sandhu KS, Wani SH, Kashyap R, Kour A, Singh S. CRISPR/Cas tool designs for multiplex genome editing and its applications in developing biotic and abiotic stress-resistant crop plants. Mol Biol Rep 2022; 49:11443-11467. [PMID: 36002653 DOI: 10.1007/s11033-022-07741-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/22/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022]
Abstract
Crop plants are prone to several yield-reducing biotic and abiotic stresses. The crop yield reductions due to these stresses need addressing to maintain an adequate balance between the increasing world population and food production to avoid food scarcities in the future. It is impossible to increase the area under food crops proportionately to meet the rising food demand. In such an adverse scenario overcoming the biotic and abiotic stresses through biotechnological interventions may serve as a boon to help meet the globe's food requirements. Under the current genomic era, the wide availability of genomic resources and genome editing technologies such as Transcription Activator-Like Effector Nucleases (TALENs), Zinc Finger Nucleases (ZFNs), and Clustered-Regularly Interspaced Palindromic Repeats/CRISPR-associated proteins (CRISPR/Cas) has widened the scope of overcoming these stresses for several food crops. These techniques have made gene editing more manageable and accessible with changes at the embryo level by adding or deleting DNA sequences of the target gene(s) from the genome. The CRISPR construct consists of a single guide RNA having complementarity with the nucleotide fragments of the target gene sequence, accompanied by a protospacer adjacent motif. The target sequence in the organism's genome is then cleaved by the Cas9 endonuclease for obtaining a desired trait of interest. The current review describes the components, mechanisms, and types of CRISPR/Cas techniques and how this technology has helped to functionally characterize genes associated with various biotic and abiotic stresses in a target organism. This review also summarizes the application of CRISPR/Cas technology targeting these stresses in crops through knocking down/out of associated genes.
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Affiliation(s)
- Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, 110012, New Delhi, India.,Guru Angad Dev Veterinary and Animal Science University, KVK, Barnala, India
| | - Dimple Sharma
- Department of Food Science and Human Nutrition, Michigan State University, 48824, East Lansing, MI, USA
| | - Gagandeep Singh Brar
- Department of Biological Sciences, North Dakota State University, 58102, Fargo, ND, USA
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, 99163, Pullman, WA, USA
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology Srinagar, Khudwani, Srinagar, Jammu, Kashmir, India
| | - Ruchika Kashyap
- Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, 57007, Brookings, SD, USA
| | - Amardeep Kour
- Regional Research Station, Punjab Agricultural University, 151001, Bathinda, Punjab, India
| | - Satnam Singh
- Regional Research Station, Punjab Agricultural University, 151203, Faridkot, Punjab, India.
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15
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Tao J, Wang Q, Mendez-Dorantes C, Burns KH, Chiarle R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat Commun 2022; 13:3685. [PMID: 35760782 PMCID: PMC9237045 DOI: 10.1038/s41467-022-31322-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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16
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Abstract
The rapid development of CRISPR-Cas genome editing tools has greatly changed the way to conduct research and holds tremendous promise for clinical applications. During genome editing, CRISPR-Cas enzymes induce DNA breaks at the target sites and subsequently the DNA repair pathways are recruited to generate diverse editing outcomes. Besides off-target cleavage, unwanted editing outcomes including chromosomal structural variations and exogenous DNA integrations have recently raised concerns for clinical safety. To eliminate these unwanted editing byproducts, we need to explore the underlying mechanisms for the formation of diverse editing outcomes from the perspective of DNA repair. Here, we describe the involved DNA repair pathways in sealing Cas enzyme-induced DNA double-stranded breaks and discuss the origins and effects of unwanted editing byproducts on genome stability. Furthermore, we propose the potential risk of inhibiting DNA repair pathways to enhance gene editing. The recent combined studies of DNA repair and CRISPR-Cas editing provide a framework for further optimizing genome editing to enhance editing safety.
