51
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Tran MH, Park H, Nobles CL, Karunadharma P, Pan L, Zhong G, Wang H, He W, Ou T, Crynen G, Sheptack K, Stiskin I, Mou H, Farzan M. A more efficient CRISPR-Cas12a variant derived from Lachnospiraceae bacterium MA2020. Mol Ther Nucleic Acids 2021; 24:40-53. [PMID: 33738137 PMCID: PMC7940699 DOI: 10.1016/j.omtn.2021.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/14/2021] [Indexed: 12/26/2022]
Abstract
CRISPR effector proteins introduce double-stranded breaks into the mammalian genome, facilitating gene editing by non-homologous end-joining or homology-directed repair. Unlike the more commonly studied Cas9, the CRISPR effector protein Cas12a/Cpf1 recognizes a T-rich protospacer adjacent motif (PAM) and can process its own CRISPR RNA (crRNA) array, simplifying the use of multiple guide RNAs. We observed that the Cas12a ortholog of Lachnospiraceae bacterium MA2020 (Lb2Cas12a) edited mammalian genes with efficiencies comparable to those of AsCas12a and LbCas12a. Compared to these well-characterized Cas12a orthologs, Lb2Cas12a is smaller and recognizes a narrow set of PAM TTTV. We introduced two mutations into Lb2Cas12a, Q571K and C1003Y, that increased its cleavage efficiency for a range of target sequences beyond those of the commonly used Cas12a orthologs AsCas12a and LbCas12a. In addition to the canonical TTTV PAM, this variant, Lb2-KY, also efficiently cleaved target regions with CTTN PAMs. Finally, we demonstrated that Lb2-KY ribonucleoprotein (RNP) complexes edited two hemoglobin target regions useful for correcting common forms of sickle-cell anemia more efficiently than commercial AsCas12a RNP complexes. Thus, Lb2-KY has distinctive properties useful for modifying a range of clinically relevant targets in the human genome.
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Affiliation(s)
- Mai H Tran
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hajeung Park
- X-ray Crystallography Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christopher L Nobles
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Li Pan
- Genomics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Guocai Zhong
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Haimin Wang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wenhui He
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tianling Ou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kelly Sheptack
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ian Stiskin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Huihui Mou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
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52
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Salisbury-Ruf CT, Larochelle A. Advances and Obstacles in Homology-Mediated Gene Editing of Hematopoietic Stem Cells. J Clin Med 2021; 10:513. [PMID: 33535527 DOI: 10.3390/jcm10030513] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Homology-directed gene editing of hematopoietic stem and progenitor cells (HSPCs) is a promising strategy for the treatment of inherited blood disorders, obviating many of the limitations associated with viral vector-mediated gene therapies. The use of CRISPR/Cas9 or other programmable nucleases and improved methods of homology template delivery have enabled precise ex vivo gene editing. These transformative advances have also highlighted technical challenges to achieve high-efficiency gene editing in HSPCs for therapeutic applications. In this review, we discuss recent pre-clinical investigations utilizing homology-mediated gene editing in HSPCs and highlight various strategies to improve editing efficiency in these cells.
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53
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Tran NT, Graf R, Wulf-Goldenberg A, Stecklum M, Strauß G, Kühn R, Kocks C, Rajewsky K, Chu VT. CRISPR-Cas9-Mediated ELANE Mutation Correction in Hematopoietic Stem and Progenitor Cells to Treat Severe Congenital Neutropenia. Mol Ther 2020; 28:2621-2634. [PMID: 32822592 PMCID: PMC7704744 DOI: 10.1016/j.ymthe.2020.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/09/2020] [Accepted: 08/05/2020] [Indexed: 01/08/2023] Open
Abstract
Severe congenital neutropenia (SCN) is a monogenic disorder. SCN patients are prone to recurrent life-threatening infections. The main causes of SCN are autosomal dominant mutations in the ELANE gene that lead to a block in neutrophil differentiation. In this study, we use CRISPR-Cas9 ribonucleoproteins and adeno-associated virus (AAV)6 as a donor template delivery system to repair the ELANEL172P mutation in SCN patient-derived hematopoietic stem and progenitor cells (HSPCs). We used a single guide RNA (sgRNA) specifically targeting the mutant allele, and an sgRNA targeting exon 4 of ELANE. Using the latter sgRNA, ∼34% of the known ELANE mutations can in principle be repaired. We achieved gene correction efficiencies of up to 40% (with sgELANE-ex4) and 56% (with sgELANE-L172P) in the SCN patient-derived HSPCs. Gene repair restored neutrophil differentiation in vitro and in vivo upon HSPC transplantation into humanized mice. Mature edited neutrophils expressed normal elastase levels and behaved normally in functional assays. Thus, we provide a proof of principle for using CRISPR-Cas9 to correct ELANE mutations in patient-derived HSPCs, which may translate into gene therapy for SCN.
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Affiliation(s)
- Ngoc Tung Tran
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Robin Graf
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | | | | | | | - Ralf Kühn
- iPS Cell Based Disease Modeling, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Christine Kocks
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Transgenics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Klaus Rajewsky
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
| | - Van Trung Chu
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; iPS Cell Based Disease Modeling, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
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54
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Butt H, Rao GS, Sedeek K, Aman R, Kamel R, Mahfouz M. Engineering herbicide resistance via prime editing in rice. Plant Biotechnol J 2020; 18:2370-2372. [PMID: 32415890 PMCID: PMC7680537 DOI: 10.1111/pbi.13399] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/02/2020] [Accepted: 05/10/2020] [Indexed: 05/04/2023]
Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering and Synthetic BiologyKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic BiologyKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic BiologyKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic BiologyKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Radwa Kamel
- Laboratory for Genome Engineering and Synthetic BiologyKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic BiologyKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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55
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Vu TV, Sivankalyani V, Kim E, Doan DTH, Tran MT, Kim J, Sung YW, Park M, Kang YJ, Kim J. Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato. Plant Biotechnol J 2020; 18:2133-2143. [PMID: 32176419 PMCID: PMC7540044 DOI: 10.1111/pbi.13373] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/08/2020] [Accepted: 02/23/2020] [Indexed: 05/04/2023]
Abstract
Genome editing via the homology-directed repair (HDR) pathway in somatic plant cells is very inefficient compared with error-prone repair by nonhomologous end joining (NHEJ). Here, we increased HDR-based genome editing efficiency approximately threefold compared with a Cas9-based single-replicon system via the use of de novo multi-replicon systems equipped with CRISPR/LbCpf1 in tomato and obtained replicon-free but stable HDR alleles. The efficiency of CRISPR/LbCpf1-based HDR was significantly modulated by physical culture conditions such as temperature and light. Ten days of incubation at 31 °C under a light/dark cycle after Agrobacterium-mediated transformation resulted in the best performance among the tested conditions. Furthermore, we developed our single-replicon system into a multi-replicon system that effectively increased HDR efficiency. Although this approach is still challenging, we showed the feasibility of HDR-based genome editing of a salt-tolerant SlHKT1;2 allele without genomic integration of antibiotic markers or any phenotypic selection. Self-pollinated offspring plants carrying the HKT1;2 HDR allele showed stable inheritance and germination tolerance in the presence of 100 mm NaCl. Our work may pave the way for transgene-free editing of alleles of interest in asexually and sexually reproducing plants.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteBac Tu LiemVietnam
| | - Velu Sivankalyani
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Eun‐Jung Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | | | - Yang Jae Kang
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
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56
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Paix A, Rasoloson D, Folkmann A, Seydoux G. Rapid Tagging of Human Proteins with Fluorescent Reporters by Genome Engineering using Double-Stranded DNA Donors. ACTA ACUST UNITED AC 2020; 129:e102. [PMID: 31710422 PMCID: PMC6935516 DOI: 10.1002/cpmb.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Tagging proteins with fluorescent reporters such as green fluorescent protein (GFP) is a powerful method to determine protein localization, especially when proteins are tagged in the endogenous context to preserve native genomic regulation. However, insertion of fluorescent reporters into the genomes of mammalian cells has required the construction of plasmids containing selection markers and/or extended sequences homologous to the site of insertion (homology arms). Here we describe a streamlined protocol that eliminates all cloning steps by taking advantage of the high propensity of linear DNAs to engage in homology‐directed repair of DNA breaks induced by the Cas9 RNA‐guided endonuclease. The protocol uses PCR amplicons, or synthetic gene fragments, with short homology arms (30‐40 bp) to insert fluorescent reporters at specific genomic locations. The linear DNAs are introduced into cells with preassembled Cas9‐crRNA‐tracrRNA complexes using one of two transfection procedures, nucleofection or lipofection. The protocol can be completed under a week, with efficiencies ranging from 0.5% to 20% of transfected cells depending on the locus targeted. © 2019 The Authors.
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Affiliation(s)
- Alexandre Paix
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dominique Rasoloson
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew Folkmann
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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57
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Shin JJ, Schröder MS, Caiado F, Wyman SK, Bray NL, Bordi M, Dewitt MA, Vu JT, Kim WT, Hockemeyer D, Manz MG, Corn JE. Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells. Cell Rep 2020; 32:108093. [PMID: 32877675 PMCID: PMC7487781 DOI: 10.1016/j.celrep.2020.108093] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/07/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Genome editing often takes the form of either error-prone sequence disruption by non-homologous end joining (NHEJ) or sequence replacement by homology-directed repair (HDR). Although NHEJ is generally effective, HDR is often difficult in primary cells. Here, we use a combination of immunophenotyping, next-generation sequencing, and single-cell RNA sequencing to investigate and reprogram genome editing outcomes in subpopulations of adult hematopoietic stem and progenitor cells. We find that although quiescent stem-enriched cells mostly use NHEJ, non-quiescent cells with the same immunophenotype use both NHEJ and HDR. Inducing quiescence before editing results in a loss of HDR in all cell subtypes. We develop a strategy of controlled cycling and quiescence that yields a 6-fold increase in the HDR/NHEJ ratio in quiescent stem cells ex vivo and in vivo. Our results highlight the tension between editing and cellular physiology and suggest strategies to manipulate quiescent cells for research and therapeutic genome editing.
