401
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Lentiviral and genome-editing strategies for the treatment of β-hemoglobinopathies. Blood 2020; 134:1203-1213. [PMID: 31467062 DOI: 10.1182/blood.2019000949] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
β-Thalassemia and sickle cell disease (SCD) are the most prevalent monogenic diseases. These disorders are caused by quantitative or qualitative defects in the production of adult hemoglobin. Gene therapy is a potential treatment option for patients lacking an allogenic compatible hematopoietic stem cell (HSC) donor. New-generation lentiviral vectors (LVs) carrying a β-globin-like gene have revolutionized this field by allowing effective HSC transduction, with no evidence of genotoxicity to date. Several clinical trials with different types of vector are underway worldwide; the initial results are encouraging with regard to the sustained production of therapeutic hemoglobin, improved biological parameters, a lower transfusion requirement, and better quality of life. Long-term follow-up studies will confirm the safety of LV-based gene therapy. The optimization of patient conditioning, HSC harvesting, and HSC transduction has further improved the therapeutic potential of this approach. Novel LV-based strategies for reactivating endogenous fetal hemoglobin (HbF) are also promising, because elevated HbF levels can reduce the severity of both β-thalassemia and SCD. Lastly, genome-editing approaches designed to correct the disease-causing mutation or reactivate HbF are currently under investigation. Here, we discuss the clinical outcomes of current LV-based gene addition trials and the promising advantages of novel alternative therapeutic strategies.
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402
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Stewart J, Banerjee S, Pettitt SJ, Lord CJ. Modelling the Cancer Phenotype in the Era of CRISPR-Cas9 Gene Editing. Clin Oncol (R Coll Radiol) 2020; 32:69-74. [PMID: 31679912 DOI: 10.1016/j.clon.2019.09.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/11/2019] [Indexed: 02/08/2023]
Affiliation(s)
- J Stewart
- Gynaecology Unit, Royal Marsden NHS Foundation Trust, London, UK; CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - S Banerjee
- Gynaecology Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - S J Pettitt
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK.
| | - C J Lord
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK.
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403
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Expanding the genome-targeting scope and the site selectivity of high-precision base editors. Nat Commun 2020; 11:629. [PMID: 32005820 PMCID: PMC6994485 DOI: 10.1038/s41467-020-14465-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/10/2020] [Indexed: 12/26/2022] Open
Abstract
Base editors (BEs) are RNA-guided CRISPR-Cas-derived genome editing tools that induce single-nucleotide changes. The limitations of current BEs lie in their low precision (especially when multiple target nucleotides of the deaminase are present within the activity window) and their restriction to targets that are in proper distance from the PAM sequence. We have recently developed high-precision cytidine BEs by engineering CDA1 truncations and nCas9 fusions that predominantly edit nucleotide C-18 relative to the PAM sequence NGG. Here, by testing fusions with Cas9 variants that recognize alternative PAMs, we provide a series of high-precision BEs that greatly expand the versatility of base editing. In addition, we obtained BEs that selectively edit C-15 or C-16. We also show that our high-precision BEs can substantially reduce off-target effect. These improved base editing tools will be widely applicable in basic research, biotechnology and gene therapy.
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404
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Banakar R, Schubert M, Collingwood M, Vakulskas C, Eggenberger AL, Wang K. Comparison of CRISPR-Cas9/Cas12a Ribonucleoprotein Complexes for Genome Editing Efficiency in the Rice Phytoene Desaturase (OsPDS) Gene. RICE (NEW YORK, N.Y.) 2020; 13:4. [PMID: 31965382 PMCID: PMC6973557 DOI: 10.1186/s12284-019-0365-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/29/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Delivery of CRISPR reagents into cells as ribonucleoprotein (RNP) complexes enables transient editing, and avoids CRISPR reagent integration in the genomes. Another technical advantage is that RNP delivery can bypass the need of cloning and vector construction steps. In this work we compared efficacies and types of edits for three Cas9 (WT Cas9 nuclease, HiFi Cas9 nuclease, Cas9 D10A nickase) and two Cas12a nucleases (AsCas12a and LbCas12a), using the rice phytoene desaturase (PDS) gene as a target site. FINDINGS Delivery of two Cas9 nucleases (WT Cas9, and HiFi Cas9) and one Cas12a nuclease (LbCas12a) resulted in targeted mutagenesis of the PDS gene. LbCas12a had a higher editing efficiency than that of WT Cas9 and HiFi Cas9. Editing by Cas9 enzymes resulted in indels (1-2 bp) or larger deletions between 20-bp to 30-bp, which included the loss of the PAM site; whereas LbCas12a editing resulted in deletions ranging between 2 bp to 20 bp without the loss of the PAM site. CONCLUSIONS In this work, when a single target site of the rice gene OsPDS was evaluated, the LbCas12a RNP complex achieved a higher targeted mutagenesis frequency than the AsCas12a or Cas9 RNPs.
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Affiliation(s)
- Raviraj Banakar
- Department of Agronomy, Iowa State University, Ames, IA, USA
- Crop Bioengineering Center, Iowa State University, Ames, IA, USA
- Present Address: Department of Plant and Microbial Genomics, University of Minnesota, St Paul, MN, 55108, USA
| | | | | | | | - Alan L Eggenberger
- Department of Agronomy, Iowa State University, Ames, IA, USA
- Crop Bioengineering Center, Iowa State University, Ames, IA, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, USA.
- Crop Bioengineering Center, Iowa State University, Ames, IA, USA.
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405
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Poletto E, Baldo G, Gomez-Ospina N. Genome Editing for Mucopolysaccharidoses. Int J Mol Sci 2020; 21:E500. [PMID: 31941077 PMCID: PMC7014411 DOI: 10.3390/ijms21020500] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Genome editing holds the promise of one-off and potentially curative therapies for many patients with genetic diseases. This is especially true for patients affected by mucopolysaccharidoses as the disease pathophysiology is amenable to correction using multiple approaches. Ex vivo and in vivo genome editing platforms have been tested primarily on MSPI and MPSII, with in vivo approaches having reached clinical testing in both diseases. Though we still await proof of efficacy in humans, the therapeutic tools established for these two diseases should pave the way for other mucopolysaccharidoses. Herein, we review the current preclinical and clinical development studies, using genome editing as a therapeutic approach for these diseases. The development of new genome editing platforms and the variety of genetic modifications possible with each tool provide potential applications of genome editing for mucopolysaccharidoses, which vastly exceed the potential of current approaches. We expect that in a not-so-distant future, more genome editing-based strategies will be established, and individual diseases will be treated through multiple approaches.
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Affiliation(s)
- Edina Poletto
- Gene Therapy Center, Hospital de Clinicas de Porto Alegre, Porto Alegre 90035-007, Brazil; (E.P.); (G.B.)
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Guilherme Baldo
- Gene Therapy Center, Hospital de Clinicas de Porto Alegre, Porto Alegre 90035-007, Brazil; (E.P.); (G.B.)
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
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406
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Agudelo D, Carter S, Velimirovic M, Duringer A, Rivest JF, Levesque S, Loehr J, Mouchiroud M, Cyr D, Waters PJ, Laplante M, Moineau S, Goulet A, Doyon Y. Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9. Genome Res 2020; 30:107-117. [PMID: 31900288 PMCID: PMC6961573 DOI: 10.1101/gr.255414.119] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/17/2019] [Indexed: 12/18/2022]
Abstract
Targeting definite genomic locations using CRISPR-Cas systems requires a set of enzymes with unique protospacer adjacent motif (PAM) compatibilities. To expand this repertoire, we engineered nucleases, cytosine base editors, and adenine base editors from the archetypal Streptococcus thermophilus CRISPR1-Cas9 (St1Cas9) system. We found that St1Cas9 strain variants enable targeting to five distinct A-rich PAMs and provide a structural basis for their specificities. The small size of this ortholog enables expression of the holoenzyme from a single adeno-associated viral vector for in vivo editing applications. Delivery of St1Cas9 to the neonatal liver efficiently rewired metabolic pathways, leading to phenotypic rescue in a mouse model of hereditary tyrosinemia. These robust enzymes expand and complement current editing platforms available for tailoring mammalian genomes.