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17
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A transgene-free method for rapid and efficient generation of precisely edited pigs without monoclonal selection. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1535-1546. [PMID: 35122622 PMCID: PMC8817169 DOI: 10.1007/s11427-021-2058-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/06/2022] [Indexed: 12/04/2022]
Abstract
Gene-edited pigs for agricultural and biomedical applications are typically generated using somatic cell nuclear transfer (SCNT). However, SCNT requires the use of monoclonal cells as donors, and the time-consuming and laborious monoclonal selection process limits the production of large populations of gene-edited animals. Here, we developed a rapid and efficient method named RE-DSRNP (reporter RNA enriched dual-sgRNA/CRISPR-Cas9 ribonucleoproteins) for generating gene-edited donor cells. RE-DSRNP takes advantage of the precise and efficient editing features of dual-sgRNA and the high editing efficiency, low off-target effects, transgene-free nature, and low cytotoxic characteristics of reporter RNA enriched RNPs (CRISPR-Cas9 ribonucleoproteins), thus eliminating the need for the selection of monoclonal cells and thereby greatly reducing the generation time of donor cells from 3–4 weeks to 1 week, while also reducing the extent of apoptosis and chromosomal aneuploidy of donor cells. We applied RE-DSRNP to produce cloned pigs bearing a deletion edit of the wild-type p53-induced phosphatase 1 (WIP1) gene: among 32 weaned cloned pigs, 31 (97%) carried WIP1 edits, and 15 (47%) were homozygous for the designed fragment deletion, and no off-target event was detected. The WIP1 knockout (KO) pigs exhibited male reproductive disorders, illustrating the utility of RE-DSRNP for rapidly generating precisely edited animals for functional genomics and disease research. RE-DSRNP’s strong editing performance in a large animal and its marked reduction in the required time for producing SCNT donor cells support its application prospects for rapidly generating populations of transgene-free cloned animals.
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18
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Montoliu L. Historical DNA Manipulation Overview. Methods Mol Biol 2022; 2495:3-28. [PMID: 35696025 DOI: 10.1007/978-1-0716-2301-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The history of DNA manipulation for the creation of genetically modified animals began in the 1970s, using viruses as the first DNA molecules microinjected into mouse embryos at different preimplantation stages. Subsequently, simple DNA plasmids were used to microinject into the pronuclei of fertilized mouse oocytes and that method became the reference for many years. The isolation of embryonic stem cells together with advances in genetics allowed the generation of gene-specific knockout mice, later on improved with conditional mutations. Cloning procedures expanded the gene inactivation to livestock and other non-model mammalian species. Lentiviruses, artificial chromosomes, and intracytoplasmic sperm injections expanded the toolbox for DNA manipulation. The last chapter of this short but intense history belongs to programmable nucleases, particularly CRISPR-Cas systems, triggering the development of genomic-editing techniques, the current revolution we are living in.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and Center for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain.
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19
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Proving that a genome-edited organism is not GMO. Trends Biotechnol 2021; 40:525-528. [PMID: 34893376 DOI: 10.1016/j.tibtech.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022]
Abstract
A genome-edited agricultural product that is proven to contain no exogenous DNA is not subject to genetically modified organism (GMO) regulations in some countries. However, whether such proof is definitive is often disputed. We discuss the approaches to substantially proving that a genome-edited organism is not GMO, while considering social aspects.
