1
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Saito S, Adachi N. Characterization and regulation of cell cycle-independent noncanonical gene targeting. Nat Commun 2024; 15:5044. [PMID: 38890315 PMCID: PMC11189520 DOI: 10.1038/s41467-024-49385-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Homology-dependent targeted DNA integration, generally referred to as gene targeting, provides a powerful tool for precise genome modification; however, its fundamental mechanisms remain poorly understood in human cells. Here we reveal a noncanonical gene targeting mechanism that does not rely on the homologous recombination (HR) protein Rad51. This mechanism is suppressed by Rad52 inhibition, suggesting the involvement of single-strand annealing (SSA). The SSA-mediated gene targeting becomes prominent when DSB repair by HR or end-joining pathways is defective and does not require isogenic DNA, permitting 5% sequence divergence. Intriguingly, loss of Msh2, loss of BLM, and induction of a target-site DNA break all significantly and synergistically enhance SSA-mediated targeted integration. Most notably, SSA-mediated integration is cell cycle-independent, occurring in the G1 phase as well. Our findings provide unequivocal evidence for Rad51-independent targeted integration and unveil multiple mechanisms to regulate SSA-mediated targeted as well as random integration.
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Affiliation(s)
- Shinta Saito
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan
| | - Noritaka Adachi
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan.
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2
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Webber BR, Johnson MJ, Skeate JG, Slipek NJ, Lahr WS, DeFeo AP, Mills LJ, Qiu X, Rathmann B, Diers MD, Wick B, Henley T, Choudhry M, Starr TK, McIvor RS, Moriarity BS. Cas9-induced targeted integration of large DNA payloads in primary human T cells via homology-mediated end-joining DNA repair. Nat Biomed Eng 2023:10.1038/s41551-023-01157-4. [PMID: 38092857 PMCID: PMC11169092 DOI: 10.1038/s41551-023-01157-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/02/2023] [Indexed: 01/12/2024]
Abstract
The reliance on viral vectors for the production of genetically engineered immune cells for adoptive cellular therapies remains a translational bottleneck. Here we report a method leveraging the DNA repair pathway homology-mediated end joining, as well as optimized reagent composition and delivery, for the Cas9-induced targeted integration of large DNA payloads into primary human T cells with low toxicity and at efficiencies nearing those of viral vectors (targeted knock-in of 1-6.7 kb payloads at rates of up to 70% at multiple targeted genomic loci and with cell viabilities of over 80%). We used the method to produce T cells with an engineered T-cell receptor or a chimaeric antigen receptor and show that the cells maintained low levels of exhaustion markers and excellent capacities for proliferation and cytokine production and that they elicited potent antitumour cytotoxicity in vitro and in mice. The method is readily adaptable to current good manufacturing practices and scale-up processes, and hence may be used as an alternative to viral vectors for the production of genetically engineered T cells for cancer immunotherapies.
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Affiliation(s)
- Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
| | - Matthew J Johnson
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Joseph G Skeate
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Anthony P DeFeo
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Lauren J Mills
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Xiaohong Qiu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Blaine Rathmann
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Miechaleen D Diers
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Bryce Wick
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | | | - Timothy K Starr
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
- Department of Ob-Gyn and Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - R Scott McIvor
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
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3
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Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis. Nat Commun 2021; 12:3854. [PMID: 34158505 PMCID: PMC8219824 DOI: 10.1038/s41467-021-24195-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/01/2021] [Indexed: 11/08/2022] Open
Abstract
Sexual reproduction constrains progeny to inherit allelic genes from both parents. Selective acquisition of target genes from only one parent in the F1 generation of plants has many potential applications including the elimination of undesired alleles and acceleration of trait stacking. CRISPR/Cas9-based gene drives can generate biased transmission of a preferred allele and convert heterozygotes to homozygotes in insects and mice, but similar strategies have not been implementable in plants because of a lack of efficient homology-directed repair (HDR). Here, we place a gene drive, which consists of cassettes that produce Cas9, guide RNAs (gRNA), and fluorescent markers, into the CRYPTOCHROME 1 (CRY1) gene through CRISPR/Cas9-mediated HDR, resulting in cry1drive lines. After crossing the cry1drive/cry1drive lines to wild type, we observe F1 plants which have DNA at the CRY1 locus from only the cry1drive/cry1drive parent. Moreover, a non-autonomous trans-acting gene drive, in which the gene drive unit and the target gene are located on different chromosomes, converts a heterozygous mutation in the target gene to homozygous. Our results demonstrate that homozygous F1 plants can be obtained through zygotic conversion using a CRISPR/Cas9-based gene drive. Unlike insects and mice, CRISPR/Cas9-based gene drives have not been achieved in plants. Here, the authors demonstrate homozygous F1 Arabidopsis plants can be obtained through zygotic conversion using CRISPR/Cas9-mediated homology-directed repair.