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Affiliation(s)
- Daniel Agudelo
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Sophie Carter
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Minja Velimirovic
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Alexis Duringer
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Jean-François Rivest
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Sébastien Levesque
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Jeremy Loehr
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Mathilde Mouchiroud
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ)-Université Laval, Québec, Québec G1V 4G5, Canada
| | - Denis Cyr
- Service de Génétique médicale, Département de Pédiatrie, Centre Hospitalier Universitaire de Sherbrooke (CHUS), et CRCHUS, Sherbrooke, Québec J1H 5N4, Canada
| | - Paula J Waters
- Service de Génétique médicale, Département de Pédiatrie, Centre Hospitalier Universitaire de Sherbrooke (CHUS), et CRCHUS, Sherbrooke, Québec J1H 5N4, Canada
| | - Mathieu Laplante
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ)-Université Laval, Québec, Québec G1V 4G5, Canada.,Université Laval Cancer Research Centre, Québec, Québec G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille Cedex 09, France.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada.,Université Laval Cancer Research Centre, Québec, Québec G1V 0A6, Canada
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407
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An overview of OECD activities related to modern techniques of biotechnology and genome editing : OECD conference on genome editing, June 2018. Transgenic Res 2020; 28:41-44. [PMID: 31321681 DOI: 10.1007/s11248-019-00131-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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408
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Abstract
A transgenic mouse carries within its genome an artificial DNA construct (transgene) that is deliberately introduced by an experimentalist. These animals are widely used to understand gene function and protein function. When addressing the history of transgenic mouse technology, it is apparent that a number of basic science research areas laid the groundwork for success. These include reproductive science, genetics and molecular biology, and micromanipulation and microscopy equipment. From reproductive physiology came applications on how to optimize mouse breeding, how to superovulate mice to produce zygotes for DNA microinjection or preimplantation embryos for combination with embryonic stem (ES) cells, and how to return zygotes and embryos to a pseudopregnant surrogate dam for gestation and birth. From developmental biology, it was learned how to micromanipulate embryos for morula aggregation and blastocyst microinjection and how to establish germline competent ES cells. From genetics came the foundational principles governing the inheritance of genes, the interactions of gene products, and an understanding of the phenotypic consequences of genetic mutations. From molecular biology came a panoply of tools and reagents that are used to clone DNA transgenes, to detect the presence of transgenes, to assess gene expression by measuring transcription, and to detect proteins in cells and tissues. Technical advances in light microscopes, micromanipulators, micropipette pullers, and ancillary equipment made it possible for experimentalists to insert thin glass needles into zygotes or embryos under controlled conditions to inject DNA solutions or ES cells. To fully discuss the breadth of contributions of these numerous scientific disciplines to a comprehensive history of transgenic science is beyond the scope of this work. Examples will be used to illustrate scientific developments central to the foundation of transgenic technology and that are in use today.
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Affiliation(s)
- Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan Medical School, Ann Arbor, MI, USA.
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
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409
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CRISPR-Cas nucleases and base editors for plant genome editing. ABIOTECH 2020; 1:74-87. [PMID: 36305010 PMCID: PMC9584094 DOI: 10.1007/s42994-019-00010-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/02/2019] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) and base editors are fundamental tools in plant genome editing. Cas9 from Streptococcus pyogenes (SpCas9), recognizing an NGG protospacer adjacent motif (PAM), is a widely used nuclease for genome editing in living cells. Cas12a nucleases, targeting T-rich PAMs, have also been recently demonstrated in several plant species. Furthermore, multiple Cas9 and Cas12a engineered variants and orthologs, with different PAM recognition sites, editing efficiencies and fidelity, have been explored in plants. These RNA-guided sequence-specific nucleases (SSN) generate double-stranded breaks (DSBs) in DNA, which trigger non-homologous end-joining (NHEJ) repair or homology-directed repair (HDR), resulting in insertion and deletion (indel) mutations or precise gene replacement, respectively. Alternatively, genome editing can be achieved by base editors without introducing DSBs. So far, several base editors have been applied in plants to introduce C-to-T or A-to-G transitions, but they are still undergoing improvement in editing window size, targeting scope, off-target effects in DNA and RNA, product purity and overall activity. Here, we summarize recent progress on the application of Cas nucleases, engineered Cas variants and base editors in plants.
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410
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Prykhozhij SV, Cordeiro-Santanach A, Caceres L, Berman JN. Genome Editing in Zebrafish Using High-Fidelity Cas9 Nucleases: Choosing the Right Nuclease for the Task. Methods Mol Biol 2020; 2115:385-405. [PMID: 32006412 DOI: 10.1007/978-1-0716-0290-4_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Shortly after the development of the CRISPR/Cas9 system, it was recognized that it is prone to induce off-target mutations at significant frequencies. Therefore, there is a strong motivation to develop Cas9 enzymes with reduced off-target activity. Multiple rational design or selection approaches have been applied to develop several Cas9 versions with reduced off-target activities (high fidelity). To make these high-fidelity Cas9s available for model systems other than human cells and bacterial strains, as, for example, in zebrafish, new specialized expression vectors need to be developed. In this chapter, we focused on the HypaCas9 and HiFi Cas9 high-fidelity enzymes and incorporated the mutations of these Cas9 versions into a codon-optimized zebrafish Cas9 vector. This optimized vector was further improved by introducing an artificial polyadenine insert (A71) since polyadenylation is known to enhance mRNA translational efficiency. The Hypa-nCas9n and HiFi-nCas9n vectors were produced by single-site mutagenesis from pT3TS-nCas9n-A71 vector. We then tested the polyadenylated mRNAs for nCas9n, Hypa-nCas9n, HiFi-nCas9n, and HiFi-Cas9 protein for editing efficiency in five genome editing strategies and found that these high-fidelity Cas9 versions had different performances ranging from activity at 2-4 sites, where the wild-type nCas9n is active, indicating that these Cas9 versions have different sgRNA preferences. In summary, the developed new high-fidelity Cas9 vectors will enable researchers to perform much more accurate genome editing.
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411
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Nguyen DN, Roth TL, Li PJ, Chen PA, Apathy R, Mamedov MR, Vo LT, Tobin VR, Goodman D, Shifrut E, Bluestone JA, Puck JM, Szoka FC, Marson A. Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency. Nat Biotechnol 2020; 38:44-49. [PMID: 31819258 PMCID: PMC6954310 DOI: 10.1038/s41587-019-0325-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022]
Abstract
Versatile and precise genome modifications are needed to create a wider range of adoptive cellular therapies1-5. Here we report two improvements that increase the efficiency of CRISPR-Cas9-based genome editing in clinically relevant primary cell types. Truncated Cas9 target sequences (tCTSs) added at the ends of the homology-directed repair (HDR) template interact with Cas9 ribonucleoproteins (RNPs) to shuttle the template to the nucleus, enhancing HDR efficiency approximately two- to fourfold. Furthermore, stabilizing Cas9 RNPs into nanoparticles with polyglutamic acid further improves editing efficiency by approximately twofold, reduces toxicity, and enables lyophilized storage without loss of activity. Combining the two improvements increases gene targeting efficiency even at reduced HDR template doses, yielding approximately two to six times as many viable edited cells across multiple genomic loci in diverse cell types, such as bulk (CD3+) T cells, CD8+ T cells, CD4+ T cells, regulatory T cells (Tregs), γδ T cells, B cells, natural killer cells, and primary and induced pluripotent stem cell-derived6 hematopoietic stem progenitor cells (HSPCs).
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Affiliation(s)
- David N Nguyen
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Theodore L Roth
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - P Jonathan Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Peixin Amy Chen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Ryan Apathy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Murad R Mamedov
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Linda T Vo
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Victoria R Tobin
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Goodman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer M Puck
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Francis C Szoka
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander Marson
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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412
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陈 果, 程 度, 陈 滨. [Development of CRISPR technology and its application in bone and cartilage tissue engineering]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:1515-1520. [PMID: 31907146 PMCID: PMC6942994 DOI: 10.12122/j.issn.1673-4254.2019.12.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Indexed: 12/09/2022]
Abstract
The CRISPR/Cas9 system, consisting of Cas9 nuclease and single guide RNA (sgRNA), is an emerging gene editing technology that can perform gene reprogramming operations such as deletion, insertion, and point mutation on DNA sequences targeted by sgRNA. In addition, CRISPR/dCas9 (a mutant that loses Cas9 nuclease activity) still retains the ability of sgRNA to target DNA. The fusion of dCas9 protein with transcriptional activator (CRISPRa) can activate the expression of the target gene, and fusion transcriptional repressors (CRISPRi) can also be used to suppress target gene expression. Efficient delivery of the CRISPR/Cas9 system is one of the main problems limiting its wide clinical application. Viral vectors are widely used to efficiently deliver CRISPR/Cas9 elements, but non-viral vector research is more attractive in terms of safety, simplicity, and flexibility. In this review, we summarize the principles and research advances of CRISPR technology, including CRISPR/ Cas9 delivery vectors, delivery methods, and obstacles to the delivery, and review the progress of CRISPR-based research in bone and cartilage tissue engineering. Finally, the challenges and future applications of CRISPR technology in bone and cartilage tissue engineering are discussed.