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20
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Kawall K. The Generic Risks and the Potential of SDN-1 Applications in Crop Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:2259. [PMID: 34834620 PMCID: PMC8622673 DOI: 10.3390/plants10112259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
The use of site-directed nucleases (SDNs) in crop plants to alter market-oriented traits is expanding rapidly. At the same time, there is an on-going debate around the safety and regulation of crops altered with the site-directed nuclease 1 (SDN-1) technology. SDN-1 applications can be used to induce a variety of genetic alterations ranging from fairly 'simple' genetic alterations to complex changes in plant genomes using, for example, multiplexing approaches. The resulting plants can contain modified alleles and associated traits, which are either known or unknown in conventionally bred plants. The European Commission recently published a study on new genomic techniques suggesting an adaption of the current GMO legislation by emphasizing that targeted mutagenesis techniques can produce genomic alterations that can also be obtained by natural mutations or conventional breeding techniques. This review highlights the need for a case-specific risk assessment of crop plants derived from SDN-1 applications considering both the characteristics of the product and the process to ensure a high level of protection of human and animal health and the environment. The published literature on so-called market-oriented traits in crop plants altered with SDN-1 applications is analyzed here to determine the types of SDN-1 application in plants, and to reflect upon the complexity and the naturalness of such products. Furthermore, it demonstrates the potential of SDN-1 applications to induce complex alterations in plant genomes that are relevant to generic SDN-associated risks. In summary, it was found that nearly half of plants with so-called market-oriented traits contain complex genomic alterations induced by SDN-1 applications, which may also pose new types of risks. It further underscores the need for data on both the process and the end-product for a case-by-case risk assessment of plants derived from SDN-1 applications.
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Affiliation(s)
- Katharina Kawall
- Fachstelle Gentechnik und Umwelt, Frohschammerstr. 14, 80807 Munich, Germany
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21
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Dehdilani N, Taemeh SY, Goshayeshi L, Dehghani H. Genetically engineered birds; pre-CRISPR and CRISPR era. Biol Reprod 2021; 106:24-46. [PMID: 34668968 DOI: 10.1093/biolre/ioab196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 11/14/2022] Open
Abstract
Generating biopharmaceuticals in genetically engineered bioreactors continues to reign supreme. Hence, genetically engineered birds have attracted considerable attention from the biopharmaceutical industry. Fairly recent genome engineering methods have made genome manipulation an easy and affordable task. In this review, we first provide a broad overview of the approaches and main impediments ahead of generating efficient and reliable genetically engineered birds, and various factors that affect the fate of a transgene. This section provides an essential background for the rest of the review, in which we discuss and compare different genome manipulation methods in the pre-CRISPR and CRISPR era in the field of avian genome engineering.
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Affiliation(s)
- Nima Dehdilani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sara Yousefi Taemeh
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Lena Goshayeshi
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.,Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.,Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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22
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Gordon DR, Jaffe G, Doane M, Glaser A, Gremillion TM, Ho MD. Responsible governance of gene editing in agriculture and the environment. Nat Biotechnol 2021; 39:1055-1057. [PMID: 34381209 DOI: 10.1038/s41587-021-01023-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Gregory Jaffe
- Center for Science in the Public Interest, Washington, DC, USA
| | | | - Aviva Glaser
- National Wildlife Federation, Washington, DC, USA
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Liu M, Zhang W, Xin C, Yin J, Shang Y, Ai C, Li J, Meng FL, Hu J. Global detection of DNA repair outcomes induced by CRISPR-Cas9. Nucleic Acids Res 2021; 49:8732-8742. [PMID: 34365511 PMCID: PMC8421148 DOI: 10.1093/nar/gkab686] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/28/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022] Open
Abstract
CRISPR–Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular DNA repair pathways for genome editing. The repair of DSBs leads to small insertions or deletions (indels) and other complex byproducts, including large deletions and chromosomal translocations. Indels are well understood to disrupt target genes, while the other deleterious byproducts remain elusive. We developed a new in silico analysis pipeline for the previously described primer-extension-mediated sequencing assay to comprehensively characterize CRISPR–Cas9-induced DSB repair outcomes in human or mouse cells. We identified tremendous deleterious DSB repair byproducts of CRISPR–Cas9 editing, including large deletions, vector integrations, and chromosomal translocations. We further elucidated the important roles of microhomology, chromosomal interaction, recurrent DSBs, and DSB repair pathways in the generation of these byproducts. Our findings provide an extra dimension for genome editing safety besides off-targets. And caution should be exercised to avoid not only off-target damages but also deleterious DSB repair byproducts during genome editing.