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Affiliation(s)
- Jiyung J Shin
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Francisco Caiado
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicolas L Bray
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Matteo Bordi
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Mark A Dewitt
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jonathan T Vu
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Won-Tae Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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58
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Martin RM, Ikeda K, Cromer MK, Uchida N, Nishimura T, Romano R, Tong AJ, Lemgart VT, Camarena J, Pavel-Dinu M, Sindhu C, Wiebking V, Vaidyanathan S, Dever DP, Bak RO, Laustsen A, Lesch BJ, Jakobsen MR, Sebastiano V, Nakauchi H, Porteus MH. Highly Efficient and Marker-free Genome Editing of Human Pluripotent Stem Cells by CRISPR-Cas9 RNP and AAV6 Donor-Mediated Homologous Recombination. Cell Stem Cell 2020; 24:821-828.e5. [PMID: 31051134 DOI: 10.1016/j.stem.2019.04.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/08/2018] [Accepted: 03/29/2019] [Indexed: 11/25/2022]
Abstract
Genome editing of human pluripotent stem cells (hPSCs) provides powerful opportunities for in vitro disease modeling, drug discovery, and personalized stem cell-based therapeutics. Currently, only small edits can be engineered with high frequency, while larger modifications suffer from low efficiency and a resultant need for selection markers. Here, we describe marker-free genome editing in hPSCs using Cas9 ribonucleoproteins (RNPs) in combination with AAV6-mediated DNA repair template delivery. We report highly efficient and bi-allelic integration frequencies across multiple loci and hPSC lines, achieving mono-allelic editing frequencies of up to 94% at the HBB locus. Using this method, we show robust bi-allelic correction of homozygous sickle cell mutations in a patient-derived induced PSC (iPSC) line. Thus, this strategy shows significant utility for generating hPSCs with large gene integrations and/or single-nucleotide changes at high frequency and without the need for introducing selection genes, enhancing the applicability of hPSC editing for research and translational uses.
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Affiliation(s)
- Renata M Martin
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Nobuko Uchida
- ReGen Med Division, BOCO Silicon Valley, Palo Alto, CA 94303, USA
| | | | - Rosa Romano
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Andrew J Tong
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Viktor T Lemgart
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Camille Sindhu
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Volker Wiebking
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Rasmus O Bak
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Anders Laustsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark; Aarhus Research Centre of Innate Immunology, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark
| | - Benjamin J Lesch
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Martin R Jakobsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark; Aarhus Research Centre of Innate Immunology, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark
| | - Vittorio Sebastiano
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA 94305, USA
| | | | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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59
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Hewes AM, Sansbury BM, Barth S, Tarcic G, Kmiec EB. gRNA Sequence Heterology Tolerance Catalyzed by CRISPR/Cas in an In Vitro Homology-Directed Repair Reaction. Mol Ther Nucleic Acids 2020; 20:568-579. [PMID: 32330873 PMCID: PMC7177190 DOI: 10.1016/j.omtn.2020.03.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 12/17/2022]
Abstract
CRISPR and associated Cas nucleases are genetic engineering tools revolutionizing innovative approaches to cancer and inherited diseases. CRISPR-directed gene editing relies heavily on proper DNA sequence alignment between the guide RNA (gRNA)/CRISPR complex and its genomic target. Accurate hybridization of complementary DNA initiates gene editing in human cells, but inherent gRNA sequence variation that could influence the gene editing reaction has been clearly established among diverse genetic populations. As this technology advances toward clinical implementation, it will be essential to assess what degree of gRNA variation generates unwanted and erroneous CRISPR activity. With the use of a system in which a cell-free extract catalyzes nonhomologous end joining (NHEJ) and homology-directed repair (HDR), it is possible to observe a more representative population of all forms of gene editing outcomes. In this manuscript, we demonstrate CRISPR/Cas complexation at heterologous binding sites that facilitate precise and error-prone HDR. The tolerance of mispairing between the gRNA and target site of the DNA to enable HDR is surprisingly high and greatly influenced by polarity of the donor DNA strand in the reaction. These results suggest that some collateral genomic activity could occur at unintended sites in CRISPR-directed gene editing in human cells.
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Affiliation(s)
- Amanda M Hewes
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA
| | - Brett M Sansbury
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Shaul Barth
- Novellus, Jerusalem Bio-Park, 1(st) Kiryat Hadassah, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel, 9112001
| | - Gabi Tarcic
- Novellus, Jerusalem Bio-Park, 1(st) Kiryat Hadassah, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel, 9112001
| | - Eric B Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA.
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60
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Li S, Zhang Y, Xia L, Qi Y. CRISPR-Cas12a enables efficient biallelic gene targeting in rice. Plant Biotechnol J 2020; 18:1351-1353. [PMID: 31730252 PMCID: PMC7206995 DOI: 10.1111/pbi.13295] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 05/03/2023]
Affiliation(s)
- Shaoya Li
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yingxiao Zhang
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Lanqin Xia
- Institute of Crop Sciences (ICS)Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
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61
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Shin SW, Lee JS. Optimized CRISPR/Cas9 strategy for homology-directed multiple targeted integration of transgenes in CHO cells. Biotechnol Bioeng 2020; 117:1895-1903. [PMID: 32086804 DOI: 10.1002/bit.27315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Site-specific integration has emerged as a promising strategy for precise Chinese hamster ovary (CHO) cell line engineering and predictable cell line development (CLD). CRISPR/Cas9 with the homology-directed repair (HDR) pathway enables precise integration of transgenes into target genomic sites. However, inherent recalcitrance to HDR-mediated targeted integration (TI) of transgenes results in low targeting efficiency, thus requiring a selection process to find a targeted integrant in CHO cells. Here, we explored several parameters that influence the targeting efficiency using a promoter-trap-based single- or double-knock-in (KI) monitoring system. A simple change in the donor template design by the addition of single-guide RNA recognition sequences strongly increased KI efficiency (2.9-36.0 fold), depending on integration sites and cell culture mode, compared to conventional circular donor plasmids. Furthermore, sequential and simultaneous KI strategies enabled us to obtain populations with ~1-4% of double-KI cells without additional enrichment procedures. Thus, this simple optimized strategy not only allows efficient CRISPR/Cas9-mediated TI in CHO cells but also paves the way for the applicability of multiplexed KIs in one experimental step without the need for sequential and independent CHO-CLD procedures.
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Affiliation(s)
- Sung Wook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
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62
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Han JP, Chang YJ, Song DW, Choi BS, Koo OJ, Yi SY, Park TS, Yeom SC. High Homology-Directed Repair Using Mitosis Phase and Nucleus Localizing Signal. Int J Mol Sci 2020; 21:E3747. [PMID: 32466470 DOI: 10.3390/ijms21113747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/24/2020] [Indexed: 12/26/2022] Open
Abstract
In homology-directed repair, mediated knock-in single-stranded oligodeoxynucleotides (ssODNs) can be used as a homologous template and present high efficiency, but there is still a need to improve efficiency. Previous studies have mainly focused on controlling double-stranded break size, ssODN stability, and the DNA repair cycle. Nevertheless, there is a lack of research on the correlation between the cell cycle and single-strand template repair (SSTR) efficiency. Here, we investigated the relationship between cell cycle and SSTR efficiency. We found higher SSTR efficiency during mitosis, especially in the metaphase and anaphase. A Cas9 protein with a nuclear localization signal (NLS) readily migrated to the nucleus; however, the nuclear envelope inhibited the nuclear import of many nucleotide templates. This seemed to result in non-homologous end joining (NHEJ) before the arrival of the homologous template. Thus, we assessed whether NLS-tagged ssODNs and free NLS peptides could circumvent problems posed by the nuclear envelope. NLS-tagging ssODNs enhanced SSTR and indel efficiency by 4-fold compared to the control. Our results suggest the following: (1) mitosis is the optimal phase for SSTR, (2) the donor template needs to be delivered to the nucleus before nuclease delivery, and (3) NLS-tagging ssODNs improve SSTR efficiency, especially high in mitosis.
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Peterson SE, Keeney S, Jasin M. Mechanistic Insight into Crossing over during Mouse Meiosis. Mol Cell 2020; 78:1252-1263.e3. [PMID: 32362315 DOI: 10.1016/j.molcel.2020.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/10/2020] [Accepted: 04/07/2020] [Indexed: 01/06/2023]
Abstract
Crossover recombination is critical for meiotic chromosome segregation, but how mammalian crossing over is accomplished is poorly understood. Here, we illuminate how strands exchange during meiotic recombination in male mice by analyzing patterns of heteroduplex DNA in recombinant molecules preserved by the mismatch correction deficiency of Msh2-/- mutants. Surprisingly, MSH2-dependent recombination suppression was not evident. However, a substantial fraction of crossover products retained heteroduplex DNA, and some provided evidence of MSH2-independent correction. Biased crossover resolution was observed, consistent with asymmetry between DNA ends in earlier intermediates. Many crossover products yielded no heteroduplex DNA, suggesting dismantling by D-loop migration. Unlike the complexity of crossovers in yeast, these simple modifications of the original double-strand break repair model-asymmetry in recombination intermediates and D-loop migration-may be sufficient to explain most meiotic crossing over in mice while also addressing long-standing questions related to Holliday junction resolution.
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Affiliation(s)
- Shaun E Peterson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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64
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Abstract
A key challenge in precise genome editing is the low efficiency of homology-directed repair (HDR). Here we describe a strategy for increasing the efficiency of HDR in cells by using a chromatin donor template instead of a naked DNA donor template. The use of chromatin, which is the natural form of DNA in the nucleus, increases the frequency of HDR-edited clones as well as homozygous editing. In addition, transfection of chromatin results in negligible cytotoxicity. These findings suggest that a chromatin donor template should be useful for a wide range of HDR applications such as the precise insertion or replacement of DNA fragments that contain the coding regions of genes. Genome editing is a powerful tool used across a wide range of biomedical research. There are several different techniques used, depending on the type of edit being made, and one known as homology-directed repair – or HDR for short – is a common technique for precisely inserting large sections of DNA, such as those needed to make desired proteins in cells. HDR takes advantage of the cell’s mechanisms for repairing damage to DNA if both strands of the DNA double helix are broken. The mechanism relies on a DNA template to stitch the strands back together. To insert or replace a new DNA sequence, scientists can add a customized piece of DNA of their choosing to the cell so that it might be incorporated into the genome. However, HDR is not very efficient, and the success rate is often less than a few percent. In HDR gene editing, the DNA template is typically added as purified, or ‘naked’, DNA. However, the natural form of DNA in cells, known as chromatin, is where the DNA helix is wrapped around a cluster of proteins known as histones. Cruz-Becerra and Kadonaga tested the idea that DNA in the form of chromatin might be more effective as a template for HDR than naked DNA. The two approaches were compared to see which was better at inserting a sequence at three different locations in the genome of lab-grown human cells. In these experiments, the chromatin templates were 2.3- to 7.4-fold more efficient than the naked DNA. Also, the DNA in human cells is organized as pairs of chromosomes, and chromatin was better than naked DNA for editing both copies of the chromosome pairs rather than only one of them. In addition, the chromatin is potentially less toxic to the cells. Cruz-Becerra and Kadonaga hope that this will be useful for increasing the success rate of HDR experiments and potentially other methods of gene editing in the future.