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Affiliation(s)
- 果 陈
- 南方医科大学南方医院创伤骨科,广东 广州 510515Department of Traumatology and Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - 度 程
- 中山大学材料科学与工程学院,广东 广州 510275School of Material Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - 滨 陈
- 南方医科大学南方医院创伤骨科,广东 广州 510515Department of Traumatology and Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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413
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Benati D, Patrizi C, Recchia A. Gene editing prospects for treating inherited retinal diseases. J Med Genet 2019; 57:437-444. [PMID: 31857428 DOI: 10.1136/jmedgenet-2019-106473] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/14/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022]
Abstract
Retinal diseases (RD) include inherited retinal dystrophy (IRD), for example, retinitis pigmentosa and Leber's congenital amaurosis, or multifactorial forms, for example, age-related macular degeneration (AMD). IRDs are clinically and genetically heterogeneous in nature. To date, more than 200 genes are known to cause IRDs, which perturb the development, function and survival of rod and cone photoreceptors or retinal pigment epithelial cells. Conversely, AMD, the most common cause of blindness in the developed world, is an acquired disease of the macula characterised by progressive visual impairment. To date, available therapeutic approaches for RD include nutritional supplements, neurotrophic factors, antiangiogenic drugs for wet AMD and gene augmentation/interference strategy for IRDs. However, these therapies do not aim at correcting the genetic defect and result in inefficient and expensive treatments. The genome editing technology based on clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein (Cas) and an RNA that guides the Cas protein to a predetermined region of the genome, represents an attractive strategy to tackle IRDs without available cure. Indeed, CRISPR/Cas system can permanently and precisely replace or remove genetic mutations causative of a disease, representing a molecular tool to cure a genetic disorder. In this review, we will introduce the mechanism of CRISPR/Cas system, presenting an updated panel of Cas variants and delivery systems, then we will focus on applications of CRISPR/Cas genome editing in the retina, and, as emerging treatment options, in patient-derived induced pluripotent stem cells followed by transplantation of retinal progenitor cells into the eye.
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Affiliation(s)
- Daniela Benati
- Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Clarissa Patrizi
- Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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414
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Okafor IC, Singh D, Wang Y, Jung M, Wang H, Mallon J, Bailey S, Lee JK, Ha T. Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding. Nucleic Acids Res 2019; 47:11880-11888. [PMID: 31713616 PMCID: PMC7145707 DOI: 10.1093/nar/gkz1058] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 12/20/2022] Open
Abstract
Cas9 has made a wide range of genomic manipulation possible. However, its specificity continues to be a challenge. Non-canonical gRNAs and new engineered variants of Cas9 have been developed to improve specificity, but at the cost of the on-target activity. DNA unwinding is a checkpoint before cleavage by Cas9, and was shown to be made more sensitive to sequence mismatches by specificity-enhancing mutations in engineered Cas9s. Here we performed single-molecule FRET-based DNA unwinding experiments using various combinations of non-canonical gRNAs and different Cas9s. All engineered Cas9s were less promiscuous than wild type when canonical gRNA was used, but HypaCas9 had much-reduced on-target unwinding. Cas9-HF1 and eCas9 showed the best balance between low promiscuity and high on-target activity with canonical gRNA. When extended gRNAs with one or two non-matching guanines added to the 5' end were used, Sniper1-Cas9 showed the lowest promiscuity while maintaining high on-target activity. Truncated gRNA generally reduced unwinding and adding a non-matching guanine to the 5' end of gRNA influenced unwinding in a sequence-context dependent manner. Our results are consistent with cell-based cleavage data and provide a mechanistic understanding of how various Cas9/gRNA combinations perform in genome engineering.
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Affiliation(s)
- Ikenna C Okafor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Digvijay Singh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Haobo Wang
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John Mallon
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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415
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CRISPR/Cas9-based targeted genome editing for correction of recessive dystrophic epidermolysis bullosa using iPS cells. Proc Natl Acad Sci U S A 2019; 116:26846-26852. [PMID: 31818947 DOI: 10.1073/pnas.1907081116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a severe inherited skin disorder caused by mutations in the COL7A1 gene encoding type VII collagen (C7). The spectrum of severity depends on the type of mutation in the COL7A1 gene. C7 is the major constituent of anchoring fibrils (AFs) at the basement membrane zone (BMZ). Patients with RDEB lack functional C7 and have severely impaired dermal-epidermal stability, resulting in extensive blistering and open wounds on the skin that greatly affect the patient's quality of life. There are currently no therapies approved for the treatment of RDEB. Here, we demonstrated the correction of mutations in exon 19 (c.2470insG) and exon 32 (c.3948insT) in the COL7A1 gene through homology-directed repair (HDR). We used the clustered regulatory interspaced short palindromic repeats (CRISPR) Cas9-gRNAs system to modify induced pluripotent stem cells (iPSCs) derived from patients with RDEB in both the heterozygous and homozygous states. Three-dimensional human skin equivalents (HSEs) were generated from gene-corrected iPSCs, differentiated into keratinocytes (KCs) and fibroblasts (FBs), and grafted onto immunodeficient mice, which showed normal expression of C7 at the BMZ as well as restored AFs 2 mo postgrafting. Safety assessment for potential off-target Cas9 cleavage activity did not reveal any unintended nuclease activity. Our findings represent a crucial advance for clinical applications of innovative autologous stem cell-based therapies for RDEB.
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416
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Ulloa-Navas MJ, García-Tárraga P, García-Verdugo JM, Herranz-Pérez V. Immunogold Labeling to Detect Streptococcus pyogenes Cas9 in Cell Culture and Tissues by Electron Microscopy. CRISPR J 2019; 2:395-405. [PMID: 31860352 DOI: 10.1089/crispr.2019.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The CRISPR-Cas9 system is a powerful and yet precise DNA-editing tool in rapid development. By combining immunogold labeling and electron microscopy with the novel CRISPR-Cas9 system, we propose a new method to gain insight into the biology of this tool. In this study, we analyzed different Cas9-induced systems such as HEK293T cell line, murine oligodendrocyte progenitor cells, brain and liver to detect Cas9 expression by immunoelectron microscopy. Our results show that while Cas9 expression could be found in the nuclei and nucleopores of transfected HEK293T cells, in transfected oligodendrocyte precursor cells, Cas9 was found in cytoplasmic vesicles. In Cas9 constitutively expressing oligodendrocyte precursors, the enzyme was located in the cytoplasm of nondividing cells. Finally, while in the liver Cas9 was detected in different cell types, in the brain we found no specifically labeled cells. In conclusion, immunoelectron microscopy opens a new spectrum of opportunities to study the CRISPR-Cas9 system in a more precise manner.
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Affiliation(s)
- María José Ulloa-Navas
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, CIBERNED, Paterna, Spain; and Faculty of Health Sciences, University Jaume I, Castelló de la Plana, Spain
| | - Patricia García-Tárraga
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, CIBERNED, Paterna, Spain; and Faculty of Health Sciences, University Jaume I, Castelló de la Plana, Spain
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, CIBERNED, Paterna, Spain; and Faculty of Health Sciences, University Jaume I, Castelló de la Plana, Spain
| | - Vicente Herranz-Pérez
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, CIBERNED, Paterna, Spain; and Faculty of Health Sciences, University Jaume I, Castelló de la Plana, Spain
- Predepartamental Unit of Medicine, Faculty of Health Sciences, University Jaume I, Castelló de la Plana, Spain
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417
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Raikwar SP, Kikkeri NS, Sakuru R, Saeed D, Zahoor H, Premkumar K, Mentor S, Thangavel R, Dubova I, Ahmed ME, Selvakumar GP, Kempuraj D, Zaheer S, Iyer SS, Zaheer A. Next Generation Precision Medicine: CRISPR-mediated Genome Editing for the Treatment of Neurodegenerative Disorders. J Neuroimmune Pharmacol 2019; 14:608-641. [PMID: 31011884 PMCID: PMC8211357 DOI: 10.1007/s11481-019-09849-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/29/2019] [Indexed: 12/13/2022]
Abstract
Despite significant advancements in the field of molecular neurobiology especially neuroinflammation and neurodegeneration, the highly complex molecular mechanisms underlying neurodegenerative diseases remain elusive. As a result, the development of the next generation neurotherapeutics has experienced a considerable lag phase. Recent advancements in the field of genome editing offer a new template for dissecting the precise molecular pathways underlying the complex neurodegenerative disorders. We believe that the innovative genome and transcriptome editing strategies offer an excellent opportunity to decipher novel therapeutic targets, develop novel neurodegenerative disease models, develop neuroimaging modalities, develop next-generation diagnostics as well as develop patient-specific precision-targeted personalized therapies to effectively treat neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, Huntington's disease, Amyotrophic lateral sclerosis, Frontotemporal dementia etc. Here, we review the latest developments in the field of CRISPR-mediated genome editing and provide unbiased futuristic insights regarding its translational potential to improve the treatment outcomes and minimize financial burden. However, despite significant advancements, we would caution the scientific community that since the CRISPR field is still evolving, currently we do not know the full spectrum of CRISPR-mediated side effects. In the wake of the recent news regarding CRISPR-edited human babies being born in China, we urge the scientific community to maintain high scientific and ethical standards and utilize CRISPR for developing in vitro disease in a dish model, in vivo testing in nonhuman primates and lower vertebrates and for the development of neurotherapeutics for the currently incurable neurodegenerative disorders. Graphical Abstract.