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Affiliation(s)
- Mengzhu Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Changchang Xin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jianhang Yin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Yafang Shang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Chen Ai
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jiaxin Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
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Boosting the potential of cattle breeding using molecular biology, genetics, and bioinformatics approaches – a review. ACTA VET BRNO 2021. [DOI: 10.2754/avb202190020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cattle are among the most important farm animals that underwent an intense selection with the aim to increase milk production and to improve growth and meat properties, meanwhile reducing the generation interval allowing for a faster herd turnover. Recently, a shift from traditional breeding methods to breeding based on genetic testing has been observed. In this perspective, we review the techniques of molecular biology, genetics, and bioinformatics that are expected to further boost the agricultural potential of cattle. We discuss embryo selection based on next-generation and Nanopore sequencing and in vitro embryo production, boosting the potential of genetically superior animals. Gene editing of embryos could further speed up the selection process, essentially introducing a change in a single generation. Lastly, we discuss the host-microbiome co-evolution and adaptation. For example, cattle already adapted to low-quality low-cost fodder could be bred to achieve desired properties for the beef and dairy industry. The challenge of breeding and genetic editing is to accompany the selection on desired consumer-oriented traits with the push for sustainability and the adaptation to a changing climate while remaining economically viable. We propose that we are yet to see the limits of what is possible to achieve with modern technology for the cattle of the future; the ultimate goal will be to produce and maintain genetically elite individuals that can sustain the growing demands on the production.
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25
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Li M, Tang X, You W, Wang Y, Chen Y, Liu Y, Yuan H, Gao C, Chen X, Xiao Z, Ouyang H, Pang D. HMEJ-mediated site-specific integration of a myostatin inhibitor increases skeletal muscle mass in porcine. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:49-62. [PMID: 34513293 PMCID: PMC8411015 DOI: 10.1016/j.omtn.2021.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/09/2021] [Indexed: 01/27/2023]
Abstract
As a robust antagonist of myostatin (MSTN), follistatin (FST) is an important regulator of skeletal muscle development, and the delivery of FST to muscle tissue represents a potential therapeutic strategy for muscular dystrophies. The N terminus and FSI domain of FST are the functional domains for MSTN binding. Here, we aimed to achieve site-specific integration of FSI-I-I, including the signal peptide, N terminus, and three FSI domains, into the last codon of the porcine MSTN gene using a homology-mediated end joining (HMEJ)-based strategy mediated by CRISPR-Cas9. Based on somatic cell nuclear transfer (SCNT) technology, we successfully obtained FSI-I-I knockin pigs. H&E staining of longissimus dorsi and gastrocnemius cross-sections showed larger myofiber sizes in FSI-I-I knockin pigs than in controls. Moreover, the Smad and Erk pathways were inhibited, whereas the PI3k/Akt pathway was activated in FSI-I-I knockin pigs. In addition, the levels of MyoD, Myf5, and MyoG transcription were upregulated while that of MRF4 was downregulated in FSI-I-I knockin pigs. These results indicate that the FSI-I-I gene mediates skeletal muscle hypertrophy through an MSTN-related signaling pathway and the expression of myogenic regulatory factors. Overall, FSI-I-I knockin pigs with hypertrophic muscle tissue hold great promise as a therapeutic model for human muscular dystrophies.
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Affiliation(s)
- Mengjing Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Xiaochun Tang
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Wenni You
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Yanbing Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Yiwu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Ying Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Hongming Yuan
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Chuang Gao
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Xue Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Zhiwei Xiao
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China,Corresponding author: Hongsheng Ouyang, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China.
| | - Daxin Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China,Corresponding author: Daxin Pang, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 130062 Changchun, Jilin Province, People’s Republic of China.