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Affiliation(s)
- Grisel Cruz-Becerra
- Section of Molecular Biology, University of California, San Diego, La Jolla, United States
| | - James T Kadonaga
- Section of Molecular Biology, University of California, San Diego, La Jolla, United States
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Billon P, Nambiar TS, Hayward SB, Zafra MP, Schatoff EM, Oshima K, Dunbar A, Breinig M, Park YC, Ryu HS, Tschaharganeh DF, Levine RL, Baer R, Ferrando A, Dow LE, Ciccia A. Detection of Marker-Free Precision Genome Editing and Genetic Variation through the Capture of Genomic Signatures. Cell Rep 2020; 30:3280-3295.e6. [PMID: 32160537 PMCID: PMC7108696 DOI: 10.1016/j.celrep.2020.02.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/13/2020] [Accepted: 02/14/2020] [Indexed: 10/29/2022] Open
Abstract
Genome editing technologies have transformed our ability to engineer desired genomic changes within living systems. However, detecting precise genomic modifications often requires sophisticated, expensive, and time-consuming experimental approaches. Here, we describe DTECT (Dinucleotide signaTurE CapTure), a rapid and versatile detection method that relies on the capture of targeted dinucleotide signatures resulting from the digestion of genomic DNA amplicons by the type IIS restriction enzyme AcuI. DTECT enables the accurate quantification of marker-free precision genome editing events introduced by CRISPR-dependent homology-directed repair, base editing, or prime editing in various biological systems, such as mammalian cell lines, organoids, and tissues. Furthermore, DTECT allows the identification of oncogenic mutations in cancer mouse models, patient-derived xenografts, and human cancer patient samples. The ease, speed, and cost efficiency by which DTECT identifies genomic signatures should facilitate the generation of marker-free cellular and animal models of human disease and expedite the detection of human pathogenic variants.
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Affiliation(s)
- Pierre Billon
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Maria P Zafra
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Emma M Schatoff
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Koichi Oshima
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrew Dunbar
- Human Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marco Breinig
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, 69120 Heidelberg, Germany
| | - Young C Park
- Human Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Han S Ryu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, 69120 Heidelberg, Germany
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard Baer
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Adolfo Ferrando
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Palmer DJ, Turner DL, Ng P. A Single "All-in-One" Helper-Dependent Adenovirus to Deliver Donor DNA and CRISPR/Cas9 for Efficient Homology-Directed Repair. Mol Ther Methods Clin Dev 2020; 17:441-447. [PMID: 32154329 PMCID: PMC7058846 DOI: 10.1016/j.omtm.2020.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/28/2020] [Indexed: 11/19/2022]
Abstract
In this study, we developed a single helper-dependent adenovirus (HDAd) to deliver all of the components (donor DNA, CRISPR-associated protein 9 [Cas9], and guide RNA [gRNA]) needed to achieve high-efficiency gene targeting and homology-directed repair in transduced cells. We show that these "all-in-one" HDAds are up to 117-fold more efficient at gene targeting than donor HDAds that do not express CRISPR/Cas9 in human induced pluripotent stem cells (iPSCs). The vast majority (>90%) of targeted recombinants had only one allele targeted, and this was accompanied by high-frequency indel formation in the non-targeted allele at the site of Cas9 cleavage. These indels varied in size and nature, and included large deletions of ∼8 kb. The remaining minority of recombinants had both alleles targeted (so-called bi-allelic targeting). These all-in-one HDAds represent an important platform for accomplishing and expanding the utility of homology-directed repair, especially for difficult-to-transfect cells and for in vivo applications.
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Affiliation(s)
- Donna J. Palmer
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Dustin L. Turner
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip Ng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Corresponding author: Philip Ng, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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67
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Ginn SL, Amaya AK, Liao SHY, Zhu E, Cunningham SC, Lee M, Hallwirth CV, Logan GJ, Tay SS, Cesare AJ, Pickett HA, Grompe M, Dilworth K, Lisowski L, Alexander IE. Efficient in vivo editing of OTC-deficient patient-derived primary human hepatocytes. JHEP Rep 2020; 2:100065. [PMID: 32039406 PMCID: PMC7005564 DOI: 10.1016/j.jhepr.2019.100065] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022] Open
Abstract
Background & Aims Genome editing technology has immense therapeutic potential and is likely to rapidly supplant contemporary gene addition approaches. Key advantages include the capacity to directly repair mutant loci with resultant recovery of physiological gene expression and maintenance of durable therapeutic effects in replicating cells. In this study, we aimed to repair a disease-causing point mutation in the ornithine transcarbamylase (OTC) locus in patient-derived primary human hepatocytes in vivo at therapeutically relevant levels. Methods Editing reagents for precise CRISPR/SaCas9-mediated cleavage and homology-directed repair (HDR) of the human OTC locus were first evaluated against an OTC minigene cassette transposed into the mouse liver. The editing efficacy of these reagents was then tested on the native OTC locus in patient-derived primary human hepatocytes xenografted into the FRG (Fah-/-Rag2-/-Il2rg-/-) mouse liver. A highly human hepatotropic capsid (NP59) was used for adeno-associated virus (AAV)-mediated gene transfer. Editing events were characterised using next-generation sequencing and restoration of OTC expression was evaluated using immunofluorescence. Results Following AAV-mediated delivery of editing reagents to patient-derived primary human hepatocytes in vivo, OTC locus-specific cleavage was achieved at efficiencies of up to 72%. Importantly, successful editing was observed in up to 29% of OTC alleles at clinically relevant vector doses. No off-target editing events were observed at the top 10 in silico-predicted sites in the genome. Conclusions We report efficient single-nucleotide correction of a disease-causing mutation in the OTC locus in patient-derived primary human hepatocytes in vivo at levels that, if recapitulated in the clinic, would provide benefit for even the most therapeutically challenging liver disorders. Key challenges for clinical translation include the cell cycle dependence of classical HDR and mitigation of unintended on- and off-target editing events. Lay summary The ability to efficiently and safely correct disease-causing mutations remains the holy grail of gene therapy. Herein, we demonstrate, for the first time, efficient in vivo correction of a patient-specific disease-causing mutation in the OTC gene in primary human hepatocytes, using therapeutically relevant vector doses. We also highlight the challenges that need to be overcome for this technology to be translated into clinical practice. Therapeutically relevant levels of single-nucleotide repair of the human OTC locus were achieved in vivo. Single-nucleotide editing of primary human hepatocytes was facilitated by a highly hepatotropic bioengineered AAV capsid. A novel human minigene platform proved highly effective for evaluation of human liver-specific genome editing reagents.
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Key Words
- 7 NGS, next-generation sequencing
- AAV, adeno-associated virus
- BrdU, bromodeoxyuridine
- CRISPR-Cas9
- FRG, Fah-/-Rag2-/-Il2rg-/-
- HDR, homology-directed repair
- ITR, inverted terminal repeats
- InDels, insertions and deletions
- LSP1, liver-specific promoter
- NHEJ, non-homologous end joining
- NP59 capsid
- OTC deficiency
- PAM, protospacer adjacent motif
- PRE, mutant form of the Woodchuck hepatitis virus posttranscriptional regulatory element
- RTA, Real Time Analysis
- SV40 pA, SV40 polyadenylation signal sequence
- SaCas9, Staphylococcus aureus Cas9 nuclease
- TBG, human thyroxine binding globulin promoter
- U6, RNA polymerase III promoter for human U6 snRNA
- WT, wild-type
- genome editing
- homology-directed repair
- humanised FRG mice
- pA, bovine growth hormone polyadenylation signal sequence
- primary human hepatocytes
- rAAV, recombinant adeno-associated virus
- recombinant AAV
- sgRNA, single guide RNA
- synthetic capsid
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Affiliation(s)
- Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Sophia H Y Liao
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Sharon C Cunningham
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Michael Lee
- Telomere Length Regulation Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Szun S Tay
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Markus Grompe
- School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Kimberley Dilworth
- Translational Vectorology Group and Vector & Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Group and Vector & Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia.,Military Institute of Hygiene and Epidemiology, Pulway, Poland
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
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68
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Hoang SM, O'Sullivan RJ. Alternative Lengthening of Telomeres: Building Bridges To Connect Chromosome Ends. Trends Cancer 2020; 6:247-60. [PMID: 32101727 DOI: 10.1016/j.trecan.2019.12.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a mechanism of telomere maintenance that is observed in many of the most recalcitrant cancer subtypes. Telomeres in ALT cancer cells exhibit a distinctive nucleoprotein architecture shaped by the mismanagement of chromatin that fosters cycles of DNA damage and replicative stress that activate homology-directed repair (HDR). Mutations in specific chromatin-remodeling factors appear to be key determinants of the emergence and survival of ALT cancer cells. However, these may represent vulnerabilities for the targeted elimination of ALT cancer cells that infiltrate tissues and organs to become devastating tumors. In this review we examine recent findings that provide new insights into the factors and mechanisms that mediate telomere length maintenance and survival of ALT cancer cells.
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69
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Yan N, Sun Y, Fang Y, Deng J, Mu L, Xu K, Mymryk JS, Zhang Z. A Universal Surrogate Reporter for Efficient Enrichment of CRISPR/Cas9-Mediated Homology-Directed Repair in Mammalian Cells. Mol Ther Nucleic Acids 2019; 19:775-789. [PMID: 31955009 PMCID: PMC6970138 DOI: 10.1016/j.omtn.2019.12.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022]
Abstract
CRISPR/Cas9-mediated homology-directed repair (HDR) can be leveraged to precisely engineer mammalian genomes. However, the inherently low efficiency of HDR often hampers to identify the desired modified cells. Here, we developed a novel universal surrogate reporter system that efficiently enriches for genetically modified cells arising from CRISPR/Cas9-induced HDR events (namely, the "HDR-USR" system). This episomally based reporter can be self-cleaved and self-repaired via HDR to create a functional puromycin selection cassette without compromising genome integrity. Co-transfection of the HDR-USR system into host cells and transient puromycin selection efficiently achieves enrichment of HDR-modified cells. We tested the system for precision point mutation at 16 loci in different human cell lines and one locus in two rodent cell lines. This system exhibited dramatic improvements in HDR efficiency at a single locus (up to 20.7-fold) and two loci at once (42% editing efficiency compared to zero in the control), as well as greatly improved knockin efficiency (8.9-fold) and biallelic deletion (35.9-fold) at test loci. Further increases were achieved by co-expression of yeast Rad52 and linear single-/double-stranded DNA donors. Taken together, our HDR-USR system provides a simple, robust and efficient surrogate reporter for the enrichment of CRISPR/Cas9-induced HDR-based precision genome editing across various targeting loci in different cell lines.
