51
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Antao AM, Karapurkar JK, Lee DR, Kim KS, Ramakrishna S. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Comput Struct Biotechnol J 2020; 18:3649-3665. [PMID: 33304462 PMCID: PMC7710510 DOI: 10.1016/j.csbj.2020.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas systems are popular genome editing tools that belong to a class of programmable nucleases and have enabled tremendous progress in the field of regenerative medicine. We here outline the structural and molecular frameworks of the well-characterized type II CRISPR system and several computational tools intended to facilitate experimental designs. The use of CRISPR tools to generate disease models has advanced research into the molecular aspects of disease conditions, including unraveling the molecular basis of immune rejection. Advances in regenerative medicine have been hindered by major histocompatibility complex-human leukocyte antigen (HLA) genes, which pose a major barrier to cell- or tissue-based transplantation. Based on progress in CRISPR, including in recent clinical trials, we hypothesize that the generation of universal donor immune-engineered stem cells is now a realistic approach to tackling a multitude of disease conditions.
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Affiliation(s)
- Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | | | - Dong Ryul Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, South Korea.,CHA Stem Cell Institute, CHA University, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
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52
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Carlson-Stevermer J, Das A, Abdeen AA, Fiflis D, Grindel BI, Saxena S, Akcan T, Alam T, Kletzien H, Kohlenberg L, Goedland M, Dombroe MJ, Saha K. Design of efficacious somatic cell genome editing strategies for recessive and polygenic diseases. Nat Commun 2020; 11:6277. [PMID: 33293555 PMCID: PMC7722885 DOI: 10.1038/s41467-020-20065-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023] Open
Abstract
Compound heterozygous recessive or polygenic diseases could be addressed through gene correction of multiple alleles. However, targeting of multiple alleles using genome editors could lead to mixed genotypes and adverse events that amplify during tissue morphogenesis. Here we demonstrate that Cas9-ribonucleoprotein-based genome editors can correct two distinct mutant alleles within a single human cell precisely. Gene-corrected cells in an induced pluripotent stem cell model of Pompe disease expressed the corrected transcript from both corrected alleles, leading to enzymatic cross-correction of diseased cells. Using a quantitative in silico model for the in vivo delivery of genome editors into the developing human infant liver, we identify progenitor targeting, delivery efficiencies, and suppression of imprecise editing outcomes at the on-target site as key design parameters that control the efficacy of various therapeutic strategies. This work establishes that precise gene editing to correct multiple distinct gene variants could be highly efficacious if designed appropriately.
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Affiliation(s)
- Jared Carlson-Stevermer
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Amritava Das
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Amr A Abdeen
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - David Fiflis
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Benjamin I Grindel
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Shivani Saxena
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Tugce Akcan
- Department of Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Tausif Alam
- Department of Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Heidi Kletzien
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Lucille Kohlenberg
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Madelyn Goedland
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Micah J Dombroe
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Retina Research Foundation Kathryn and Latimer Murfee Chair, Madison, WI, USA.
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53
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Lau CH, Tin C, Suh Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Fac Rev 2020; 9:20. [PMID: 33659952 PMCID: PMC7886068 DOI: 10.12703/r/9-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
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54
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Marsh S, Hanson B, Wood MJA, Varela MA, Roberts TC. Application of CRISPR-Cas9-Mediated Genome Editing for the Treatment of Myotonic Dystrophy Type 1. Mol Ther 2020; 28:2527-2539. [PMID: 33171139 PMCID: PMC7704741 DOI: 10.1016/j.ymthe.2020.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/03/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a debilitating multisystemic disorder, caused by expansion of a CTG microsatellite repeat in the 3' untranslated region of the DMPK (dystrophia myotonica protein kinase) gene. To date, novel therapeutic approaches have focused on transient suppression of the mutant, repeat-expanded RNA. However, recent developments in the field of genome editing have raised the exciting possibility of inducing permanent correction of the DM1 genetic defect. Specifically, repurposing of the prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) system has enabled programmable, site-specific, and multiplex genome editing. CRISPR-based strategies for the treatment of DM1 can be applied either directly to patients, or indirectly through the ex vivo modification of patient-derived cells, and they include excision of the repeat expansion, insertion of synthetic polyadenylation signals upstream of the repeat, steric interference with RNA polymerase II procession through the repeat leading to transcriptional downregulation of DMPK, and direct RNA targeting of the mutant RNA species. Potential obstacles to such therapies are discussed, including the major challenge of Cas9 and guide RNA transgene/ribonuclear protein delivery, off-target gene editing, vector genome insertion at cut sites, on-target unintended mutagenesis (e.g., repeat inversion), pre-existing immunity to Cas9 or AAV antigens, immunogenicity, and Cas9 persistence.