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Affiliation(s)
- Sudhanshu P Raikwar
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA
| | - Nidhi S Kikkeri
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Ragha Sakuru
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Daniyal Saeed
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Haris Zahoor
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Keerthivaas Premkumar
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Shireen Mentor
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Republic of South Africa
| | - Ramasamy Thangavel
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA
| | - Iuliia Dubova
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA
| | - Mohammad Ejaz Ahmed
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA
| | - Govindhasamy P Selvakumar
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA
| | - Duraisamy Kempuraj
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA
| | - Smita Zaheer
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Shankar S Iyer
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA
| | - Asgar Zaheer
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA.
- U.S. Department of Veterans Affairs, Harry S. Truman Memorial Veteran's Hospital, Columbia, MO, USA.
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418
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Wu J, Yin H. Engineering guide RNA to reduce the off-target effects of CRISPR. J Genet Genomics 2019; 46:523-529. [PMID: 31902584 DOI: 10.1016/j.jgg.2019.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/26/2022]
Abstract
As versatile and robust genome editing tools, clustered regularly interspaced short palindromic repeats (CRISPR) technologies have been broadly used in basic research, biotechnology, and therapeutic development. Off-target mutagenesis by CRISPR systems has been demonstrated, and various methods have been developed to markedly increase their specificity. In this review, we highlight the efforts of producing and modifying guide RNA (gRNA) to minimize off-target activities, including sequence and structure design, tuning expression and chemical modification. The modalities of gRNA engineering can be applied across CRISPR systems. In conjunction with CRISPR protein effectors, the engineered gRNA enables efficient and precise genome editing.
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Affiliation(s)
- Jing Wu
- Department of Pathology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, 430071, China
| | - Hao Yin
- Department of Pathology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, 430071, China; Department of Urology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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419
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Hematopoietic stem cell gene therapy: The optimal use of lentivirus and gene editing approaches. Blood Rev 2019; 40:100641. [PMID: 31761379 DOI: 10.1016/j.blre.2019.100641] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 12/26/2022]
Abstract
Due to pioneering in vitro investigations on gene modification, gene engineering platforms have incredibly improved to a safer and more powerful tool for the treatment of multiple blood and immune disorders. Likewise, several clinical trials have been initiated combining autologous hematopoietic stem cell transplantation (auto-HSCT) with gene therapy (GT) tools. As several GT modalities such as lentivirus and gene editing tools have a long developmental path ahead to diminish its negative side effects, it is hard to decide which modality is optimal for treating a specific disease. Gene transfer by lentiviruses is the platform of choice for loss-of-mutation diseases, whereas gene correction/addition or gene disruption by gene editing tools, mainly CRISPR/Cas9, is likely to be more efficient in diseases where tight regulation is needed. Therefore, in this review, we compiled pertinent information about lentiviral gene transfer and CRISPR/Cas9 gene editing, their evolution to a safer platform for HSCT, and their applications on other types of gene disorders based on the etiology of the disease and cell fitness.
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420
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Genome-Wide Off-Target Analysis in CRISPR-Cas9 Modified Mice and Their Offspring. G3-GENES GENOMES GENETICS 2019; 9:3645-3651. [PMID: 31492696 PMCID: PMC6829146 DOI: 10.1534/g3.119.400503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The emergence of the CRISPR-Cas9 system has triggered a technical revolution in mammalian genome editing. Compared to traditional gene-targeting strategies, CRISPR-Cas9 technology offers a more efficient and cost-effective approach for generating genetically modified animal models. However, off-target cleavage in CRISPR-mediated genome editing is a major concern in the analysis of phenotypes as well as the selection of therapeutic targets. Here, we analyzed whole-genome sequencing (WGS) data from two knock-out (KO) mouse strains generated by using the CRISPR-Cas9 system targeting the Mmd and Paqr8 loci. A total of nine individuals were sequenced including two parents, four F1 offspring and three uninjected control mice. Using GATK and bcftools software, we identified two off-target events in the founder mice. The two CRISPR-Cas9-induced off-target events were predictable using Cas-OFFinder and were not passed on to the offspring that we investigated. In addition, our results indicated that the number of CRISPR-Cas9-induced mutations was not statistically distinguishable from the background de novo mutations (DNMs).
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421
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Abstract
A recent report from Dr He Jiankui concerning the birth of twin girls harbouring mutations engineered by CRISPR/Cas nucleases has been met with international condemnation. Beside the serious ethical concerns, there are known technical risks associated with CRISPR/Cas gene editing which further raise questions about how these events could have been allowed to occur. Numerous studies have reported unexpected genomic mutation and mosaicism following the use of CRISPR/Cas nucleases, and it is currently unclear how prevalent these disadvantageous events are and how robust and sensitive the strategies to detect these unwanted events may be. Although Dr Jiankui's study appears to have involved certain checks to ascertain these risks, the decision to implant the manipulated embryos, given these unknowns, must nonetheless be considered reckless. Here I review the technical concerns surrounding genome editing and consider the available data from Dr Jiankui in this context. Although the data remains unpublished, preventing a thorough assessment of what was performed, it seems clear that the rationale behind the undertaking was seriously flawed; the procedures involved substantial technical risks which, when added to the serious ethical concerns, fully justify the widespread criticism that the events have received.
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Affiliation(s)
- Benjamin Davies
- Welcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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422
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Tong S, Moyo B, Lee CM, Leong K, Bao G. Engineered materials for in vivo delivery of genome-editing machinery. NATURE REVIEWS. MATERIALS 2019; 4:726-737. [PMID: 34094589 PMCID: PMC8174554 DOI: 10.1038/s41578-019-0145-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 05/22/2023]
Abstract
Genome editing technologies, such as CRISPR/Cas9, are promising for treating otherwise incurable genetic diseases. Great progress has been made for ex vivo genome editing; however, major bottlenecks exist in the development of efficient, safe, and targetable in vivo delivery systems, which are needed for the treatment of many diseases. To achieve high efficacy and safety in therapeutic in vivo genome editing, editing activities must be controlled spatially and temporally in the body, which requires novel materials, delivery strategies, and control mechanisms. Thus, there is currently a tremendous opportunity for the biomaterials research community to develop in vivo delivery systems that overcome the problems of low editing efficiency, off-targeting effect, safety, and cell and tissue specificity. In this Review, we summarize delivery approaches and provide perspectives on the challenges and possible solutions, aiming to stimulate further development of engineered materials for in vivo delivery of genome-editing machinery.
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Affiliation(s)
- Sheng Tong
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Buhle Moyo
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ciaran M. Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kam Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
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423
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Alisjahbana A, Mohammad I, Gao Y, Evren E, Ringqvist E, Willinger T. Human macrophages and innate lymphoid cells: Tissue-resident innate immunity in humanized mice. Biochem Pharmacol 2019; 174:113672. [PMID: 31634458 DOI: 10.1016/j.bcp.2019.113672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022]
Abstract
Macrophages and innate lymphoid cells (ILCs) are tissue-resident cells that play important roles in organ homeostasis and tissue immunity. Their intricate relationship with the organs they reside in allows them to quickly respond to perturbations of organ homeostasis and environmental challenges, such as infection and tissue injury. Macrophages and ILCs have been extensively studied in mice, yet important species-specific differences exist regarding innate immunity between humans and mice. Complementary to ex-vivo studies with human cells, humanized mice (i.e. mice with a human immune system) offer the opportunity to study human macrophages and ILCs in vivo within their surrounding tissue microenvironments. In this review, we will discuss how humanized mice have helped gain new knowledge about the basic biology of these cells, as well as their function in infectious and malignant conditions. Furthermore, we will highlight active areas of investigation related to human macrophages and ILCs, such as their cellular heterogeneity, ontogeny, tissue residency, and plasticity. In the near future, we expect more fundamental discoveries in these areas through the combined use of improved humanized mouse models together with state-of-the-art technologies, such as single-cell RNA-sequencing and CRISPR/Cas9 genome editing.
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Affiliation(s)
- Arlisa Alisjahbana
- Center for Infectious Medicine, Karolinska Institutet, Alfred Nobels allé 8, 141 52 Stockholm, Sweden
| | - Imran Mohammad
- Center for Infectious Medicine, Karolinska Institutet, Alfred Nobels allé 8, 141 52 Stockholm, Sweden
| | - Yu Gao
- Center for Infectious Medicine, Karolinska Institutet, Alfred Nobels allé 8, 141 52 Stockholm, Sweden
| | - Elza Evren
- Center for Infectious Medicine, Karolinska Institutet, Alfred Nobels allé 8, 141 52 Stockholm, Sweden
| | - Emma Ringqvist
- Center for Infectious Medicine, Karolinska Institutet, Alfred Nobels allé 8, 141 52 Stockholm, Sweden
| | - Tim Willinger
- Center for Infectious Medicine, Karolinska Institutet, Alfred Nobels allé 8, 141 52 Stockholm, Sweden.