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Affiliation(s)
- Nana Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongsen Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanyuan Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingrong Deng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Mu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Joe S Mymryk
- Department of Microbiology & Immunology, Oncology and Otolaryngology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Attwood KM, Salsman J, Chung D, Mathavarajah S, Van Iderstine C, Dellaire G. PML isoform expression and DNA break location relative to PML nuclear bodies impacts the efficiency of homologous recombination. Biochem Cell Biol 2019; 98:314-326. [PMID: 31671275 DOI: 10.1139/bcb-2019-0115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML NBs) are nuclear subdomains that respond to genotoxic stress by increasing in number via changes in chromatin structure. However, the role of the PML protein and PML NBs in specific mechanisms of DNA repair has not been fully characterized. Here, we have directly examined the role of PML in homologous recombination (HR) using I-SceI extrachromosomal and chromosome-based homology-directed repair (HDR) assays, and in HDR by CRISPR/Cas9-mediated gene editing. We determined that PML loss can inhibit HR in an extrachromosomal HDR assay but had less of an effect on CRISPR/Cas9-mediated chromosomal HDR. Overexpression of PML also inhibited both CRISPR HDR and I-SceI-induced HDR using a chromosomal reporter, and in an isoform-specific manner. However, the impact of PML overexpression on the chromosomal HDR reporter was dependent on the intranuclear chromosomal positioning of the reporter. Specifically, HDR at the TAP1 gene locus, which is associated with PML NBs, was reduced compared with a locus not associated with a PML NB; yet, HDR could be reduced at the non-PML NB-associated locus by PML overexpression. Thus, both loss and overexpression of PML isoforms can inhibit HDR, and proximity of a chromosomal break to a PML NB can impact HDR efficiency.
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Affiliation(s)
- Kathleen M Attwood
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | | | - Graham Dellaire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.,Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Reuven N, Adler J, Broennimann K, Myers N, Shaul Y. Recruitment of DNA Repair MRN Complex by Intrinsically Disordered Protein Domain Fused to Cas9 Improves Efficiency of CRISPR-Mediated Genome Editing. Biomolecules 2019; 9:E584. [PMID: 31597252 PMCID: PMC6843829 DOI: 10.3390/biom9100584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 is a powerful tool for genome editing in cells and organisms. Nevertheless, introducing directed templated changes by homology-directed repair (HDR) requires the cellular DNA repair machinery, such as the MRN complex (Mre11/Rad50/Nbs1). To improve the process, we tailored chimeric constructs of Cas9, in which SpCas9 was fused at its N- or C-terminus to a 126aa intrinsically disordered domain from HSV-1 alkaline nuclease (UL12) that recruits the MRN complex. The chimeric Cas9 constructs were two times more efficient in homology-directed editing of endogenous loci in tissue culture cells. This effect was dependent upon the MRN-recruiting activity of the domain and required lower amounts of the chimeric Cas9 in comparison with unmodified Cas9. The new constructs improved the yield of edited cells when making endogenous point mutations or inserting small tags encoded by oligonucleotide donor DNA (ssODN), and also with larger insertions encoded by plasmid DNA donor templates. Improved editing was achieved with both transfected plasmid-encoded Cas9 constructs as well as recombinant Cas9 protein transfected as ribonucleoprotein complexes. Our strategy was highly efficient in restoring a genetic defect in a cell line, exemplifying the possible implementation of our strategy in gene therapy. These constructs provide a simple approach to improve directed editing.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Karin Broennimann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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72
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Barroso-González J, García-Expósito L, Hoang SM, Lynskey ML, Roncaioli JL, Ghosh A, Wallace CT, de Vitis M, Modesti M, Bernstein KA, Sarkar SN, Watkins SC, O'Sullivan RJ. RAD51AP1 Is an Essential Mediator of Alternative Lengthening of Telomeres. Mol Cell 2019; 76:11-26.e7. [PMID: 31400850 PMCID: PMC6778027 DOI: 10.1016/j.molcel.2019.06.043] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/23/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a homology-directed repair (HDR) mechanism of telomere elongation that controls proliferation in aggressive cancers. We show that the disruption of RAD51-associated protein 1 (RAD51AP1) in ALT+ cancer cells leads to generational telomere shortening. This is due to RAD51AP1's involvement in RAD51-dependent homologous recombination (HR) and RAD52-POLD3-dependent break induced DNA synthesis. RAD51AP1 KO ALT+ cells exhibit telomere dysfunction and cytosolic telomeric DNA fragments that are sensed by cGAS. Intriguingly, they activate ULK1-ATG7-dependent autophagy as a survival mechanism to mitigate DNA damage and apoptosis. Importantly, RAD51AP1 protein levels are elevated in ALT+ cells due to MMS21 associated SUMOylation. Mutation of a single SUMO-targeted lysine residue perturbs telomere dynamics. These findings indicate that RAD51AP1 is an essential mediator of the ALT mechanism and is co-opted by post-translational mechanisms to maintain telomere length and ensure proliferation of ALT+ cancer cells.
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Song My Hoang
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Michelle L Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Arundhati Ghosh
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Callen T Wallace
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Marco de Vitis
- Department of Science, University of Rome "ROMA TRE", 00146 Rome, Italy
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm UMR1068, Aix Marseille Université U105; Institut Paoli Calmettes, 27 Boulevard Lei Roure CS30059, 13273 Marseille, Cedex 09, France
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Saumendra N Sarkar
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA.
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73
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Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM, Reddy ST. Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells. MAbs 2019; 11:1367-1380. [PMID: 31478465 PMCID: PMC6816377 DOI: 10.1080/19420862.2019.1662691] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in cellular engineering enabled by CRISPR-Cas9 genome editing have made it possible to expand the use of mammalian cells in biotechnological applications. Here, we describe an antibody engineering and screening approach where complete variable light (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, we are able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, we could isolate a diverse panel of >40 unique antigen-binding variants. Additionally, we successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | | | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
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74
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Rogers GL, Chen HY, Morales H, Cannon PM. Homologous Recombination-Based Genome Editing by Clade F AAVs Is Inefficient in the Absence of a Targeted DNA Break. Mol Ther 2019; 27:1726-1736. [PMID: 31540849 DOI: 10.1016/j.ymthe.2019.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 12/26/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are frequently used as donor templates for genome editing by homologous recombination. Although modification rates are typically under 1%, they are greatly enhanced by targeted double-stranded DNA breaks (DSBs). A recent report described clade F AAVs mediating high-efficiency homologous recombination-based editing in the absence of DSBs. The clade F vectors included AAV9 and a series isolated from human hematopoietic stem and progenitor cells (HSPCs). We evaluated these vectors by packaging homology donors into AAV9 and an AAVHSC capsid and examining their ability to insert GFP at the CCR5 and AAVS1 loci in human HSPCs and cell lines. As a control, we used AAV6, which effectively edits HSPCs but only when combined with a targeted DSB. Each AAV vector promoted GFP insertion in the presence of matched CCR5 or AAVS1 zinc-finger nucleases (ZFNs), but none supported detectable editing in the absence of the nucleases. Rates of editing with ZFNs correlated with transduction efficiencies for each vector, implying no differences in the ability of donor sequences delivered by the different vectors to direct genome editing. Our results, therefore, do not support that clade F AAVs can perform high-efficiency genome editing in the absence of a DSB.
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Affiliation(s)
- Geoffrey L Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Hsu-Yu Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Heidy Morales
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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75
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Pattabhi S, Lotti SN, Berger MP, Singh S, Lux CT, Jacoby K, Lee C, Negre O, Scharenberg AM, Rawlings DJ. In Vivo Outcome of Homology-Directed Repair at the HBB Gene in HSC Using Alternative Donor Template Delivery Methods. Mol Ther Nucleic Acids 2019; 17:277-288. [PMID: 31279229 PMCID: PMC6611979 DOI: 10.1016/j.omtn.2019.05.025] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022]
Abstract
Gene editing following designer nuclease cleavage in the presence of a DNA donor template can revert mutations in disease-causing genes. For optimal benefit, reversion of the point mutation in HBB leading to sickle cell disease (SCD) would permit precise homology-directed repair (HDR) while concurrently limiting on-target non-homologous end joining (NHEJ)-based HBB disruption. In this study, we directly compared the relative efficiency of co-delivery of a novel CRISPR/Cas9 ribonucleoprotein targeting HBB in association with recombinant adeno-associated virus 6 (rAAV6) versus single-stranded oligodeoxynucleotides (ssODNs) to introduce the sickle mutation (GTC or GTG; encoding E6V) or a silent change (GAA; encoding E6optE) in human CD34+ mobilized peripheral blood stem cells (mPBSCs) derived from healthy donors. In vitro, rAAV6 outperformed ssODN donor template delivery and mediated greater HDR correction, leading to both higher HDR rates and a higher HDR:NHEJ ratio. In contrast, at 12-14 weeks post-transplant into recipient, immunodeficient, NOD, B6, SCID Il2rγ-/- Kit(W41/W41) (NBSGW) mice, a ∼6-fold higher proportion of ssODN-modified cells persisted in vivo compared to recipients of rAAV6-modified mPBSCs. Together, our findings highlight that methodology for donor template delivery markedly impacts long-term persistence of HBB gene-modified mPBSCs, and they suggest that the ssODN platform is likely to be most amenable to direct clinical translation.
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Affiliation(s)
- Sowmya Pattabhi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Samantha N Lotti
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Mason P Berger
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Swati Singh
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Christopher T Lux
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kyle Jacoby
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Andrew M Scharenberg
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Casebia Therapeutics, Cambridge, MA, USA; Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA, USA; Department of Immunology, University of Washington, School of Medicine, Seattle, WA, USA
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA, USA; Department of Immunology, University of Washington, School of Medicine, Seattle, WA, USA.
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76
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Philip NS, Escobedo F, Bahr LL, Berry BJ, Wojtovich AP. Mos1 Element-Mediated CRISPR Integration of Transgenes in Caenorhabditis elegans. G3 (Bethesda) 2019; 9:2629-35. [PMID: 31186306 DOI: 10.1534/g3.119.400399] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The introduction of exogenous genes in single-copy at precise genomic locations is a powerful tool that has been widely used in the model organism Caenorhabditis elegans. Here, we have streamlined the process by creating a rapid, cloning-free method of single-copy transgene insertion we call Mos1 element-mediated CRISPR integration (mmCRISPi). The protocol combines the impact of Mos1 mediated single-copy gene insertion (mosSCI) with the ease of CRISPR/Cas9 mediated gene editing, allowing in vivo construction of transgenes from linear DNA fragments integrated at defined loci in the C. elegans genome. This approach was validated by defining its efficiency at different integration sites in the genome and by testing transgene insert size. The mmCRISPi method benefits from in vivo recombination of overlapping PCR fragments, allowing researchers to mix-and-match between promoters, protein-coding sequences, and 3′ untranslated regions, all inserted in a single step at a defined Mos1 loci.