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26
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Zhang W, Yin J, Zhang-Ding Z, Xin C, Liu M, Wang Y, Ai C, Hu J. In-depth assessment of the PAM compatibility and editing activities of Cas9 variants. Nucleic Acids Res 2021; 49:8785-8795. [PMID: 34133740 PMCID: PMC8421146 DOI: 10.1093/nar/gkab507] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
A series of Cas9 variants have been developed to improve the editing fidelity or targeting range of CRISPR-Cas9. Here, we employ a high-throughput sequencing approach primer-extension-mediated sequencing to analyze the editing efficiency, specificity and protospacer adjacent motif (PAM) compatibility of a dozen of SpCas9 variants at multiple target sites in depth, and our findings validate the high fidelity or broad editing range of these SpCas9 variants. With regard to the PAM-flexible SpCas9 variants, we detect significantly increased levels of off-target activity and propose a trade-off between targeting range and editing specificity for them, especially for the near-PAM-less SpRY. Moreover, we use a deep learning model to verify the consistency and predictability of SpRY off-target sites. Furthermore, we combine high-fidelity SpCas9 variants with SpRY to generate three new SpCas9 variants with both high fidelity and broad editing range. Finally, we also find that the existing SpCas9 variants are not effective in suppressing genome instability elicited by CRISPR-Cas9 editing, raising an urgent issue to be addressed.
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Affiliation(s)
- Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jianhang Yin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Zhengrong Zhang-Ding
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Changchang Xin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Mengzhu Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Yuhong Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Chen Ai
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
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27
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Kurgan G, Turk R, Li H, Roberts N, Rettig GR, Jacobi AM, Tso L, Sturgeon M, Mertens M, Noten R, Florus K, Behlke MA, Wang Y, McNeill MS. CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing. Mol Ther Methods Clin Dev 2021; 21:478-491. [PMID: 33981780 PMCID: PMC8082044 DOI: 10.1016/j.omtm.2021.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/26/2022]
Abstract
CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair fingerprints that result from non-homologous end joining (NHEJ) after double-stranded breaks (DSBs) were introduced by Cas9 or Cas12a for >500 paired treatment/control experiments. We found that building biological understanding of the repair into a novel analysis tool (CRISPAltRations) improved the quality of the results. We validated our software using simulated, targeted amplicon sequencing data (11 guide RNAs [gRNAs] and 603 on- and off-target locations) and demonstrated that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR-associated indels and homology-directed repair (HDR) events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user interface (GUI) and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a user interface (UI), we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.
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Affiliation(s)
- Gavin Kurgan
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | | | | | - Lauren Tso
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | | | | | | | | | | | - Yu Wang
- Integrated DNA Technologies, Coralville, IA 52241, USA
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28
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Epstein LR, Lee SS, Miller MF, Lombardi HA. CRISPR, animals, and FDA oversight: Building a path to success. Proc Natl Acad Sci U S A 2021; 118:e2004831117. [PMID: 34050010 PMCID: PMC8179205 DOI: 10.1073/pnas.2004831117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Technological advances, such as genome editing and specifically CRISPR, offer exciting promise for the creation of products that address public health concerns, such as disease transmission and a sustainable food supply and enable production of human therapeutics, such as organs and tissues for xenotransplantation or recombinant human proteins to treat disease. The Food and Drug Administration recognizes the need for such innovative solutions and plays a key role in bringing safe and effective animal biotechnology products to the marketplace. In this article, we (the Food and Drug Administration/Center for Veterinary Medicine) describe the current state of the science, including advances in technology as well as scientific limitations and considerations for how researchers and commercial developers working to create intentional genomic alterations in animals can work within these limitations. We also describe our risk-based approach and how it strikes a balance between our regulatory responsibilities and the need to get innovative products to market efficiently. We continue to seek input from our stakeholders and hope to use this feedback to improve the transparency, predictability, and efficiency of our process. We think that working together, using appropriate science- and risk-based oversight, is the foundation to a successful path forward.