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424
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Functional profiling of single CRISPR/Cas9-edited human long-term hematopoietic stem cells. Nat Commun 2019; 10:4730. [PMID: 31628330 PMCID: PMC6802205 DOI: 10.1038/s41467-019-12726-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/29/2019] [Indexed: 12/20/2022] Open
Abstract
In the human hematopoietic system, rare self-renewing multipotent long-term hematopoietic stem cells (LT-HSCs) are responsible for the lifelong production of mature blood cells and are the rational target for clinical regenerative therapies. However, the heterogeneity in the hematopoietic stem cell compartment and variable outcomes of CRISPR/Cas9 editing make functional interrogation of rare LT-HSCs challenging. Here, we report high efficiency LT-HSC editing at single-cell resolution using electroporation of modified synthetic gRNAs and Cas9 protein. Targeted short isoform expression of the GATA1 transcription factor elicit distinct differentiation and proliferation effects in single highly purified LT-HSC when analyzed with functional in vitro differentiation and long-term repopulation xenotransplantation assays. Our method represents a blueprint for systematic genetic analysis of complex tissue hierarchies at single-cell resolution. Previous gene editing in haematopoietic stem cells (HSCs) has focussed on a heterogeneous CD34+ population. Here, the authors demonstrate high efficiency CRISPR/Cas9-based editing of purified long-term HSCs using non-homologous end joining and homology-directed repair, by directing isoform-specific expression of GATA1.
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425
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Ikeda A, Fujii W, Sugiura K, Naito K. High-fidelity endonuclease variant HypaCas9 facilitates accurate allele-specific gene modification in mouse zygotes. Commun Biol 2019; 2:371. [PMID: 31633062 PMCID: PMC6787007 DOI: 10.1038/s42003-019-0627-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 09/23/2019] [Indexed: 02/04/2023] Open
Abstract
CRISPR/Cas9 has been widely used for the efficient generation of genetically modified animals; however, this system could have unexpected off-target effects. In the present study, we confirmed the validity of a high-fidelity Cas9 variant, HypaCas9, for accurate genome editing in mouse zygotes. HypaCas9 efficiently modified the target locus while minimizing off-target effects even in a single-nucleotide mismatched sequence. Furthermore, by applying HypaCas9 to the discrimination of SNP in hybrid strain-derived zygotes, we accomplished allele-specific gene modifications and successfully generated mice with a monoallelic mutation in an essential gene. These results suggest that the improved accuracy of HypaCas9 facilitates the generation of genetically modified animals.
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Affiliation(s)
- Arisa Ikeda
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Wataru Fujii
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Koji Sugiura
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Kunihiko Naito
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
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426
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Zheng Q, Zhang X, Yang H, Xie J, Xie Y, Chen J, Yu C, Zhong C. Internal Ribosome Entry Site Dramatically Reduces Transgene Expression in Hematopoietic Cells in a Position-Dependent Manner. Viruses 2019; 11:v11100920. [PMID: 31597367 PMCID: PMC6833044 DOI: 10.3390/v11100920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/21/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
Bicistronic transgene expression mediated by internal ribosome entry site (IRES) elements has been widely used. It co-expresses heterologous transgene products from a message RNA driven by a single promoter. Hematologic gene delivery is a promising treatment for both inherited and acquired diseases. A combined strategy was recently documented for potential genome editing in hematopoietic cells. A transduction efficiency exceeding ~90% can be achieved by capsid-optimized recombinant adeno-associated virus serotype 6 (rAAV6) vectors. In this study, to deliver an encephalomyocarditis virus (EMCV) IRES-containing rAAV6 genome into hematopoietic cells, we observed that EMCV IRES almost completely shut down the transgene expression during the process of mRNA–protein transition. In addition, position-dependent behavior was observed, in which only the EMCV IRES element located between a promoter and the transgenes had an inhibitory effect. Although further studies are warranted to evaluate the involvement of cellular translation machinery, our results propose the use of specific IRES elements or an alternative strategy, such as the 2A system, to achieve bicistronic transgene expression in hematopoietic cells.
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Affiliation(s)
- Qingyun Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Xueyan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA.
| | - Hua Yang
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA.
- Department of Radiology, Central South University, Changsha, Hunan 410013, China.
| | - Jinyan Xie
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Yilin Xie
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Jinzhong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
- Yeda Research Institute of Gene and Cell Therapy, Taizhou, Zhejiang 318000, China.
| | - Chenghui Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA.
- Yeda Research Institute of Gene and Cell Therapy, Taizhou, Zhejiang 318000, China.
| | - Chen Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
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427
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Improved Double-Nicking Strategies for COL7A1-Editing by Homologous Recombination. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:496-507. [PMID: 31670199 PMCID: PMC6838546 DOI: 10.1016/j.omtn.2019.09.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 11/21/2022]
Abstract
Current gene-editing approaches for treatment of recessive dystrophic epidermolysis bullosa (RDEB), an inherited, severe form of blistering skin disease, suffer from low efficiencies and safety concerns that complicate implementation in clinical settings. We present a strategy for efficient and precise repair of RDEB-associated mutations in the COL7A1 gene. We compared the efficacy of double-strand breaks (induced by CRISPR/Cas9), single nicks, or double nicks (induced by Cas9n) in mediating repair of a COL7A1 splice-site mutation in exon 3 by homologous recombination (HR). We accomplished remarkably high HR frequencies of 89% with double nicking while at the same time keeping unwanted repair outcomes, such as non-homologous end joining (NHEJ), at a minimum (11%). We also investigated the effects of subtle differences in repair template design on HR rates and found that strategic template-nicking can enhance COL7A1-editing efficiency. In RDEB patient keratinocytes, application of double-nicking led to restoration and subsequent secretion of type VII collagen at high efficiency. Comprehensive analysis of 25 putative off-target sites revealed no off-target activity for double-nicking, while usage of Cas9 resulted in 54% modified alleles at one site. Taken together, our work provides a framework for efficient, precise, and safe repair of COL7A1, which lies at the heart of a future curative therapy of RDEB.
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428
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The Potential Use of the CRISPR-Cas System for HIV-1 Gene Therapy. Int J Genomics 2019; 2019:8458263. [PMID: 31531340 PMCID: PMC6721108 DOI: 10.1155/2019/8458263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/14/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023] Open
Abstract
The HIV-1 virus (human immunodeficiency virus) affects 36.9 million people worldwide, with approximately 900000 deaths in 2017. The virus carrier can develop severe immunodeficiency since CD4+ T lymphocytes are the main target, leading to acquired immunodeficiency syndrome (AIDS). Despite advances in pharmacological treatment, it is still difficult to eliminate latent reservoirs, becoming one of the main obstacles for viral eradication. The CRISPR- (clustered regularly interspaced short palindromic repeat-) Cas system is a genome-editing method which uses a guide RNA, a complementary sequence to the interested site, recruiting a nuclease that can break the viral or the host cell genetic material. From this double-stranded break, cellular repair mechanisms are activated being able to generate deletions, insertions, or substitutions, in order to inactivate specific gene loci, leading to loss of function. The objective of this minireview is to synthesize the current knowledge on the application of CRISPR-Cas-based gene therapy for HIV-1. The strategies encompass all steps of the viral infection cycle, from inhibition of cell invasion, through viral replication and integration inhibition, to excision of the latent provirus. Off-target effects and ethical implications were also discussed to evaluate the safety of the approach and viability of its application in humans, respectively. Although preclinical and clinical tests are still needed, the recent results establish an exciting possibility of applying this technology for prophylaxis and treatment of HIV-1.
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429
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Klatt D, Cheng E, Philipp F, Selich A, Dahlke J, Schmidt RE, Schott JW, Büning H, Hoffmann D, Thrasher AJ, Schambach A. Targeted Repair of p47-CGD in iPSCs by CRISPR/Cas9: Functional Correction without Cleavage in the Highly Homologous Pseudogenes. Stem Cell Reports 2019; 13:590-598. [PMID: 31543470 PMCID: PMC6829751 DOI: 10.1016/j.stemcr.2019.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 10/26/2022] Open
Abstract
Mutations in the NADPH oxidase, which is crucial for the respiratory burst in phagocytes, result in chronic granulomatous disease (CGD). The only curative treatment option for CGD patients, who suffer from severe infections, is allogeneic bone marrow transplantation. Over 90% of patients with mutations in the p47phox subunit of the oxidase complex carry the deletion c.75_76delGT (ΔGT). This frequent mutation most likely originates via gene conversion from one of the two pseudogenes NCF1B or NCF1C, which are highly homologous to NCF1 (encodes p47phox) but carry the ΔGT mutation. We applied CRISPR/Cas9 to generate patient-like p47-ΔGT iPSCs for disease modeling. To avoid unpredictable chromosomal rearrangements by CRISPR/Cas9-mediated cleavage in the pseudogenes, we developed a gene-correction approach to specifically target NCF1 but leave the pseudogenes intact. Functional assays revealed restored NADPH oxidase activity and killing of bacteria in corrected phagocytes as well as the specificity of this approach.