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77
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van Sluis M, McStay B. Nucleolar DNA Double-Strand Break Responses Underpinning rDNA Genomic Stability. Trends Genet 2019; 35:743-53. [PMID: 31353047 DOI: 10.1016/j.tig.2019.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022]
Abstract
Nucleoli, the sites of ribosome biogenesis, form around ribosomal gene (rDNA) arrays termed nucleolar organiser regions (NORs). These are the most transcriptionally active regions of the human genome and specialised responses have evolved to ensure their genomic stability. This review focuses on nucleolar responses to DNA double-strand breaks (DSBs) introduced into rDNA arrays using sequence-specific endonucleases, including CRISPR/Cas9. Repair of rDNA DSBs is predominantly carried out by the homology-directed repair (HDR) pathway that is facilitated by inhibition of transcription by RNA polymerase-I (Pol-I) and ensuing dramatic nucleolar reorganisation. Additionally, we review evidence that nucleoli can sense and respond to DSBs elsewhere in the genome.
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78
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Kaul T, Raman NM, Eswaran M, Thangaraj A, Verma R, Sony SK, Sathelly KM, Kaul R, Yadava P, Agrawal PK. Data Mining by Pluralistic Approach on CRISPR Gene Editing in Plants. Front Plant Sci 2019; 10:801. [PMID: 31354748 PMCID: PMC6632506 DOI: 10.3389/fpls.2019.00801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Genome engineering by site-specific nucleases enables reverse genetics and targeted editing of genomes in an efficacious manner. Contemporary revolutionized progress in targeted-genome engineering technologies based on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-related RNA-guided endonucleases facilitate coherent interrogation of crop genome function. Evolved as an innate component of the adaptive immune response in bacterial and archaeal systems, CRISPR/Cas system is now identified as a versatile molecular tool that ensures specific and targeted genome modification in plants. Applications of this genome redaction tool-kit include somatic genome editing, rectification of genetic disorders or gene therapy, treatment of infectious diseases, generation of animal models, and crop improvement. We review the utilization of these synthetic nucleases as precision, targeted-genome editing platforms with the inherent potential to accentuate basic science "strengths and shortcomings" of gene function, complement plant breeding techniques for crop improvement, and charter a knowledge base for effective use of editing technology for ever-increasing agricultural demands. Furthermore, the emerging importance of Cpf1, Cas9 nickase, C2c2, as well as other innovative candidates that may prove more effective in driving novel applications in crops are also discussed. The mined data has been prepared as a library and opened for public use at www.lipre.org.
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Affiliation(s)
- Tanushri Kaul
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nitya Meenakshi Raman
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Murugesh Eswaran
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Arulprakash Thangaraj
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rachana Verma
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sonia Khan Sony
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Krishnamurthy M. Sathelly
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rashmi Kaul
- Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pranjal Yadava
- Department of Biotechnology, Indian Institute of Maize Research, Indian Institute of Agricultural Biotechnology (ICAR), New Delhi, India
| | - Pawan Kumar Agrawal
- National Agricultural Science Fund, Indian Council of Agricultural Research, New Delhi, India
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79
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Farboud B, Severson AF, Meyer BJ. Strategies for Efficient Genome Editing Using CRISPR-Cas9. Genetics 2019; 211:431-57. [PMID: 30504364 DOI: 10.1534/genetics.118.301775] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
The targetable DNA endonuclease CRISPR-Cas9 has transformed analysis of biological processes by enabling robust genome editing in model and nonmodel organisms. Although rules directing Cas9 to its target DNA via a guide RNA are straightforward, wide variation occurs in editing efficiency and repair outcomes for both imprecise error-prone repair and precise templated repair. We found that imprecise and precise DNA repair from double-strand breaks (DSBs) is asymmetric, favoring repair in one direction. Using this knowledge, we designed RNA guides and repair templates that increased the frequency of imprecise insertions and deletions and greatly enhanced precise insertion of point mutations in Caenorhabditis elegans We also devised strategies to insert long (10 kb) exogenous sequences and incorporate multiple nucleotide substitutions at a considerable distance from DSBs. We expanded the repertoire of co-conversion markers appropriate for diverse nematode species. These selectable markers enable rapid identification of Cas9-edited animals also likely to carry edits in desired targets. Lastly, we explored the timing, location, frequency, sex dependence, and categories of DSB repair events by developing loci with allele-specific Cas9 targets that can be contributed during mating from either male or hermaphrodite germ cells. We found a striking difference in editing efficiency between maternally and paternally contributed genomes. Furthermore, imprecise repair and precise repair from exogenous repair templates occur with high frequency before and after fertilization. Our strategies enhance Cas9-targeting efficiency, lend insight into the timing and mechanisms of DSB repair, and establish guidelines for achieving predictable precise and imprecise repair outcomes with high frequency.
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80
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Pickett CJ, Zeller RW. Efficient genome editing using CRISPR-Cas-mediated homology directed repair in the ascidian Ciona robusta. Genesis 2018; 56:e23260. [PMID: 30375719 DOI: 10.1002/dvg.23260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/21/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
Eliminating or silencing a gene's level of activity is one of the classic approaches developmental biologists employ to determine a gene's function. A recently developed method of gene perturbation called CRISPR-Cas, which was derived from a prokaryotic adaptive immune system, has been adapted for use in eukaryotic cells. This technology has been established in several model organisms as a powerful and efficient tool for knocking out or knocking down the function of a gene of interest. It has been recently shown that CRISPR-Cas functions with fidelity and efficiency in Ciona robusta. Here, we show that in C. robusta CRISPR-Cas mediated genomic knock-ins can be efficiently generated. Electroporating a tissue-specific transgene driving Cas9 and a U6-driven gRNA transgene together with a fluorescent protein-containing homology directed repair (FP-HDR) template results in gene-specific patterns of fluorescence consistent with a targeted genomic insertion. Using the Tyrosinase locus to optimize reagents, we first characterize a new Pol III promoter for expressing gRNAs from the Ciona savignyi H1 gene, and then adapt technology that flanks gRNAs by ribozymes allowing cell-specific expression from Pol II promoters. Next, we examine homology arm-length efficiencies of FP-HDR templates. Reagents were then developed for targeting Brachyury and Pou4 that resulted in expected patterns of fluorescence, and sequenced PCR amplicons derived from single embryos validated predicted genomic insertions. Finally, using two differentially colored FP-HDR templates, we show that biallelic FP-HDR template insertion can be detected in live embryos of the F0 generation.
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Affiliation(s)
- C J Pickett
- Department of Biology, San Diego State University, San Diego, California
| | - Robert W Zeller
- Department of Biology, San Diego State University, San Diego, California.,Coastal and Marine Institute, San Diego State University, San Diego, California.,Center for Applied and Experimental Genomics, San Diego State University, San Diego, California
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81
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Abstract
Binary transcription systems are powerful genetic tools widely used for visualizing and manipulating cell fate and gene expression in specific groups of cells or tissues in model organisms. These systems contain two components as separate transgenic lines. A driver line expresses a transcriptional activator under the control of tissue-specific promoters/enhancers, and a reporter/effector line harbors a target gene placed downstream to the binding site of the transcription activator. Animals harboring both components induce tissue-specific transactivation of a target gene expression. Precise spatiotemporal expression of the gene in targeted tissues is critical for unbiased interpretation of cell/gene activity. Therefore, developing a method for generating exclusive cell/tissue-specific driver lines is essential. Here we present a method to generate highly tissue-specific targeted expression system by employing a "Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated" (CRISPR/Cas)-based genome editing technique. In this method, the endonuclease Cas9 is targeted by two chimeric guide RNAs (gRNA) to specific sites in the first coding exon of a gene in the Drosophila genome to create double-strand breaks (DSB). Subsequently, using an exogenous donor plasmid containing the transactivator sequence, the cell-autonomous repair machinery enables homology-directed repair (HDR) of the DSB, resulting in precise deletion and replacement of the exon with the transactivator sequence. The knocked-in transactivator is expressed exclusively in cells where the cis-regulatory elements of the replaced gene are functional. The detailed step-by-step protocol presented here for generating a binary transcriptional driver expressed in Drosophila fgf/branchless-producing epithelial/neuronal cells can be adopted for any gene- or tissue-specific expression.
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Affiliation(s)
- Lijuan Du
- Department of Cell Biology and Molecular Genetics, University of Maryland
| | - Amy Zhou
- Department of Cell Biology and Molecular Genetics, University of Maryland
| | - Alex Sohr
- Department of Cell Biology and Molecular Genetics, University of Maryland
| | - Sougata Roy
- Department of Cell Biology and Molecular Genetics, University of Maryland;
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82
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Izmiryan A, Ganier C, Bovolenta M, Schmitt A, Mavilio F, Hovnanian A. Ex Vivo COL7A1 Correction for Recessive Dystrophic Epidermolysis Bullosa Using CRISPR/Cas9 and Homology-Directed Repair. Mol Ther Nucleic Acids 2018; 12:554-567. [PMID: 30195791 PMCID: PMC6077132 DOI: 10.1016/j.omtn.2018.06.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/04/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Recessive dystrophic epidermolysis bullosa is a rare and severe genetic skin disease resulting in blistering of the skin and mucosa. Recessive dystrophic epidermolysis bullosa (RDEB) is caused by a wide variety of mutations in COL7A1-encoding type VII collagen, which is essential for dermal-epidermal adhesion. Here we demonstrate the feasibility of ex vivo COL7A1 editing in primary RDEB cells and in grafted 3D skin equivalents through CRISPR/Cas9-mediated homology-directed repair. We designed five guide RNAs to correct a RDEB causative null mutation in exon 2 (c.189delG; p.Leu64Trpfs*40). Among the site-specific guide RNAs tested, one showed significant cleavage activity in primary RDEB keratinocytes and in fibroblasts when delivered as integration-deficient lentivirus. Genetic correction was detected in transduced keratinocytes and fibroblasts by allele-specific highly sensitive TaqMan-droplet digital PCR (ddPCR), resulting in 11% and 15.7% of corrected COL7A1 mRNA expression, respectively, without antibiotic selection. Grafting of genetically corrected 3D skin equivalents onto nude mice showed up to 26% re-expression and normal localization of type VII collagen as well as anchoring fibril formation at the dermal-epidermal junction. Our study provides evidence that precise genome editing in primary RDEB cells is a relevant strategy to genetically correct COL7A1 mutations for the development of future ex vivo clinical applications.