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Affiliation(s)
- Seren Marsh
- University of Oxford Medical School, Medical Sciences Division, University of Oxford, Oxford OX3 9DU, UK
| | - Britt Hanson
- Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, UK; Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK; MDUK Oxford Neuromuscular Centre, UK
| | - Miguel A Varela
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
| | - Thomas C Roberts
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK; MDUK Oxford Neuromuscular Centre, UK.
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55
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Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing. Biochem Pharmacol 2020; 182:114195. [DOI: 10.1016/j.bcp.2020.114195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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56
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Gavande NS, VanderVere-Carozza PS, Pawelczak KS, Mendoza-Munoz P, Vernon TL, Hanakahi LA, Summerlin M, Dynlacht JR, Farmer AH, Sears CR, Nasrallah NA, Garrett J, Turchi JJ. Discovery and development of novel DNA-PK inhibitors by targeting the unique Ku-DNA interaction. Nucleic Acids Res 2020; 48:11536-11550. [PMID: 33119767 PMCID: PMC7672428 DOI: 10.1093/nar/gkaa934] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/02/2020] [Accepted: 10/09/2020] [Indexed: 01/05/2023] Open
Abstract
DNA-dependent protein kinase (DNA-PK) plays a critical role in the non-homologous end joining (NHEJ) repair pathway and the DNA damage response (DDR). DNA-PK has therefore been pursued for the development of anti-cancer therapeutics in combination with ionizing radiation (IR). We report the discovery of a new class of DNA-PK inhibitors that act via a novel mechanism of action, inhibition of the Ku-DNA interaction. We have developed a series of highly potent and specific Ku-DNA binding inhibitors (Ku-DBi's) that block the Ku-DNA interaction and inhibit DNA-PK kinase activity. Ku-DBi's directly interact with the Ku and inhibit in vitro NHEJ, cellular NHEJ, and potentiate the cellular activity of radiomimetic agents and IR. Analysis of Ku-null cells demonstrates that Ku-DBi's cellular activity is a direct result of Ku inhibition, as Ku-null cells are insensitive to Ku-DBi's. The utility of Ku-DBi's was also revealed in a CRISPR gene-editing model where we demonstrate that the efficiency of gene insertion events was increased in cells pre-treated with Ku-DBi's, consistent with inhibition of NHEJ and activation of homologous recombination to facilitate gene insertion. These data demonstrate the discovery and application of new series of compounds that modulate DNA repair pathways via a unique mechanism of action.
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Affiliation(s)
- Navnath S Gavande
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN 46202, USA
- Department of Pharmaceutical Sciences, Wayne State University College of Pharmacy and Health Sciences, Detroit, MI 48201, USA
| | | | | | - Pamela Mendoza-Munoz
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Tyler L Vernon
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Leslyn A Hanakahi
- Department of Biopharmaceutical Sciences, University of Illinois College of Pharmacy, Rockford, IL 61107, USA
| | - Matthew Summerlin
- Department of Biopharmaceutical Sciences, University of Illinois College of Pharmacy, Rockford, IL 61107, USA
| | - Joseph R Dynlacht
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Annabelle H Farmer
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Catherine R Sears
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Nawar Al Nasrallah
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Joy Garrett
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - John J Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN 46202, USA
- NERx Biosciences, 212 W 10th St. Suite A480, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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57
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Bashir S, Dang T, Rossius J, Wolf J, Kühn R. Enhancement of CRISPR-Cas9 induced precise gene editing by targeting histone H2A-K15 ubiquitination. BMC Biotechnol 2020; 20:57. [PMID: 33097066 PMCID: PMC7585302 DOI: 10.1186/s12896-020-00650-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Precise genetic modifications are preferred products of CRISPR-Cas9 mediated gene editing in mammalian cells but require the repair of induced double-strand breaks (DSB) through homology directed repair (HDR). Since HDR competes with the prevailing non-homologous end joining (NHEJ) pathway and depends on the presence of repair templates its efficiency is often limited and demands optimized methodology. RESULTS For the enhancement of HDR we redirect the DSB repair pathway choice by targeting the Ubiquitin mark for damaged chromatin at Histone H2A-K15. We used fusions of the Ubiquitin binding domain (UBD) of Rad18 or RNF169 with BRCA1 to promote HDR initiation and UBD fusions with DNA binding domains to attract donor templates and facilitate HDR processing. Using a traffic light reporter system in human HEK293 cells we found that the coexpression of both types of UBD fusion proteins promotes HDR, reduces NHEJ and shifts the HDR/NHEJ balance up to 6-fold. The HDR enhancing effect of UBD fusion proteins was confirmed at multiple endogenous loci. CONCLUSIONS Our findings provide a novel efficient approach to promote precise gene editing in human cells.