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4
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He X, Xie H, Liu X, Gu F. Basic and Clinical Application of Adeno-Associated Virus-Mediated Genome Editing. Hum Gene Ther 2019; 30:673-681. [PMID: 30588843 DOI: 10.1089/hum.2018.190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Traditional gene therapy (gene replacement) has made a breakthrough in treating inherited diseases. Adeno-associated virus (AAV) has emerged as a highly promising vector with innate ability, boosting the development of gene replacement and gene targeting. With the recent advance of engineered nucleases that work efficiently in human cells, AAV mediated-genome editing with nucleases has raised hopes for in situ gene therapy of inherited and non-inherited diseases. Here, the applications of AAV-mediated genome editing are highlighted, and the prospect of AAV and nucleases that will render extension of such success in clinical gene therapy is discussed.
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Affiliation(s)
- Xiubin He
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, P.R. China
| | - Haihua Xie
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, P.R. China
| | - Xiexie Liu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, P.R. China
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, P.R. China
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5
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Hiramoto T, Li LB, Funk SE, Hirata RK, Russell DW. Nuclease-free Adeno-Associated Virus-Mediated Il2rg Gene Editing in X-SCID Mice. Mol Ther 2018; 26:1255-1265. [PMID: 29606506 DOI: 10.1016/j.ymthe.2018.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022] Open
Abstract
X-linked severe combined immunodeficiency (X-SCID) has been successfully treated by hematopoietic stem cell (HSC) transduction with retroviral vectors expressing the interleukin-2 receptor subunit gamma gene (IL2RG), but several patients developed malignancies due to vector integration near cellular oncogenes. This adverse side effect could in principle be avoided by accurate IL2RG gene editing with a vector that does not contain a functional promoter or IL2RG gene. Here, we show that adeno-associated virus (AAV) gene editing vectors can insert a partial Il2rg cDNA at the endogenous Il2rg locus in X-SCID murine bone marrow cells and that these ex vivo-edited cells repopulate transplant recipients and produce CD4+ and CD8+ T cells. Circulating, edited lymphocytes increased over time and appeared in secondary transplant recipients, demonstrating successful editing in long-term repopulating cells. Random vector integration events were nearly undetectable, and malignant transformation of the transplanted cells was not observed. Similar editing frequencies were observed in human hematopoietic cells. Our results demonstrate that therapeutically relevant HSC gene editing can be achieved by AAV vectors in the absence of site-specific nucleases and suggest that this may be a safe and effective therapy for hematopoietic diseases where in vivo selection can increase edited cell numbers.