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Affiliation(s)
- Araksya Izmiryan
- Laboratory of Genetic Skin Diseases, INSERM UMR 1163, Imagine Institute, 24 bd du Montparnasse, Paris, France; University Paris Descartes-Sorbonne Cité, Paris, France
| | - Clarisse Ganier
- Laboratory of Genetic Skin Diseases, INSERM UMR 1163, Imagine Institute, 24 bd du Montparnasse, Paris, France; University Paris Descartes-Sorbonne Cité, Paris, France
| | | | - Alain Schmitt
- Electronic Microscopy Facility, INSERM UMR 1016, Cochin Institute, Paris, France
| | - Fulvio Mavilio
- University Paris Descartes-Sorbonne Cité, Paris, France; Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy; Imagine Institute, Paris, France
| | - Alain Hovnanian
- Laboratory of Genetic Skin Diseases, INSERM UMR 1163, Imagine Institute, 24 bd du Montparnasse, Paris, France; University Paris Descartes-Sorbonne Cité, Paris, France; Department of Genetics, Necker Hospital for Sick Children, APHP, Paris, France.
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83
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Savic N, Ringnalda FCAS, Lindsay H, Berk C, Bargsten K, Li Y, Neri D, Robinson MD, Ciaudo C, Hall J, Jinek M, Schwank G. Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. eLife 2018; 7:e33761. [PMID: 29809142 PMCID: PMC6023611 DOI: 10.7554/elife.33761] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 05/26/2018] [Indexed: 12/22/2022] Open
Abstract
The CRISPR-Cas9 targeted nuclease technology allows the insertion of genetic modifications with single base-pair precision. The preference of mammalian cells to repair Cas9-induced DNA double-strand breaks via error-prone end-joining pathways rather than via homology-directed repair mechanisms, however, leads to relatively low rates of precise editing from donor DNA. Here we show that spatial and temporal co-localization of the donor template and Cas9 via covalent linkage increases the correction rates up to 24-fold, and demonstrate that the effect is mainly caused by an increase of donor template concentration in the nucleus. Enhanced correction rates were observed in multiple cell types and on different genomic loci, suggesting that covalently linking the donor template to the Cas9 complex provides advantages for clinical applications where high-fidelity repair is desired.
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Affiliation(s)
- Natasa Savic
- The Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
| | | | - Helen Lindsay
- The Institute of Molecular Life Sciences, University of ZurichZurichSwitzerland
- SIB Swiss Institute of BioinformaticsZurichSwitzerland
| | - Christian Berk
- Institute for Pharmaceutical Sciences, ETH ZurichZurichSwitzerland
| | - Katja Bargsten
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Yizhou Li
- Institute for Pharmaceutical Sciences, ETH ZurichZurichSwitzerland
| | - Dario Neri
- Institute for Pharmaceutical Sciences, ETH ZurichZurichSwitzerland
| | - Mark D Robinson
- The Institute of Molecular Life Sciences, University of ZurichZurichSwitzerland
- SIB Swiss Institute of BioinformaticsZurichSwitzerland
| | - Constance Ciaudo
- The Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
| | - Jonathan Hall
- Institute for Pharmaceutical Sciences, ETH ZurichZurichSwitzerland
| | - Martin Jinek
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Gerald Schwank
- The Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
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84
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Paul B, Ibarra GSR, Hubbard N, Einhaus T, Astrakhan A, Rawlings DJ, Kiem HP, Peterson CW. Efficient Enrichment of Gene-Modified Primary T Cells via CCR5-Targeted Integration of Mutant Dihydrofolate Reductase. Mol Ther Methods Clin Dev 2018; 9:347-357. [PMID: 30038938 PMCID: PMC6054698 DOI: 10.1016/j.omtm.2018.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/01/2018] [Indexed: 12/19/2022]
Abstract
Targeted gene therapy strategies utilizing homology-driven repair (HDR) allow for greater control over transgene integration site, copy number, and expression-significant advantages over traditional vector-mediated gene therapy with random genome integration. However, the relatively low efficiency of HDR-based strategies limits their clinical application. Here, we used HDR to knock in a mutant dihydrofolate reductase (mDHFR) selection gene at the gene-edited CCR5 locus in primary human CD4+ T cells and selected for mDHFR-modified cells in the presence of methotrexate (MTX). Cells were transfected with CCR5-megaTAL nuclease mRNA and transduced with adeno-associated virus containing an mDHFR donor template flanked by CCR5 homology arms, leading to up to 40% targeted gene insertion. Clinically relevant concentrations of MTX led to a greater than 5-fold enrichment for mDHFR-modified cells, which maintained a diverse TCR repertoire over the course of expansion and drug selection. Our results demonstrate that mDHFR/MTX-based selection can be used to enrich for gene-modified T cells ex vivo, paving the way for analogous approaches to increase the percentage of HIV-resistant, autologous CD4+ T cells infused into HIV+ patients, and/or for in vivo selection of gene-edited T cells for the treatment of cancer.
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Affiliation(s)
- Biswajit Paul
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Guillermo S Romano Ibarra
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nicholas Hubbard
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA, USA
| | - Teresa Einhaus
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - David J Rawlings
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Department of Immunology, University of Washington, Seattle, WA, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
| | - Christopher W Peterson
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
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85
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Sin YY, Ballantyne LL, Richmond CR, Funk CD. Transplantation of Gene-Edited Hepatocyte-like Cells Modestly Improves Survival of Arginase-1-Deficient Mice. Mol Ther Nucleic Acids 2018; 10:122-130. [PMID: 29499927 PMCID: PMC5862027 DOI: 10.1016/j.omtn.2017.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/06/2017] [Accepted: 11/17/2017] [Indexed: 12/25/2022]
Abstract
Progress in gene editing research has been accelerated by utilizing engineered nucleases in combination with induced pluripotent stem cell (iPSC) technology. Here, we report transcription activator-like effector nuclease (TALEN)-mediated reincorporation of Arg1 exons 7 and 8 in iPSCs derived from arginase-1-deficient mice possessing Arg1Δ alleles lacking these terminal exons. The edited cells could be induced to differentiate into hepatocyte-like cells (iHLCs) in vitro and were subsequently used for transplantation into our previously described (Sin et al., PLoS ONE 2013) tamoxifen-inducible Arg1-Cre arginase-1-deficient mouse model. While successful gene-targeted repair was achieved in iPSCs containing Arg1Δ alleles, only minimal restoration of urea cycle function could be observed in the iHLC-transplanted mice compared to control mice, and survival in this lethal model was extended by up to a week in some mice. The partially rescued phenotype may be due to inadequate regenerative capacity of arginase-1-expressing cells in the correct metabolic zones. Technical hurdles exist and will need to be overcome for gene-edited iPSC to iHLC rescue of arginase-1 deficiency, a rare urea cycle disorder.
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Affiliation(s)
- Yuan Yan Sin
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Laurel L Ballantyne
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Christopher R Richmond
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Colin D Funk
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
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86
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Croglio MP, Haake JM, Ryan CP, Wang VS, Lapier J, Schlarbaum JP, Dayani Y, Artuso E, Prandi C, Koltai H, Agama K, Pommier Y, Chen Y, Tricoli L, LaRocque JR, Albanese C, Yarden RI. Analogs of the novel phytohormone, strigolactone, trigger apoptosis and synergize with PARP inhibitors by inducing DNA damage and inhibiting DNA repair. Oncotarget 2017; 7:13984-4001. [PMID: 26910887 PMCID: PMC4924693 DOI: 10.18632/oncotarget.7414] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 01/16/2016] [Indexed: 12/28/2022] Open
Abstract
Strigolactones are a novel class of plant hormones produced in roots that regulate shoot and root development. We previously reported that strigolactone analogs (SLs) induce G2/M cell cycle arrest and apoptosis in a variety of human cancer cells and inhibit tumor growth of human breast cancer xenografts in mice. SLs had no significant influences on non-transformed cells. Here we report for the first time that SLs induce DNA damage in the form of DNA double-strand breaks (DSBs) and activate the DNA damage response signaling by inducing phosphorylation of ATM, ATR and DNA-PKcs and co-localization of the DNA damage signaling protein, 53BP1, with γH2AX nuclear foci. We further report that in addition to DSBs induction, SLs simultaneously impair DSBs repair, mostly homology-directed repair (HDR) and to a lesser extent non-homologous end joining (NHEJ). In response to SLs, RAD51, the homologous DSB repair protein, is ubiquitinated and targeted for proteasomal degradation and it fails to co-localize with γH2AX foci. Interestingly, SLs synergize with DNA damaging agents-based therapeutics. The combination of PARP inhibitors and SLs showed an especially potent synergy, but only in BRCA1-proficient cells. No synergy was observed between SLs and PARP inhibitors in BRCA1-deficient cells, supporting a role for SLs in HDR impairment. Together, our data suggest that SLs increase genome instability and cell death by a unique mechanism of inducing DNA damage and inhibiting DNA repair.
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Affiliation(s)
- Michael P Croglio
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Jefferson M Haake
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Colin P Ryan
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Victor S Wang
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Jennifer Lapier
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Jamie P Schlarbaum
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Yaron Dayani
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Emma Artuso
- Department of Chemistry, University of Turin, Turin, Italy
| | | | - Hinanit Koltai
- Institute of Plant Sciences, ARO, Volcani Center, Bet Dagan, Israel
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yu Chen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lucas Tricoli
- The Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, NW, Washington DC, USA
| | - Jeannine R LaRocque
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Christopher Albanese
- The Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, NW, Washington DC, USA.,Department of Pathology, Georgetown University Medical Center, NW, Washington DC, USA
| | - Ronit I Yarden
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA.,The Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, NW, Washington DC, USA
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87
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Gundry MC, Brunetti L, Lin A, Mayle AE, Kitano A, Wagner D, Hsu JI, Hoegenauer KA, Rooney CM, Goodell MA, Nakada D. Highly Efficient Genome Editing of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9. Cell Rep 2017; 17:1453-1461. [PMID: 27783956 DOI: 10.1016/j.celrep.2016.09.092] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/01/2016] [Accepted: 09/28/2016] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the mechanisms that regulate hematopoietic stem/progenitor cells (HSPCs) has been advanced by the ability to genetically manipulate mice; however, germline modification is time consuming and expensive. Here, we describe fast, efficient, and cost-effective methods to directly modify the genomes of mouse and human HSPCs using the CRISPR/Cas9 system. Using plasmid and virus-free delivery of guide RNAs alone into Cas9-expressing HSPCs or Cas9-guide RNA ribonucleoprotein (RNP) complexes into wild-type cells, we have achieved extremely efficient gene disruption in primary HSPCs from mouse (>60%) and human (∼75%). These techniques enabled rapid evaluation of the functional effects of gene loss of Eed, Suz12, and DNMT3A. We also achieved homology-directed repair in primary human HSPCs (>20%). These methods will significantly expand applications for CRISPR/Cas9 technologies for studying normal and malignant hematopoiesis.