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Affiliation(s)
- Laura R Epstein
- Office of the Director, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855
| | - Stella S Lee
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855
| | - Mayumi F Miller
- Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD 20708
| | - Heather A Lombardi
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855;
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29
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Pineda PS, Flores EB, Herrera JRV, Low WY. Opportunities and Challenges for Improving the Productivity of Swamp Buffaloes in Southeastern Asia. Front Genet 2021; 12:629861. [PMID: 33828581 PMCID: PMC8021093 DOI: 10.3389/fgene.2021.629861] [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: 11/16/2020] [Accepted: 02/26/2021] [Indexed: 11/18/2022] Open
Abstract
The swamp buffalo is a domesticated animal commonly found in Southeast Asia. It is a highly valued agricultural animal for smallholders, but the production of this species has unfortunately declined in recent decades due to rising farm mechanization. While swamp buffalo still plays a role in farmland cultivation, this species' purposes has shifted from draft power to meat, milk, and hide production. The current status of swamp buffaloes in Southeast Asia is still understudied compared to its counterparts such as the riverine buffaloes and cattle. This review discusses the background of swamp buffalo, with an emphasis on recent work on this species in Southeast Asia, and associated genetics and genomics work such as cytogenetic studies, phylogeny, domestication and migration, genetic sequences and resources. Recent challenges to realize the potential of this species in the agriculture industry are also discussed. Limited genetic resource for swamp buffalo has called for more genomics work to be done on this species including decoding its genome. As the economy progresses and farm mechanization increases, research and development for swamp buffaloes are focused on enhancing its productivity through understanding the genetics of agriculturally important traits. The use of genomic markers is a powerful tool to efficiently utilize the potential of this animal for food security and animal conservation. Understanding its genetics and retaining and maximizing its adaptability to harsher environments are a strategic move for food security in poorer nations in Southeast Asia in the face of climate change.
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Affiliation(s)
- Paulene S. Pineda
- Philippine Carabao Center National Headquarters and Genepool, Science City of Muñoz, Philippines
| | - Ester B. Flores
- Philippine Carabao Center National Headquarters and Genepool, Science City of Muñoz, Philippines
| | | | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
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30
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Owen JR, Hennig SL, McNabb BR, Mansour TA, Smith JM, Lin JC, Young AE, Trott JF, Murray JD, Delany ME, Ross PJ, Van Eenennaam AL. One-step generation of a targeted knock-in calf using the CRISPR-Cas9 system in bovine zygotes. BMC Genomics 2021; 22:118. [PMID: 33581720 PMCID: PMC7881600 DOI: 10.1186/s12864-021-07418-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 01/31/2021] [Indexed: 12/31/2022] Open
Abstract
Background The homologous recombination (HR) pathway is largely inactive in early embryos prior to the first cell division, making it difficult to achieve targeted gene knock-ins. The homology-mediated end joining (HMEJ)-based strategy has been shown to increase knock-in efficiency relative to HR, non-homologous end joining (NHEJ), and microhomology-mediated end joining (MMEJ) strategies in non-dividing cells. Results By introducing gRNA/Cas9 ribonucleoprotein complex and a HMEJ-based donor template with 1 kb homology arms flanked by the H11 safe harbor locus gRNA target site, knock-in rates of 40% of a 5.1 kb bovine sex-determining region Y (SRY)-green fluorescent protein (GFP) template were achieved in Bos taurus zygotes. Embryos that developed to the blastocyst stage were screened for GFP, and nine were transferred to recipient cows resulting in a live phenotypically normal bull calf. Genomic analyses revealed no wildtype sequence at the H11 target site, but rather a 26 bp insertion allele, and a complex 38 kb knock-in allele with seven copies of the SRY-GFP template and a single copy of the donor plasmid backbone. An additional minor 18 kb allele was detected that looks to be a derivative of the 38 kb allele resulting from the deletion of an inverted repeat of four copies of the SRY-GFP template. Conclusion The allelic heterogeneity in this biallelic knock-in calf appears to have resulted from a combination of homology directed repair, homology independent targeted insertion by blunt-end ligation, NHEJ, and rearrangement following editing of the gRNA target site in the donor template. This study illustrates the potential to produce targeted gene knock-in animals by direct cytoplasmic injection of bovine embryos with gRNA/Cas9, although further optimization is required to ensure a precise single-copy gene integration event. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07418-3.