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Affiliation(s)
- Denise Klatt
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Erica Cheng
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Friederike Philipp
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, 30625 Hannover, Germany
| | - Anton Selich
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Julia Dahlke
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Reinhold E Schmidt
- Department of Immunology and Rheumatology, Hannover Medical School, 30625 Hannover, Germany
| | - Juliane W Schott
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Program, Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; Great Ormond Street Hospital NHS Foundation Trust, London WC1N 1EH, UK
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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430
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Wang D, Zhang C, Wang B, Li B, Wang Q, Liu D, Wang H, Zhou Y, Shi L, Lan F, Wang Y. Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning. Nat Commun 2019; 10:4284. [PMID: 31537810 PMCID: PMC6753114 DOI: 10.1038/s41467-019-12281-8] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 07/24/2019] [Indexed: 12/16/2022] Open
Abstract
Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA activity for two highly specific SpCas9 variants (eSpCas9(1.1) and SpCas9-HF1) and wild-type SpCas9 (WT-SpCas9) in human cells, and obtain indel rates of over 50,000 gRNAs for each nuclease, covering ~20,000 genes. We evaluate the contribution of 1,031 features to gRNA activity and develope models for activity prediction. Our data reveals that a combination of RNN with important biological features outperforms other models for activity prediction. We further demonstrate that our model outperforms other popular gRNA design tools. Finally, we develop an online design tool DeepHF for the three Cas9 nucleases. The database, as well as the designer tool, is freely accessible via a web server, http://www.DeepHF.com/ .
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Affiliation(s)
- Daqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Chengdong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Bei Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Qiang Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Dong Liu
- Co-innovation Center of Neuroregeneration, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Hongyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, 200011, China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
- Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Feng Lan
- Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Disease, Capital Medical University, Beijing, 100029, China.
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China.
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431
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Dudek AM, Porteus MH. AAV6 Is Superior to Clade F AAVs in Stimulating Homologous Recombination-Based Genome Editing in Human HSPCs. Mol Ther 2019; 27:1701-1705. [PMID: 31537456 DOI: 10.1016/j.ymthe.2019.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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432
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CRISPR technologies for stem cell engineering and regenerative medicine. Biotechnol Adv 2019; 37:107447. [PMID: 31513841 DOI: 10.1016/j.biotechadv.2019.107447] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022]
Abstract
CRISPR/Cas9 system exploits the concerted action of Cas9 nuclease and programmable single guide RNA (sgRNA), and has been widely used for genome editing. The Cas9 nuclease activity can be abolished by mutation to yield the catalytically deactivated Cas9 (dCas9). Coupling with the customizable sgRNA for targeting, dCas9 can be fused with transcription repressors to inhibit specific gene expression (CRISPR interference, CRISPRi) or fused with transcription activators to activate the expression of gene of interest (CRISPR activation, CRISPRa). Here we introduce the principles and recent advances of these CRISPR technologies, their delivery vectors and review their applications in stem cell engineering and regenerative medicine. In particular, we focus on in vitro stem cell fate manipulation and in vivo applications such as prevention of retinal and muscular degeneration, neural regeneration, bone regeneration, cartilage tissue engineering, as well as treatment of diseases in blood, skin and liver. Finally, the challenges to translate CRISPR to regenerative medicine and future perspectives are discussed and proposed.
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433
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Gomez-Ospina N, Scharenberg SG, Mostrel N, Bak RO, Mantri S, Quadros RM, Gurumurthy CB, Lee C, Bao G, Suarez CJ, Khan S, Sawamoto K, Tomatsu S, Raj N, Attardi LD, Aurelian L, Porteus MH. Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I. Nat Commun 2019; 10:4045. [PMID: 31492863 PMCID: PMC6731271 DOI: 10.1038/s41467-019-11962-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022] Open
Abstract
Lysosomal enzyme deficiencies comprise a large group of genetic disorders that generally lack effective treatments. A potential treatment approach is to engineer the patient’s own hematopoietic system to express high levels of the deficient enzyme, thereby correcting the biochemical defect and halting disease progression. Here, we present an efficient ex vivo genome editing approach using CRISPR-Cas9 that targets the lysosomal enzyme iduronidase to the CCR5 safe harbor locus in human CD34+ hematopoietic stem and progenitor cells. The modified cells secrete supra-endogenous enzyme levels, maintain long-term repopulation and multi-lineage differentiation potential, and can improve biochemical and phenotypic abnormalities in an immunocompromised mouse model of Mucopolysaccharidosis type I. These studies provide support for the development of genome-edited CD34+ hematopoietic stem and progenitor cells as a potential treatment for Mucopolysaccharidosis type I. The safe harbor approach constitutes a flexible platform for the expression of lysosomal enzymes making it applicable to other lysosomal storage disorders. Mucopolysaccharidosis type I (MPSI) is a lysosomal storage disease caused by insufficient iduronidase (IDUA) activity. Here, the authors use an ex vivo genome editing approach to overexpress IDUA in human hematopoietic stem and progenitor cells and show it can phenotypically correct MSPI in mouse model.
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Affiliation(s)
- Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | | | - Nathalie Mostrel
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C., Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000, Aarhus C., Denmark
| | - Sruthi Mantri
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaukat Khan
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Kazuki Sawamoto
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Shunji Tomatsu
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Nitin Raj
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laure Aurelian
- Stanford University School of Medicine, Stanford, CA, 94305, USA.,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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434
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Park SH, Lee CM, Dever DP, Davis TH, Camarena J, Srifa W, Zhang Y, Paikari A, Chang AK, Porteus MH, Sheehan VA, Bao G. Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease. Nucleic Acids Res 2019; 47:7955-7972. [PMID: 31147717 PMCID: PMC6735704 DOI: 10.1093/nar/gkz475] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/14/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022] Open
Abstract
Sickle cell disease (SCD) is a monogenic disorder that affects millions worldwide. Allogeneic hematopoietic stem cell transplantation is the only available cure. Here, we demonstrate the use of CRISPR/Cas9 and a short single-stranded oligonucleotide template to correct the sickle mutation in the β-globin gene in hematopoietic stem and progenitor cells (HSPCs) from peripheral blood or bone marrow of patients with SCD, with 24.5 ± 7.6% efficiency without selection. Erythrocytes derived from gene-edited cells showed a marked reduction of sickle cells, with the level of normal hemoglobin (HbA) increased to 25.3 ± 13.9%. Gene-corrected SCD HSPCs retained the ability to engraft when transplanted into non-obese diabetic (NOD)-SCID-gamma (NSG) mice with detectable levels of gene correction 16-19 weeks post-transplantation. We show that, by using a high-fidelity SpyCas9 that maintained the same level of on-target gene modification, the off-target effects including chromosomal rearrangements were significantly reduced. Taken together, our results demonstrate efficient gene correction of the sickle mutation in both peripheral blood and bone marrow-derived SCD HSPCs, a significant reduction in sickling of red blood cells, engraftment of gene-edited SCD HSPCs in vivo and the importance of reducing off-target effects; all are essential for moving genome editing based SCD treatment into clinical practice.
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Affiliation(s)
- So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Yankai Zhang
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alireza Paikari
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia K Chang
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Vivien A Sheehan
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
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435
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Shelake RM, Pramanik D, Kim JY. Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era. Microorganisms 2019; 7:E269. [PMID: 31426522 PMCID: PMC6723455 DOI: 10.3390/microorganisms7080269] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant-microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
- Division of Life Science (CK1 Program), Gyeongsang National University, Jinju 660-701, Korea.
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436
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Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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437
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Choi GCG, Zhou P, Yuen CTL, Chan BKC, Xu F, Bao S, Chu HY, Thean D, Tan K, Wong KH, Zheng Z, Wong ASL. Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9. Nat Methods 2019; 16:722-730. [PMID: 31308554 DOI: 10.1038/s41592-019-0473-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 06/03/2019] [Indexed: 01/01/2023]
Abstract
The combined effect of multiple mutations on protein function is hard to predict; thus, the ability to functionally assess a vast number of protein sequence variants would be practically useful for protein engineering. Here we present a high-throughput platform that enables scalable assembly and parallel characterization of barcoded protein variants with combinatorial modifications. We demonstrate this platform, which we name CombiSEAL, by systematically characterizing a library of 948 combination mutants of the widely used Streptococcus pyogenes Cas9 (SpCas9) nuclease to optimize its genome-editing activity in human cells. The ease with which the editing activities of the pool of SpCas9 variants can be assessed at multiple on- and off-target sites accelerates the identification of optimized variants and facilitates the study of mutational epistasis. We successfully identify Opti-SpCas9, which possesses enhanced editing specificity without sacrificing potency and broad targeting range. This platform is broadly applicable for engineering proteins through combinatorial modifications en masse.