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Affiliation(s)
- Sanum Bashir
- Max-Delbrück-Centrum für Molekulare Medizin, 13125, Berlin, Germany
- Present Address: BioNTech Cell & Gene Therapies GmbH, Mainz, Germany
| | - Tu Dang
- Max-Delbrück-Centrum für Molekulare Medizin, 13125, Berlin, Germany
| | - Jana Rossius
- Max-Delbrück-Centrum für Molekulare Medizin, 13125, Berlin, Germany
| | - Johanna Wolf
- Present Address: Glycotope GmbH, 13125, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Centrum für Molekulare Medizin, 13125, Berlin, Germany.
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58
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Shin SW, Lee JS. CHO Cell Line Development and Engineering via Site-specific Integration: Challenges and Opportunities. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0093-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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59
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Yang H, Ren S, Yu S, Pan H, Li T, Ge S, Zhang J, Xia N. Methods Favoring Homology-Directed Repair Choice in Response to CRISPR/Cas9 Induced-Double Strand Breaks. Int J Mol Sci 2020; 21:E6461. [PMID: 32899704 PMCID: PMC7555059 DOI: 10.3390/ijms21186461] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 12/15/2022] Open
Abstract
Precise gene editing is-or will soon be-in clinical use for several diseases, and more applications are under development. The programmable nuclease Cas9, directed by a single-guide RNA (sgRNA), can introduce double-strand breaks (DSBs) in target sites of genomic DNA, which constitutes the initial step of gene editing using this novel technology. In mammals, two pathways dominate the repair of the DSBs-nonhomologous end joining (NHEJ) and homology-directed repair (HDR)-and the outcome of gene editing mainly depends on the choice between these two repair pathways. Although HDR is attractive for its high fidelity, the choice of repair pathway is biased in a biological context. Mammalian cells preferentially employ NHEJ over HDR through several mechanisms: NHEJ is active throughout the cell cycle, whereas HDR is restricted to S/G2 phases; NHEJ is faster than HDR; and NHEJ suppresses the HDR process. This suggests that definitive control of outcome of the programmed DNA lesioning could be achieved through manipulating the choice of cellular repair pathway. In this review, we summarize the DSB repair pathways, the mechanisms involved in choice selection based on DNA resection, and make progress in the research investigating strategies that favor Cas9-mediated HDR based on the manipulation of repair pathway choice to increase the frequency of HDR in mammalian cells. The remaining problems in improving HDR efficiency are also discussed. This review should facilitate the development of CRISPR/Cas9 technology to achieve more precise gene editing.
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Affiliation(s)
| | | | | | | | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Collaborative Innovation Centers of Biological Products, School of Public Health, Xiamen University, Xiamen 361102, China; (H.Y.); (S.R.); (S.Y.); (H.P.); (J.Z.); (N.X.)
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Collaborative Innovation Centers of Biological Products, School of Public Health, Xiamen University, Xiamen 361102, China; (H.Y.); (S.R.); (S.Y.); (H.P.); (J.Z.); (N.X.)
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60
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Modulation of DNA double-strand break repair as a strategy to improve precise genome editing. Oncogene 2020; 39:6393-6405. [PMID: 32884115 DOI: 10.1038/s41388-020-01445-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
In the present day, it is possible to incorporate targeted mutations or replace a gene using genome editing techniques such as customisable CRISPR/Cas9 system. Although induction of DNA double-strand breaks (DSBs) by genome editing tools can be repaired by both non-homologous end joining (NHEJ) and homologous recombination (HR), the skewness of the former pathway in human and other mammals normally result in imprecise repair. Scientists working at the crossroads of DNA repair and genome editing have devised new strategies for using a specific pathway to their advantage. Refinement in the efficiency of precise gene editing was witnessed upon downregulation of NHEJ by knockdown or using small molecule inhibitors on one hand, and upregulation of HR proteins and addition of HR stimulators, other hand. The exploitation of cell cycle phase differences together with appropriate donor DNA length/sequence and small molecules has provided further improvement in precise genome editing. The present article reviews the mechanisms of improving the efficiency of precise genome editing in several model organisms and in clinics.