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Affiliation(s)
- Joseph R Owen
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Sadie L Hennig
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Bret R McNabb
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt
| | - Justin M Smith
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Jason C Lin
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Amy E Young
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Josephine F Trott
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - James D Murray
- Department of Animal Science, University of California - Davis, Davis, CA, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Mary E Delany
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Pablo J Ross
- Department of Animal Science, University of California - Davis, Davis, CA, USA
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Mueller ML, Cole JB, Connors NK, Johnston DJ, Randhawa IAS, Van Eenennaam AL. Comparison of Gene Editing Versus Conventional Breeding to Introgress the POLLED Allele Into the Tropically Adapted Australian Beef Cattle Population. Front Genet 2021; 12:593154. [PMID: 33643378 PMCID: PMC7905321 DOI: 10.3389/fgene.2021.593154] [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: 08/09/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Dehorning is the process of physically removing horns to protect animals and humans from injury, but the process is costly, unpleasant, and faces increasing public scrutiny. Genetic selection for polled (hornless), which is genetically dominant to horned, is a long-term solution to eliminate the need for dehorning. However, due to the limited number of polled Australian Brahman bulls, the northern Australian beef cattle population remains predominantly horned. The potential to use gene editing to produce high-genetic-merit polled cattle was recently demonstrated. To further explore the concept, this study simulated introgression of the POLLED allele into a tropically adapted Australian beef cattle population via conventional breeding or gene editing (top 1% or 10% of seedstock bulls/year) for 3 polled mating schemes and compared results to baseline selection on genetic merit (Japan Ox selection index, $JapOx) alone, over the course of 20 years. The baseline scenario did not significantly decrease the 20-year HORNED allele frequency (80%), but resulted in one of the fastest rates of genetic gain ($8.00/year). Compared to the baseline, the conventional breeding scenarios where polled bulls were preferentially used for breeding, regardless of their genetic merit, significantly decreased the 20-year HORNED allele frequency (30%), but resulted in a significantly slower rate of genetic gain ($6.70/year, P ≤ 0.05). The mating scheme that required the exclusive use of homozygous polled bulls, resulted in the lowest 20-year HORNED allele frequency (8%), but this conventional breeding scenario resulted in the slowest rate of genetic gain ($5.50/year). The addition of gene editing the top 1% or 10% of seedstock bull calves/year to each conventional breeding scenario resulted in significantly faster rates of genetic gain (up to $8.10/year, P ≤ 0.05). Overall, our study demonstrates that, due to the limited number of polled Australian Brahman bulls, strong selection pressure on polled will be necessary to meaningfully increase the number of polled animals in this population. Moreover, these scenarios illustrate how gene editing could be a tool for accelerating the development of high-genetic-merit homozygous polled sires to mitigate the current trade-off of slower genetic gain associated with decreasing HORNED allele frequency in the Australian Brahman population.