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Affiliation(s)
- Gigi C G Choi
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Peng Zhou
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Chaya T L Yuen
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Becky K C Chan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Feng Xu
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Siyu Bao
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China
| | - Hoi Yee Chu
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China
| | - Dawn Thean
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau, China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau, China
- Institute of Translational Medicine, University of Macau, Macau, China
| | - Zongli Zheng
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Alan S L Wong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China.
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438
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Abstract
The prokaryote-derived CRISPR-Cas genome editing systems have transformed our ability to manipulate, detect, image and annotate specific DNA and RNA sequences in living cells of diverse species. The ease of use and robustness of this technology have revolutionized genome editing for research ranging from fundamental science to translational medicine. Initial successes have inspired efforts to discover new systems for targeting and manipulating nucleic acids, including those from Cas9, Cas12, Cascade and Cas13 orthologues. Genome editing by CRISPR-Cas can utilize non-homologous end joining and homology-directed repair for DNA repair, as well as single-base editing enzymes. In addition to targeting DNA, CRISPR-Cas-based RNA-targeting tools are being developed for research, medicine and diagnostics. Nuclease-inactive and RNA-targeting Cas proteins have been fused to a plethora of effector proteins to regulate gene expression, epigenetic modifications and chromatin interactions. Collectively, the new advances are considerably improving our understanding of biological processes and are propelling CRISPR-Cas-based tools towards clinical use in gene and cell therapies.
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Affiliation(s)
- Adrian Pickar-Oliver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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439
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Miller JC, Patil DP, Xia DF, Paine CB, Fauser F, Richards HW, Shivak DA, Bendaña YR, Hinkley SJ, Scarlott NA, Lam SC, Reik A, Zhou Y, Paschon DE, Li P, Wangzor T, Lee G, Zhang L, Rebar EJ. Enhancing gene editing specificity by attenuating DNA cleavage kinetics. Nat Biotechnol 2019; 37:945-952. [PMID: 31359006 DOI: 10.1038/s41587-019-0186-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/11/2019] [Indexed: 12/22/2022]
Abstract
Engineered nucleases have gained broad appeal for their ability to mediate highly efficient genome editing. However the specificity of these reagents remains a concern, especially for therapeutic applications, given the potential mutagenic consequences of off-target cleavage. Here we have developed an approach for improving the specificity of zinc finger nucleases (ZFNs) that engineers the FokI catalytic domain with the aim of slowing cleavage, which should selectively reduce activity at low-affinity off-target sites. For three ZFN pairs, we engineered single-residue substitutions in the FokI domain that preserved full on-target activity but showed a reduction in off-target indels of up to 3,000-fold. By combining this approach with substitutions that reduced the affinity of zinc fingers, we developed ZFNs specific for the TRAC locus that mediated 98% knockout in T cells with no detectable off-target activity at an assay background of ~0.01%. We anticipate that this approach, and the FokI variants we report, will enable routine generation of nucleases for gene editing with no detectable off-target activity.
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Affiliation(s)
| | | | - Danny F Xia
- Sangamo Therapeutics, Inc., Richmond, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Patrick Li
- Sangamo Therapeutics, Inc., Richmond, CA, USA
| | | | - Gary Lee
- Sangamo Therapeutics, Inc., Richmond, CA, USA
| | - Lei Zhang
- Sangamo Therapeutics, Inc., Richmond, CA, USA
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440
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Skarnes WC, Pellegrino E, McDonough JA. Improving homology-directed repair efficiency in human stem cells. Methods 2019; 164-165:18-28. [PMID: 31216442 DOI: 10.1016/j.ymeth.2019.06.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 11/30/2022] Open
Abstract
The generation of induced pluripotent stem cell models of human disease requires efficient modification of one or both alleles depending on dominant or recessive inheritance of the disease. To faithfully recapitulate many disease variants, the introduction of a single base change is required. The introduction of additional silent mutations designed to prevent re-cutting of the modified allele by Cas9 is not an optimal strategy, particularly for non-coding variants. Here, we developed an improved protocol for efficient engineering of single nucleotide variants in human iPS cells. Using a fluorescent BFP->GFP assay to monitor the incorporation of a single base pair change, we optimized the protocol to achieve HDR in 70% of unselected human iPS cells. The additive effects of cold shock, a small molecule enhancer of HDR and chemically modified ssODN dramatically shift the bias of repair in favor of HDR, resulting in a seven-fold higher ratio of HDR to NHEJ from 0.5 to 3.7.
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Affiliation(s)
- William C Skarnes
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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441
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Spiegel A, Bachmann M, Jurado Jiménez G, Sarov M. CRISPR/Cas9-based knockout pipeline for reverse genetics in mammalian cell culture. Methods 2019; 164-165:49-58. [PMID: 31051255 DOI: 10.1016/j.ymeth.2019.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/04/2019] [Accepted: 04/24/2019] [Indexed: 12/14/2022] Open
Abstract
We present a straightforward protocol for reverse genetics in cultured mammalian cells, using CRISPR/Cas9-mediated homology-dependent repair (HDR) based insertion of a protein trap cassette, resulting in a termination of the endogenous gene expression. Complete loss of function can be achieved with monoallelic trap cassette insertion, as the second allele is frequently disrupted by an error-prone non-homologous end joining (NHEJ) mechanism. The method should be applicable to any expressed gene in most cell lines, including those with low HDR efficiency, as the knockout alleles can be directly selected for.
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Affiliation(s)
- Aleksandra Spiegel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mandy Bachmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Gabriel Jurado Jiménez
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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442
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Schatoff EM, Zafra MP, Dow LE. Base editing the mammalian genome. Methods 2019; 164-165:100-108. [PMID: 30836137 PMCID: PMC6684841 DOI: 10.1016/j.ymeth.2019.02.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/27/2019] [Indexed: 02/03/2023] Open
Abstract
Base editing is a powerful technology that enables programmable conversion of single nucleotides in the mammalian genome. Base editors consist of a partially active Cas9 nuclease (Cas9D10A) tethered to a natural or synthetic DNA modifying enzyme. Though only recently described, BE has already shown enormous potential for basic and translational research, allowing the creation or repair of disease alleles in a variety of cell types and model organisms. In the past 2 years, a vast array of new and modified base editor variants have been described, expanding the flexibility and usefulness of the approach. Though simple in concept, effective implementation of base editing requires an understanding of the advantages and limitations of each of these tools. Here, we provide an overview of the concepts of DNA base editing, and discuss the recent progress toward the development of optimized base editing systems for mammalian cells. In addition, we highlight key technical aspects of designing and executing BE experiments, and provide detailed experimental examples of successful base editing in cell lines and organoids to help guide the effective use of these tools for genome modification.
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Affiliation(s)
- Emma M Schatoff
- Sandra and Edward Meyer Cancer Center, United States; Weill Cornell/Rockefeller/Sloan Kettering Tri-I MD-PhD Program, New York 10065, United States
| | - Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, United States; Department of Medicine, United States
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, United States; Department of Medicine, United States; Department of Biochemistry, Weill Cornell Medicine, New York 10021, United States.
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443
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Gene therapy of hematological disorders: current challenges. Gene Ther 2019; 26:296-307. [PMID: 31300728 DOI: 10.1038/s41434-019-0093-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 12/13/2022]
Abstract
Recent advances in genetic engineering technology and stem cell biology have spurred great interest in developing gene therapies for hereditary, as well as acquired hematological disorders. Currently, hematopoietic stem cell transplantation is used to cure disorders such as hemoglobinopathies and primary immunodeficiencies; however, this method is limited by the availability of immune-matched donors. Using autologous cells coupled with genome editing bypasses this limitation and therefore became the focus of many research groups aiming to develop efficient and safe genomic modification. Hence, gene therapy research has witnessed a noticeable growth in recent years with numerous successful achievements; however, several challenges have to be overcome before gene therapy becomes widely available for patients. In this review, I discuss tools used in gene therapy for hematological disorders, choices of target cells, and delivery vehicles with emphasis on current hurdles and attempts to solve them, and present examples of successful clinical trials to give a glimpse of current progress.