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Affiliation(s)
- Michael C Gundry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06156 Perugia, Italy
| | - Angelique Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Allison E Mayle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ayumi Kitano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dimitrios Wagner
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital and Houston Methodist Hospital, Houston, TX 77030, USA; Institute for Medical Immunology, Charité University Medicine Berlin, 13353 Berlin, Germany
| | - Joanne I Hsu
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA; Translational Biology and Molecular Medicine Program, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin A Hoegenauer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cliona M Rooney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital and Houston Methodist Hospital, Houston, TX 77030, USA
| | - Margaret A Goodell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital and Houston Methodist Hospital, Houston, TX 77030, USA.
| | - Daisuke Nakada
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA.
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88
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Hainzl S, Peking P, Kocher T, Murauer EM, Larcher F, Del Rio M, Duarte B, Steiner M, Klausegger A, Bauer JW, Reichelt J, Koller U. COL7A1 Editing via CRISPR/Cas9 in Recessive Dystrophic Epidermolysis Bullosa. Mol Ther 2017; 25:2573-84. [PMID: 28800953 DOI: 10.1016/j.ymthe.2017.07.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 12/20/2022] Open
Abstract
Designer nucleases allow specific and precise genomic modifications and represent versatile molecular tools for the correction of disease-associated mutations. In this study, we have exploited an ex vivo CRISPR/Cas9-mediated homology-directed repair approach for the correction of a frequent inherited mutation in exon 80 of COL7A1, which impairs type VII collagen expression, causing the severe blistering skin disease recessive dystrophic epidermolysis bullosa. Upon CRISPR/Cas9 treatment of patient-derived keratinocytes, using either the wild-type Cas9 or D10A nickase, corrected single-cell clones expressed and secreted similar levels of type VII collagen as control keratinocytes. Transplantation of skin equivalents grown from corrected keratinocytes onto immunodeficient mice showed phenotypic reversion with normal localization of type VII collagen at the basement membrane zone, compared with uncorrected keratinocytes, as well as fully stratified and differentiated skin layers without indication of blister development. Next-generation sequencing revealed on-target efficiency of up to 30%, whereas nuclease-mediated off-target site modifications at predicted genomic loci were not detected. These data demonstrate the potential of the CRISPR/Cas9 technology as a possible ex vivo treatment option for genetic skin diseases in the future.
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89
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Chen CC, Kass EM, Yen WF, Ludwig T, Moynahan ME, Chaudhuri J, Jasin M. ATM loss leads to synthetic lethality in BRCA1 BRCT mutant mice associated with exacerbated defects in homology-directed repair. Proc Natl Acad Sci U S A 2017; 114:7665-70. [PMID: 28659469 DOI: 10.1073/pnas.1706392114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BRCA1 is essential for homology-directed repair (HDR) of DNA double-strand breaks in part through antagonism of the nonhomologous end-joining factor 53BP1. The ATM kinase is involved in various aspects of DNA damage signaling and repair, but how ATM participates in HDR and genetically interacts with BRCA1 in this process is unclear. To investigate this question, we used the Brca1S1598F mouse model carrying a mutation in the BRCA1 C-terminal domain of BRCA1. Whereas ATM loss leads to a mild HDR defect in adult somatic cells, we find that ATM inhibition leads to severely reduced HDR in Brca1S1598F cells. Consistent with a critical role for ATM in HDR in this background, loss of ATM leads to synthetic lethality of Brca1S1598F mice. Whereas both ATM and BRCA1 promote end resection, which can be regulated by 53BP1, 53bp1 deletion does not rescue the HDR defects of Atm mutant cells, in contrast to Brca1 mutant cells. These results demonstrate that ATM has a role in HDR independent of the BRCA1-53BP1 antagonism and that its HDR function can become critical in certain contexts.
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90
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Norton EL, Sherwood RK, Bennett RJ. Development of a CRISPR-Cas9 System for Efficient Genome Editing of Candida lusitaniae. mSphere 2017; 2:e00217-17. [PMID: 28657072 DOI: 10.1128/mSphere.00217-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 05/29/2017] [Indexed: 11/20/2022] Open
Abstract
Candida lusitaniae is a member of the Candida clade that includes a diverse group of fungal species relevant to both human health and biotechnology. This species exhibits a full sexual cycle to undergo interconversion between haploid and diploid forms. C. lusitaniae is also an emerging opportunistic pathogen that can cause serious bloodstream infections in the clinic and yet has often proven to be refractory to facile genetic manipulations. In this work, we develop a clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (Cas9) system to enable genome editing of C. lusitaniae. We demonstrate that expression of CRISPR-Cas9 components under species-specific promoters is necessary for efficient gene targeting and can be successfully applied to multiple genes in both haploid and diploid isolates. Gene deletion efficiencies with CRISPR-Cas9 were further enhanced in C. lusitaniae strains lacking the established nonhomologous end joining (NHEJ) factors Ku70 and DNA ligase 4. These results indicate that NHEJ plays an important role in directing the repair of DNA double-strand breaks (DSBs) in C. lusitaniae and that removal of this pathway increases integration of gene deletion templates by homologous recombination. The described approaches significantly enhance the ability to perform genetic studies in, and promote understanding of, this emerging human pathogen and model sexual species. IMPORTANCE The ability to perform efficient genome editing is a key development for detailed mechanistic studies of a species. Candida lusitaniae is an important member of the Candida clade and is relevant both as an emerging human pathogen and as a model for understanding mechanisms of sexual reproduction. We highlight the development of a CRISPR-Cas9 system for efficient genome manipulation in C. lusitaniae and demonstrate the importance of species-specific promoters for expression of CRISPR components. We also demonstrate that the NHEJ pathway contributes to non-template-mediated repair of DNA DSBs and that removal of this pathway enhances efficiencies of gene targeting by CRISPR-Cas9. These results therefore establish important genetic tools for further exploration of C. lusitaniae biology.
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91
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Spraggon L, Martelotto LG, Hmeljak J, Hitchman TD, Wang J, Wang L, Slotkin EK, Fan PD, Reis-Filho JS, Ladanyi M. Generation of conditional oncogenic chromosomal translocations using CRISPR-Cas9 genomic editing and homology-directed repair. J Pathol 2017; 242:102-112. [PMID: 28188619 DOI: 10.1002/path.4883] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 01/11/2023]
Abstract
Chromosomal rearrangements encoding oncogenic fusion proteins are found in a wide variety of malignancies. The use of programmable nucleases to generate specific double-strand breaks in endogenous loci, followed by non-homologous end joining DNA repair, has allowed several of these translocations to be generated as constitutively expressed fusion genes within a cell population. Here, we describe a novel approach that combines CRISPR-Cas9 technology with homology-directed repair to engineer, capture, and modulate the expression of chromosomal translocation products in a human cell line. We have applied this approach to the genetic modelling of t(11;22)(q24;q12) and t(11;22)(p13;q12), translocation products of the EWSR1 gene and its 3' fusion partners FLI1 and WT1, present in Ewing's sarcoma and desmoplastic small round cell tumour, respectively. Our innovative approach allows for temporal control of the expression of engineered endogenous chromosomal rearrangements, and provides a means to generate models to study tumours driven by fusion genes. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Lee Spraggon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julija Hmeljak
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler D Hitchman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiang Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pang-Dian Fan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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92
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Vanoli F, Tomishima M, Feng W, Lamribet K, Babin L, Brunet E, Jasin M. CRISPR-Cas9-guided oncogenic chromosomal translocations with conditional fusion protein expression in human mesenchymal cells. Proc Natl Acad Sci U S A 2017; 114:3696-701. [PMID: 28325870 DOI: 10.1073/pnas.1700622114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gene editing techniques have been extensively used to attempt to model recurrent genomic rearrangements found in tumor cells. These methods involve the induction of double-strand breaks at endogenous loci followed by the identification of breakpoint junctions within a population, which typically arise by nonhomologous end joining. The low frequency of these events, however, has hindered the cloning of cells with the desired rearrangement before oncogenic transformation. Here we present a strategy combining CRISPR-Cas9 technology and homology-directed repair to allow for the selection of human mesenchymal stem cells harboring the oncogenic translocation EWSR1-WT1 found in the aggressive desmoplastic small round cell tumor. The expression of the fusion transcript is under the control of the endogenous EWSR1 promoter and, importantly, can be conditionally expressed using Cre recombinase. This method is easily adapted to generate any cancer-relevant rearrangement.
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93
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MacLeod DT, Antony J, Martin AJ, Moser RJ, Hekele A, Wetzel KJ, Brown AE, Triggiano MA, Hux JA, Pham CD, Bartsevich VV, Turner CA, Lape J, Kirkland S, Beard CW, Smith J, Hirsch ML, Nicholson MG, Jantz D, McCreedy B. Integration of a CD19 CAR into the TCR Alpha Chain Locus Streamlines Production of Allogeneic Gene-Edited CAR T Cells. Mol Ther 2017; 25:949-61. [PMID: 28237835 DOI: 10.1016/j.ymthe.2017.02.005] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 11/25/2022] Open
Abstract
Adoptive cellular therapy using chimeric antigen receptor (CAR) T cell therapies have produced significant objective responses in patients with CD19+ hematological malignancies, including durable complete responses. Although the majority of clinical trials to date have used autologous patient cells as the starting material to generate CAR T cells, this strategy poses significant manufacturing challenges and, for some patients, may not be feasible because of their advanced disease state or difficulty with manufacturing suitable numbers of CAR T cells. Alternatively, T cells from a healthy donor can be used to produce an allogeneic CAR T therapy, provided the cells are rendered incapable of eliciting graft versus host disease (GvHD). One approach to the production of these cells is gene editing to eliminate expression of the endogenous T cell receptor (TCR). Here we report a streamlined strategy for generating allogeneic CAR T cells by targeting the insertion of a CAR transgene directly into the native TCR locus using an engineered homing endonuclease and an AAV donor template. We demonstrate that anti-CD19 CAR T cells produced in this manner do not express the endogenous TCR, exhibit potent effector functions in vitro, and mediate clearance of CD19+ tumors in an in vivo mouse model.