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Affiliation(s)
- Takafumi Hiramoto
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Li B Li
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sarah E Funk
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Roli K Hirata
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - David W Russell
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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6
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Chaterji S, Ahn EH, Kim DH. CRISPR Genome Engineering for Human Pluripotent Stem Cell Research. Theranostics 2017; 7:4445-4469. [PMID: 29158838 PMCID: PMC5695142 DOI: 10.7150/thno.18456] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
The emergence of targeted and efficient genome editing technologies, such as repurposed bacterial programmable nucleases (e.g., CRISPR-Cas systems), has abetted the development of cell engineering approaches. Lessons learned from the development of RNA-interference (RNA-i) therapies can spur the translation of genome editing, such as those enabling the translation of human pluripotent stem cell engineering. In this review, we discuss the opportunities and the challenges of repurposing bacterial nucleases for genome editing, while appreciating their roles, primarily at the epigenomic granularity. First, we discuss the evolution of high-precision, genome editing technologies, highlighting CRISPR-Cas9. They exist in the form of programmable nucleases, engineered with sequence-specific localizing domains, and with the ability to revolutionize human stem cell technologies through precision targeting with greater on-target activities. Next, we highlight the major challenges that need to be met prior to bench-to-bedside translation, often learning from the path-to-clinic of complementary technologies, such as RNA-i. Finally, we suggest potential bioinformatics developments and CRISPR delivery vehicles that can be deployed to circumvent some of the challenges confronting genome editing technologies en route to the clinic.
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7
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Garate Z, Quintana-Bustamante O, Crane AM, Olivier E, Poirot L, Galetto R, Kosinski P, Hill C, Kung C, Agirre X, Orman I, Cerrato L, Alberquilla O, Rodriguez-Fornes F, Fusaki N, Garcia-Sanchez F, Maia TM, Ribeiro ML, Sevilla J, Prosper F, Jin S, Mountford J, Guenechea G, Gouble A, Bueren JA, Davis BR, Segovia JC. Generation of a High Number of Healthy Erythroid Cells from Gene-Edited Pyruvate Kinase Deficiency Patient-Specific Induced Pluripotent Stem Cells. Stem Cell Reports 2015; 5:1053-1066. [PMID: 26549847 PMCID: PMC4682065 DOI: 10.1016/j.stemcr.2015.10.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 01/30/2023] Open
Abstract
Pyruvate kinase deficiency (PKD) is a rare erythroid metabolic disease caused by mutations in the PKLR gene. Erythrocytes from PKD patients show an energetic imbalance causing chronic non-spherocytic hemolytic anemia, as pyruvate kinase defects impair ATP production in erythrocytes. We generated PKD induced pluripotent stem cells (PKDiPSCs) from peripheral blood mononuclear cells (PB-MNCs) of PKD patients by non-integrative Sendai viral vectors. PKDiPSCs were gene edited to integrate a partial codon-optimized R-type pyruvate kinase cDNA in the second intron of the PKLR gene by TALEN-mediated homologous recombination (HR). Notably, we found allele specificity of HR led by the presence of a single-nucleotide polymorphism. High numbers of erythroid cells derived from gene-edited PKDiPSCs showed correction of the energetic imbalance, providing an approach to correct metabolic erythroid diseases and demonstrating the practicality of this approach to generate the large cell numbers required for comprehensive biochemical and metabolic erythroid analyses. Patient-specific PKDiPSCs are generated from PB-MNCs by a non-integrative system PKDiPSCs are gene edited to insert a partial co-RPK in the PKLR locus mediated by TALEN An SNP in the homology arm leads to allele-specific homologous recombination Gene-edited PKDiPSCs generate a high number of metabolically corrected erythroid cells
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Affiliation(s)
- Zita Garate
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain; Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Oscar Quintana-Bustamante
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain.