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Affiliation(s)
- Maci L. Mueller
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agricultural, Beltsville, MD, United States
| | - Natalie K. Connors
- Animal Genetics and Breeding Unit (AGBU), University of New England, Armidale, NSW, Australia
| | - David J. Johnston
- Animal Genetics and Breeding Unit (AGBU), University of New England, Armidale, NSW, Australia
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Naegeli H, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Mullins E, Nogué F, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Casacuberta J, Gennaro A, Paraskevopoulos K, Raffaello T, Rostoks N. Applicability of the EFSA Opinion on site-directed nucleases type 3 for the safety assessment of plants developed using site-directed nucleases type 1 and 2 and oligonucleotide-directed mutagenesis. EFSA J 2020; 18:e06299. [PMID: 33281977 PMCID: PMC7684970 DOI: 10.2903/j.efsa.2020.6299] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The European Commission requested the EFSA Panel on Genetically Modified Organisms (GMO) to assess whether section 4 (hazard identification) and the conclusions of EFSA's Scientific opinion on the risk assessment of plants developed using zinc finger nuclease type 3 technique (ZFN-3) and other site-directed nucleases (SDN) with similar function are valid for plants developed via SDN-1, SDN-2 and oligonucleotide-directed mutagenesis (ODM). In delivering this Opinion, the GMO Panel compared the hazards associated with plants produced via SDN-1, SDN-2 and ODM with those associated with plants obtained via both SDN-3 and conventional breeding. Unlike for SDN-3 methods, the application of SDN-1, SDN-2 and ODM approaches aims to modify genomic sequences in a way which can result in plants not containing any transgene, intragene or cisgene. Consequently, the GMO Panel concludes that those considerations which are specifically related to the presence of a transgene, intragene or cisgene included in section 4 and the conclusions of the Opinion on SDN-3 are not relevant to plants obtained via SDN-1, SDN-2 or ODM as defined in this Opinion. Overall, the GMO Panel did not identify new hazards specifically linked to the genomic modification produced via SDN-1, SDN-2 or ODM as compared with both SDN-3 and conventional breeding. Furthermore, the GMO Panel considers that the existing Guidance for risk assessment of food and feed from genetically modified plants and the Guidance on the environmental risk assessment of genetically modified plants are sufficient but are only partially applicable to plants generated via SDN-1, SDN-2 or ODM. Indeed, those guidance documents' requirements that are linked to the presence of exogenous DNA are not relevant for the risk assessment of plants developed via SDN-1, SDN-2 or ODM approaches if the genome of the final product does not contain exogenous DNA.
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Moro LN, Viale DL, Bastón JI, Arnold V, Suvá M, Wiedenmann E, Olguín M, Miriuka S, Vichera G. Generation of myostatin edited horse embryos using CRISPR/Cas9 technology and somatic cell nuclear transfer. Sci Rep 2020; 10:15587. [PMID: 32973188 PMCID: PMC7518276 DOI: 10.1038/s41598-020-72040-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
The application of new technologies for gene editing in horses may allow the generation of improved sportive individuals. Here, we aimed to knock out the myostatin gene (MSTN), a negative regulator of muscle mass development, using CRISPR/Cas9 and to generate edited embryos for the first time in horses. We nucleofected horse fetal fibroblasts with 1, 2 or 5 µg of 2 different gRNA/Cas9 plasmids targeting the first exon of MSTN. We observed that increasing plasmid concentrations improved mutation efficiency. The average efficiency was 63.6% for gRNA1 (14/22 edited clonal cell lines) and 96.2% for gRNA2 (25/26 edited clonal cell lines). Three clonal cell lines were chosen for embryo generation by somatic cell nuclear transfer: one with a monoallelic edition, one with biallelic heterozygous editions and one with a biallelic homozygous edition, which rendered edited blastocysts in each case. Both MSTN editions and off-targets were analyzed in the embryos. In conclusion, CRISPR/Cas9 proved an efficient method to edit the horse genome in a dose dependent manner with high specificity. Adapting this technology sport advantageous alleles could be generated, and a precision breeding program could be developed.
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Affiliation(s)
- Lucia Natalia Moro
- LIAN-CONICET, Fundación FLENI, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Diego Luis Viale
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Neurología y Citogenética Molecular, CESyMA, Buenos Aires, Argentina
| | | | | | - Mariana Suvá
- KHEIRON BIOTECH S.A, Pilar, Buenos Aires, Argentina
| | | | | | - Santiago Miriuka
- LIAN-CONICET, Fundación FLENI, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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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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Affiliation(s)
- Steven M Solomon
- Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD, USA.
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