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94
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Brookhouser N, Raman S, Potts C, Brafman DA. May I Cut in? Gene Editing Approaches in Human Induced Pluripotent Stem Cells. Cells. 2017;6. [PMID: 28178187 PMCID: PMC5371870 DOI: 10.3390/cells6010005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 01/20/2017] [Accepted: 01/30/2017] [Indexed: 12/16/2022] Open
Abstract
In the decade since Yamanaka and colleagues described methods to reprogram somatic cells into a pluripotent state, human induced pluripotent stem cells (hiPSCs) have demonstrated tremendous promise in numerous disease modeling, drug discovery, and regenerative medicine applications. More recently, the development and refinement of advanced gene transduction and editing technologies have further accelerated the potential of hiPSCs. In this review, we discuss the various gene editing technologies that are being implemented with hiPSCs. Specifically, we describe the emergence of technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 that can be used to edit the genome at precise locations, and discuss the strengths and weaknesses of each of these technologies. In addition, we present the current applications of these technologies in elucidating the mechanisms of human development and disease, developing novel and effective therapeutic molecules, and engineering cell-based therapies. Finally, we discuss the emerging technological advances in targeted gene editing methods.
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95
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Zhang WW, Lypaczewski P, Matlashewski G. Optimized CRISPR-Cas9 Genome Editing for Leishmania and Its Use To Target a Multigene Family, Induce Chromosomal Translocation, and Study DNA Break Repair Mechanisms. mSphere 2017; 2:e00340-16. [PMID: 28124028 DOI: 10.1128/mSphere.00340-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022] Open
Abstract
Leishmania parasites cause human leishmaniasis. To accelerate characterization of Leishmania genes for new drug and vaccine development, we optimized and simplified the CRISPR-Cas9 genome-editing tool for Leishmania. We show that co-CRISPR targeting of the miltefosine transporter gene and serial transfections of an oligonucleotide donor significantly eased isolation of edited mutants. This cotargeting strategy was efficiently used to delete all 11 members of the A2 virulence gene family. This technical advancement is valuable, since there are many gene clusters and supernumerary chromosomes in the various Leishmania species and isolates. We simplified this CRISPR system by developing a gRNA and Cas9 coexpression vector which could be used to delete genes in various Leishmania species. This CRISPR system could also be used to generate specific chromosomal translocations, which will help in the study of Leishmania gene expression and transcription control. This study also provides new information about double-strand DNA break repair mechanisms in Leishmania. CRISPR-Cas9-mediated genome editing has recently been adapted for Leishmania spp. parasites, the causative agents of human leishmaniasis. We have optimized this genome-editing tool by selecting for cells with CRISPR-Cas9 activity through cotargeting the miltefosine transporter gene; mutation of this gene leads to miltefosine resistance. This cotargeting strategy integrated into a triple guide RNA (gRNA) expression vector was used to delete all 11 copies of the A2 multigene family; this was not previously possible with the traditional gene-targeting method. We found that the Leishmania donovani rRNA promoter is more efficient than the U6 promoter in driving gRNA expression, and sequential transfections of the oligonucleotide donor significantly eased the isolation of edited mutants. A gRNA and Cas9 coexpression vector was developed that was functional in all tested Leishmania species, including L. donovani, L. major, and L. mexicana. By simultaneously targeting sites from two different chromosomes, all four types of targeted chromosomal translocations were generated, regardless of the polycistronic transcription direction from the parent chromosomes. It was possible to use this CRISPR system to create a single conserved amino acid substitution (A189G) mutation for both alleles of RAD51, a DNA recombinase involved in homology-directed repair. We found that RAD51 is essential for L. donovani survival based on direct observation of the death of mutants with both RAD51 alleles disrupted, further confirming that this CRISPR system can reveal gene essentiality. Evidence is also provided that microhomology-mediated end joining (MMEJ) plays a major role in double-strand DNA break repair in L. donovani. IMPORTANCELeishmania parasites cause human leishmaniasis. To accelerate characterization of Leishmania genes for new drug and vaccine development, we optimized and simplified the CRISPR-Cas9 genome-editing tool for Leishmania. We show that co-CRISPR targeting of the miltefosine transporter gene and serial transfections of an oligonucleotide donor significantly eased isolation of edited mutants. This cotargeting strategy was efficiently used to delete all 11 members of the A2 virulence gene family. This technical advancement is valuable, since there are many gene clusters and supernumerary chromosomes in the various Leishmania species and isolates. We simplified this CRISPR system by developing a gRNA and Cas9 coexpression vector which could be used to delete genes in various Leishmania species. This CRISPR system could also be used to generate specific chromosomal translocations, which will help in the study of Leishmania gene expression and transcription control. This study also provides new information about double-strand DNA break repair mechanisms in Leishmania.
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Abstract
DNA damage tolerance (DDT) mechanisms allow cells to synthesize a new DNA strand when the template is damaged. Many mutations resulting from DNA damage in eukaryotes are generated during DDT when cells use the mutagenic translesion polymerases, Rev1 and Polζ, rather than mechanisms with higher fidelity. The coordination among DDT mechanisms is not well understood. We used live-cell imaging to study the function of DDT mechanisms throughout the cell cycle of the fission yeast Schizosaccharomyces pombe. We report that checkpoint-dependent mitotic delay provides a cellular mechanism to ensure the completion of high fidelity DDT, largely by homology-directed repair (HDR). DDT by mutagenic polymerases is suppressed during the checkpoint delay by a mechanism dependent on Rad51 recombinase. When cells pass the G2/M checkpoint and can no longer delay mitosis, they completely lose the capacity for HDR and simultaneously exhibit a requirement for Rev1 and Polζ. Thus, DDT is coordinated with the checkpoint response so that the activity of mutagenic polymerases is confined to a vulnerable period of the cell cycle when checkpoint delay and HDR are not possible.
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Affiliation(s)
- A John Callegari
- a Molecular Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| | - Thomas J Kelly
- a Molecular Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
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97
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Abstract
Gene conversions occur when genomic double-strand DNA breaks (DSBs) trigger unidirectional transfer of genetic material from a homologous template sequence. Exogenous or mutated sequence can be introduced through this homology-directed repair (HDR). We leveraged gene conversion to develop a method for genomic editing of existing transgenic insertions in Drosophila melanogaster The clustered regularly-interspaced palindromic repeats (CRISPR)/Cas9 system is used in the H: omology A: ssisted C: RISPR K: nock-in (HACK) method to induce DSBs in a GAL4 transgene, which is repaired by a single-genomic transgenic construct containing GAL4 homologous sequences flanking a T2A-QF2 cassette. With two crosses, this technique converts existing GAL4 lines, including enhancer traps, into functional QF2 expressing lines. We used HACK to convert the most commonly-used GAL4 lines (labeling tissues such as neurons, fat, glia, muscle, and hemocytes) to QF2 lines. We also identified regions of the genome that exhibited differential efficiencies of HDR. The HACK technique is robust and readily adaptable for targeting and replacement of other genomic sequences, and could be a useful approach to repurpose existing transgenes as new genetic reagents become available.
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Affiliation(s)
- Chun-Chieh Lin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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98
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Abstract
Recent advances in gene editing with engineered nucleases have transformed our ability to manipulate the genome from diverse organisms for applications ranging from biomedical research to disease treatment. A major complication with these engineered nucleases is the binding of the nuclease to unintended genomic sites that share sequence homology with the on-target site. Cleavage of these off-target sites followed by DNA repair using normal cellular DNA repair mechanisms can cause gene mutation or gross chromosome rearrangement. Identification of nuclease-generated off-target sites is a daunting task due to the size and complexity of the mammalian genome. Five unbiased, genome-wide strategies have been developed to detect the off-target cleavage. Some of these strategies reach the sensitivity near the detection limit of directed deep sequencing and have sufficient precision and resolution to objectively assessing the off-target effect of any engineered nuclease. Significant progress has also been made recently to boost the nuclease targeting specificity by protein engineering to modify the structure of the nuclease and alter the interaction with its genomic target. In several studied cases, the off-target effect generated by the modified nuclease is completely eliminated. These modified nucleases significantly improve the overall fidelity of gene editing. These developments will enable gene editing tools to be applied more broadly and safely in basic research and disease treatment.
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Affiliation(s)
- Jiing-Kuan Yee
- Department of Diabetes and Metabolic Diseases Research, City of Hope National Medical Center, Duarte, CA, USA
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99
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Lee JS, Grav LM, Pedersen LE, Lee GM, Kildegaard HF. Accelerated homology-directed targeted integration of transgenes in Chinese hamster ovary cells via CRISPR/Cas9 and fluorescent enrichment. Biotechnol Bioeng 2016; 113:2518-23. [PMID: 27159230 DOI: 10.1002/bit.26002] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 12/29/2022]
Abstract
Targeted gene integration into site-specific loci can be achieved in Chinese hamster ovary (CHO) cells via CRISPR/Cas9 genome editing technology and the homology-directed repair (HDR) pathway. The low efficiency of HDR often requires antibiotic selection, which limits targeted integration of multiple genes at multiple sites. To improve HDR-mediated targeted integration, while avoiding the use of selection markers, chemical treatment for increased HDR, and fluorescent enrichment of genome-edited cells was assessed in CHO cells. Chemical treatment did not improve HDR-mediated targeted integration. In contrast, fluorescent markers in Cas9 and donor constructs enable FACS enrichment, resulting in a threefold increase in the number of cells with HDR-mediated genome editing. Combined with this enrichment method, large transgenes encoding model proteins (including an antibody) were successfully targeted integrated. This approach provides a simple and fast strategy for targeted generation of stable CHO production cell lines in a rational way. Biotechnol. Bioeng. 2016;113: 2518-2523. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jae Seong Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark.,Department of Biological Sciences, KAIST, Yuseong-gu, Daejeon, Republic of Korea
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark.
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100
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Lee J, Chung JH, Kim HM, Kim DW, Kim H. Designed nucleases for targeted genome editing. Plant Biotechnol J 2016; 14:448-62. [PMID: 26369767 DOI: 10.1111/pbi.12465] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 05/20/2023]
Abstract
Targeted genome-editing technology using designed nucleases has been evolving rapidly, and its applications are widely expanding in research, medicine and biotechnology. Using this genome-modifying technology, researchers can precisely and efficiently insert, remove or change specific sequences in various cultured cells, micro-organisms, animals and plants. This genome editing is based on the generation of double-strand breaks (DSBs), repair of which modifies the genome through nonhomologous end-joining (NHEJ) or homology-directed repair (HDR). In addition, designed nickase-induced generation of single-strand breaks can also lead to precise genome editing through HDR, albeit at relatively lower efficiencies than that induced by nucleases. Three kinds of designed nucleases have been used for targeted DSB formation: zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases derived from the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system. A growing number of researchers are using genome-editing technologies, which have become more accessible and affordable since the discovery and adaptation of CRISPR-Cas9. Here, the repair mechanism and outcomes of DSBs are reviewed and the three types of designed nucleases are discussed with the hope that such understanding will facilitate applications to genome editing.
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Affiliation(s)
- Junwon Lee
- Department of Physiology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Hee Chung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Dong-Wook Kim
- Department of Physiology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hyongbum Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Graduate Program of Nano Science and Technology, Yonsei University, Seoul, Korea
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