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444
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Bueren JA, Quintana-Bustamante O, Almarza E, Navarro S, Río P, Segovia JC, Guenechea G. Advances in the gene therapy of monogenic blood cell diseases. Clin Genet 2019; 97:89-102. [PMID: 31231794 DOI: 10.1111/cge.13593] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/12/2019] [Accepted: 05/21/2019] [Indexed: 01/19/2023]
Abstract
Hematopoietic gene therapy has markedly progressed during the last 15 years both in terms of safety and efficacy. While a number of serious adverse events (SAE) were initially generated as a consequence of genotoxic insertions of gamma-retroviral vectors in the cell genome, no SAEs and excellent outcomes have been reported in patients infused with autologous hematopoietic stem cells (HSCs) transduced with self-inactivated lentiviral and gammaretroviral vectors. Advances in the field of HSC gene therapy have extended the number of monogenic diseases that can be treated with these approaches. Nowadays, evidence of clinical efficacy has been shown not only in primary immunodeficiencies, but also in other hematopoietic diseases, including beta-thalassemia and sickle cell anemia. In addition to the rapid progression of non-targeted gene therapies in the clinic, new approaches based on gene editing have been developed thanks to the discovery of designed nucleases and improved non-integrative vectors, which have markedly increased the efficacy and specificity of gene targeting to levels compatible with its clinical application. Based on advances achieved in the field of gene therapy, it can be envisaged that these therapies will soon be part of the therapeutic approaches used to treat life-threatening diseases of the hematopoietic system.
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Affiliation(s)
- Juan A Bueren
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Oscar Quintana-Bustamante
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Elena Almarza
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Susana Navarro
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Paula Río
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - José C Segovia
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Guillermo Guenechea
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
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445
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Çiçek YA, Luther DC, Kretzmann JA, Rotello VM. Advances in CRISPR/Cas9 Technology for in Vivo Translation. Biol Pharm Bull 2019; 42:304-311. [PMID: 30828060 DOI: 10.1248/bpb.b18-00811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has revolutionized therapeutic gene editing by providing researchers with a new method to study and cure diseases previously considered untreatable. While the full range and power of CRISPR technology for therapeutics is being elucidated through in vitro studies, translation to in vivo studies is slow. To date there is no totally effective delivery strategy to carry CRISPR components to the target site in vivo. The complexity of in vivo delivery is furthered by the number of potential delivery methods, the different forms in which CRISPR can be delivered as a therapeutic, and the disease target and tissue type in question. There are major challenges and limitations to delivery strategies, and it is imperative that future directions are guided by well-conducted studies that consider the full effect these variables have on the eventual outcome. In this review we will discuss the advances of the latest in vivo CRISPR/Cas9 delivery strategies and highlight the challenges yet to be overcome.
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Affiliation(s)
- Yağız Anıl Çiçek
- Department of Chemistry, Middle East Technical University (METU)
| | | | - Jessica A Kretzmann
- Department of Chemistry, University of Massachusetts.,School of Molecular Sciences, The University of Western Australia
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446
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Zhong Z, Sretenovic S, Ren Q, Yang L, Bao Y, Qi C, Yuan M, He Y, Liu S, Liu X, Wang J, Huang L, Wang Y, Baby D, Wang D, Zhang T, Qi Y, Zhang Y. Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG. MOLECULAR PLANT 2019; 12:1027-1036. [PMID: 30928637 DOI: 10.1016/j.molp.2019.03.011] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/21/2019] [Accepted: 03/23/2019] [Indexed: 05/22/2023]
Abstract
Two recently engineered SpCas9 variants, namely xCas9 and Cas9-NG, show promising potential in improving targeting specificity and broadening the targeting range. In this study, we evaluated these Cas9 variants in the model and crop plant, rice. We first tested xCas9-3.7, the most effective xCas9 variant in mammalian cells, for targeted mutagenesis at 16 possible NGN PAM (protospacer adjacent motif) combinations in duplicates. xCas9 exhibited nearly equivalent editing efficiency to wild-type Cas9 (Cas9-WT) at most canonical NGG PAM sites tested, whereas it showed limited activity at non-canonical NGH (H = A, C, T) PAM sites. High editing efficiency of xCas9 at NGG PAMs was further demonstrated with C to T base editing by both rAPOBEC1 and PmCDA1 cytidine deaminases. With mismatched sgRNAs, we found that xCas9 had improved targeting specificity over the Cas9-WT. Furthermore, we tested two Cas9-NG variants, Cas9-NGv1 and Cas9-NG, for targeting NGN PAMs. Both Cas9-NG variants showed higher editing efficiency at most non-canonical NG PAM sites tested, and enabled much more efficient editing than xCas9 at AT-rich PAM sites such as GAT, GAA, and CAA. Nevertheless, we found that Cas9-NG variants showed significant reduced activity at the canonical NGG PAM sites. In stable transgenic rice lines, we demonstrated that Cas9-NG had much higher editing efficiency than Cas9-NGv1 and xCas9 at NG PAM sites. To expand the base-editing scope, we developed an efficient C to T base-editing system by making fusion of Cas9-NG nickase (D10A version), PmCDA1, and UGI. Taken together, our work benchmarked xCas9 as a high-fidelity nuclease for targeting canonical NGG PAMs and Cas9-NG as a preferred variant for targeting relaxed PAMs for plant genome editing.
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Affiliation(s)
- Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Lijia Yang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Caiyan Qi
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Mingzhu Yuan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Xiaopei Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Jiaheng Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Lan Huang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Yan Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Dibin Baby
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh 517507, India
| | - David Wang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Seven Lakes High School, Katy, TX 77494, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China.
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447
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Puig-Saus C, Ribas A. Gene editing: Towards the third generation of adoptive T-cell transfer therapies. IMMUNO-ONCOLOGY TECHNOLOGY 2019; 1:19-26. [PMID: 35755321 PMCID: PMC9216344 DOI: 10.1016/j.iotech.2019.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
First-generation adoptive T-cell transfer (ACT) administering tumor-infiltrating lymphocytes (TILs), and second-generation ACT using autologous T cells genetically modified to express tumor-specific T-cell receptors (TCRs) or chimeric antigen receptors (CARs) have both shown promise for the treatment of several cancers, including melanoma, leukemia and lymphoma. However, these treatments require labor-intensive manufacturing of the cell product for each patient, frequently utilize lentiviral or retroviral vectors to genetically modify the T cells, and have limited antitumor efficacy in solid tumors. Gene editing is revolutionizing the field of gene therapy, and ACT is at the forefront of this revolution. Gene-editing technologies can be used to re-engineer the phenotype of T cells to increase their antitumor potency, to generate off-the-shelf ACT products, and to replace endogenous TCRs with tumor-specific TCRs or CARs using homology-directed repair (HDR) donor templates. Adeno-associated viral vectors or linear DNA have been used as HDR donor templates. Of note, non-viral delivery substantially reduces the time required to generate clinical-grade reagents for manufacture of T-cell products—a critical step for the translation of personalized T-cell therapies. These technological advances in the field using gene editing open the door to the third generation of ACT therapies. CRISPR-Cas9 allows the generation of tumor-specific T cells for adoptive T-cell transfer (ACT). Gene editing allows generation of off-the-shelf ACT products. Gene editing can tailor T-cell phenotype and increase antitumor potency. Non-viral gene editing is a requirement for personalized ACT. Personalized third-generation ACT: gene-edited neoantigen-specific T cells.
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Affiliation(s)
- Cristina Puig-Saus
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, USA
| | - Antoni Ribas
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, USA.,Division of Surgical Oncology, Department of Surgery, UCLA, Los Angeles, USA.,Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, USA.,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, USA
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448
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De Luca M, Aiuti A, Cossu G, Parmar M, Pellegrini G, Robey PG. Advances in stem cell research and therapeutic development. Nat Cell Biol 2019; 21:801-811. [PMID: 31209293 DOI: 10.1038/s41556-019-0344-z] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/09/2019] [Indexed: 12/12/2022]
Abstract
Despite many reports of putative stem-cell-based treatments in genetic and degenerative disorders or severe injuries, the number of proven stem cell therapies has remained small. In this Review, we survey advances in stem cell research and describe the cell types that are currently being used in the clinic or are close to clinical trials. Finally, we analyse the scientific rationale, experimental approaches, caveats and results underpinning the clinical use of such stem cells.
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Affiliation(s)
- Michele De Luca
- Center for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Giulio Cossu
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund, Sweden.,Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Graziella Pellegrini
- Center for Regenerative Medicine "Stefano Ferrari", Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Pamela Gehron Robey
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
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449
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Abstract
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.
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450
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Schober K, Müller TR, Gökmen F, Grassmann S, Effenberger M, Poltorak M, Stemberger C, Schumann K, Roth TL, Marson A, Busch DH. Orthotopic replacement of T-cell receptor α- and β-chains with preservation of near-physiological T-cell function. Nat Biomed Eng 2019; 3:974-984. [DOI: 10.1038/s41551-019-0409-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 04/26/2019] [Indexed: 02/07/2023]
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