| | - Ana M Crane
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Emmanuel Olivier
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | | | - Collin Hill
- Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA
| | - Charles Kung
- Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA
| | - Xabi Agirre
- Hematology and Cell Therapy, Clinica Universidad de Navarra and CIMA, Pamplona 31008, Spain
| | - Israel Orman
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Laura Cerrato
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Omaira Alberquilla
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Fatima Rodriguez-Fornes
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Noemi Fusaki
- JST PRESTO and Ophthalmology, Keio University, Tokyo 108-8345, Japan
| | - Felix Garcia-Sanchez
- Histocompatibility and Molecular Biology Laboratory, Centro de Transfusion de Madrid, Madrid 28032, Spain
| | - Tabita M Maia
- Serviço de Hematologia, Centro Hospitalar e Universitario de Coimbra, Coimbra 3000-075, Portugal
| | - Maria L Ribeiro
- Serviço de Hematologia, Centro Hospitalar e Universitario de Coimbra, Coimbra 3000-075, Portugal
| | | | - Felipe Prosper
- Hematology and Cell Therapy, Clinica Universidad de Navarra and CIMA, Pamplona 31008, Spain
| | - Shengfang Jin
- Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA
| | - Joanne Mountford
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Guillermo Guenechea
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | | | - Juan A Bueren
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jose C Segovia
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain.
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8
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Byrne SM, Church GM. Crispr-mediated Gene Targeting of Human Induced Pluripotent Stem Cells. ACTA ACUST UNITED AC 2015; 35:5A.8.1-5A.8.22. [PMID: 26949444 DOI: 10.1002/9780470151808.sc05a08s35] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 nuclease systems can create double-stranded DNA breaks at specific sequences to efficiently and precisely disrupt, excise, mutate, insert, or replace genes. However, human embryonic stem or induced pluripotent stem cells (iPSCs) are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe an optimized protocol for genome engineering of human iPSCs using a simple transient transfection of plasmids and/or single-stranded oligonucleotides. With this protocol, we achieve transfection efficiencies greater than 60%, with gene disruption efficiencies from 1-25% and gene insertion/replacement efficiencies from 0.5-10% without any further selection or enrichment steps. We also describe how to design and assess optimal sgRNA target sites and donor targeting vectors; cloning individual iPSC by single cell FACS sorting, and genotyping successfully edited cells.
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Affiliation(s)
- Susan M Byrne
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
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9
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Silent IL2RG Gene Editing in Human Pluripotent Stem Cells. Mol Ther 2015; 24:582-91. [PMID: 26444081 DOI: 10.1038/mt.2015.190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/30/2015] [Indexed: 12/19/2022] Open
Abstract
Many applications of pluripotent stem cells (PSCs) require efficient editing of silent chromosomal genes. Here, we show that a major limitation in isolating edited clones is silencing of the selectable marker cassette after homologous recombination and that this can be overcome by using a ubiquitous chromatin opening element (UCOE) promoter-driven transgene. We use this strategy to edit the silent IL2RG locus in human PSCs with a recombinant adeno-associated virus (rAAV)-targeting vector in the absence of potentially genotoxic, site-specific nucleases and show that IL2RG is required for natural killer and T-cell differentiation of human PSCs. Insertion of an active UCOE promoter into a silent locus altered the histone modification and cytosine methylation pattern of surrounding chromatin, but these changes resolved when the UCOE promoter was removed. This same approach could be used to correct IL2RG mutations in X-linked severe combined immunodeficiency patient-derived induced PSCs (iPSCs), to prevent graft versus host disease in regenerative medicine applications, or to edit other silent genes.
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10
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Crane AM, Kramer P, Bui JH, Chung WJ, Li XS, Gonzalez-Garay ML, Hawkins F, Liao W, Mora D, Choi S, Wang J, Sun HC, Paschon DE, Guschin DY, Gregory PD, Kotton DN, Holmes MC, Sorscher EJ, Davis BR. Targeted correction and restored function of the CFTR gene in cystic fibrosis induced pluripotent stem cells. Stem Cell Reports 2015; 4:569-77. [PMID: 25772471 PMCID: PMC4400651 DOI: 10.1016/j.stemcr.2015.02.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/13/2022] Open
Abstract
Recently developed reprogramming and genome editing technologies make possible the derivation of corrected patient-specific pluripotent stem cell sources-potentially useful for the development of new therapeutic approaches. Starting with skin fibroblasts from patients diagnosed with cystic fibrosis, we derived and characterized induced pluripotent stem cell (iPSC) lines. We then utilized zinc-finger nucleases (ZFNs), designed to target the endogenous CFTR gene, to mediate correction of the inherited genetic mutation in these patient-derived lines via homology-directed repair (HDR). We observed an exquisitely sensitive, homology-dependent preference for targeting one CFTR allele versus the other. The corrected cystic fibrosis iPSCs, when induced to differentiate in vitro, expressed the corrected CFTR gene; importantly, CFTR correction resulted in restored expression of the mature CFTR glycoprotein and restoration of CFTR chloride channel function in iPSC-derived epithelial cells.
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Affiliation(s)
- Ana M Crane
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Philipp Kramer
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jacquelin H Bui
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Wook Joon Chung
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, AL 35294, USA
| | - Xuan Shirley Li
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Manuel L Gonzalez-Garay
- Center for Molecular Imaging, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Finn Hawkins
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Wei Liao
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Daniela Mora
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Sangbum Choi
- Division of Clinical and Translational Sciences, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jianbin Wang
- Sangamo BioSciences, Inc., Richmond, CA 94804, USA
| | - Helena C Sun
- Sangamo BioSciences, Inc., Richmond, CA 94804, USA
| | | | | | | | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | | | - Eric J Sorscher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, AL 35294, USA
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA.
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11
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Alexander IE, Russell DW. The Potential of AAV-Mediated Gene Targeting for Gene and Cell Therapy Applications. CURRENT STEM CELL REPORTS 2015. [DOI: 10.1007/s40778-014-0001-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Abstract
The use of custom-engineered sequence-specific nucleases (including CRISPR/Cas9, ZFN, and TALEN) allows genetic changes in human cells to be easily made with much greater efficiency and precision than before. Engineered double-stranded DNA breaks can efficiently disrupt genes, or, with the right donor vector, engineer point mutations and gene insertions. However, a number of design considerations should be taken into account to ensure maximum gene targeting efficiency and specificity. This is especially true when engineering human embryonic stem or induced pluripotent stem cells (iPSCs), which are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe a protocol for easily engineering genetic changes in human iPSCs, through which we typically achieve targeting efficiencies between 1% and 10% without any subsequent selection steps. Since this protocol only uses the simple transient transfection of plasmids and/or single-stranded oligonucleotides, most labs will easily be able to perform it. We also describe strategies for identifying, cloning, and genotyping successfully edited cells, and how to design the optimal sgRNA target sites and donor vectors. Finally, we discuss alternative methods for gene editing including viral delivery vectors, Cas9 nickases, and orthogonal Cas9 systems.
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13
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Abstract
The use of custom-engineered sequence-specific nucleases (including CRISPR/Cas9, ZFN, and TALEN) allows genetic changes in human cells to be easily made with much greater efficiency and precision than before. Engineered double-stranded DNA breaks can efficiently disrupt genes, or, with the right donor vector, engineer point mutations and gene insertions. However, a number of design considerations should be taken into account to ensure maximum gene targeting efficiency and specificity. This is especially true when engineering human embryonic stem or induced pluripotent stem cells (iPSCs), which are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe a protocol for easily engineering genetic changes in human iPSCs, through which we typically achieve targeting efficiencies between 1% and 10% without any subsequent selection steps. Since this protocol only uses the simple transient transfection of plasmids and/or single-stranded oligonucleotides, most labs will easily be able to perform it. We also describe strategies for identifying, cloning, and genotyping successfully edited cells, and how to design the optimal sgRNA target sites and donor vectors. Finally, we discuss alternative methods for gene editing including viral delivery vectors, Cas9 nickases, and orthogonal Cas9 systems.
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Affiliation(s)
- Susan M Byrne
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Prashant Mali
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
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