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61
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Aulicino F, Capin J, Berger I. Synthetic Virus-Derived Nanosystems (SVNs) for Delivery and Precision Docking of Large Multifunctional DNA Circuitry in Mammalian Cells. Pharmaceutics 2020; 12:E759. [PMID: 32796680 PMCID: PMC7466058 DOI: 10.3390/pharmaceutics12080759] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 12/12/2022] Open
Abstract
DNA delivery is at the forefront of current research efforts in gene therapy and synthetic biology. Viral vectors have traditionally dominated the field; however, nonviral delivery systems are increasingly gaining traction. Baculoviruses are arthropod-specific viruses that can be easily engineered and repurposed to accommodate and deliver large sequences of exogenous DNA into mammalian cells, tissues, or ultimately organisms. These synthetic virus-derived nanosystems (SVNs) are safe, readily customized, and can be manufactured at scale. By implementing clustered regularly interspaced palindromic repeats (CRISPR) associated protein (CRISPR/Cas) modalities into this system, we developed SVNs capable of inserting complex DNAs into genomes, at base pair precision. We anticipate a major role for SVNs as an attractive alternative to viral vectors in accelerating genome engineering and gene therapy applications in the future.
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Affiliation(s)
- Francesco Aulicino
- Bristol Synthetic Biology Centre BrisSynBio, School of Biochemistry, 1 Tankard’s Close, University of Bristol, Bristol BS8 1TD, UK;
| | - Julien Capin
- Bristol Synthetic Biology Centre BrisSynBio, School of Biochemistry, 1 Tankard’s Close, University of Bristol, Bristol BS8 1TD, UK;
| | - Imre Berger
- Bristol Synthetic Biology Centre BrisSynBio, School of Biochemistry, 1 Tankard’s Close, University of Bristol, Bristol BS8 1TD, UK;
- Max Planck Bristol Centre for Minimal Biology, School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, UK
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62
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Gu B. Light up the embryos: knock-in reporter generation for mouse developmental biology. Anim Reprod 2020; 17:e20200055. [PMID: 33029220 PMCID: PMC7534580 DOI: 10.1590/1984-3143-ar2020-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Developmental biology seeks to understand the sophisticated regulated process through which a single cell – a fertilized egg – generates a highly organized organism. The most effective way to reveal the nature of these processes is to follow single cells and cell lineages in real-time. Recent advances in imaging equipment, fluorescent tags and computational tools have made long term multi-color imaging of cells and embryos possible. However, there is still one major challenging for achieving live imaging of mammalian embryos- the generation of embryos carrying reporters that recapitulate the endogenous expression pattern of marker genes. Recent developments of genome editing technology played important roles in enabling efficient generation of reporter mouse models. This mini review discusses recent developments of technologies for efficiently generate knock-in reporter mice and the application of these models in live imaging development. With these developments, we are starting to realize the long-sought promises of realtime analysis of mammalian development.
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Affiliation(s)
- Bin Gu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Canada.,Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Michigan, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, Michigan, USA
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63
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Zhang W, Chen Y, Yang J, Zhang J, Yu J, Wang M, Zhao X, Wei K, Wan X, Xu X, Jiang Y, Chen J, Gao S, Mao Z. A high-throughput small molecule screen identifies farrerol as a potentiator of CRISPR/Cas9-mediated genome editing. eLife 2020; 9:56008. [PMID: 32644042 PMCID: PMC7380943 DOI: 10.7554/elife.56008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022] Open
Abstract
Directly modulating the choice between homologous recombination (HR) and non-homologous end joining (NHEJ) - two independent pathways for repairing DNA double-strand breaks (DSBs) - has the potential to improve the efficiency of gene targeting by CRISPR/Cas9. Here, we have developed a rapid and easy-to-score screening approach for identifying small molecules that affect the choice between the two DSB repair pathways. Using this tool, we identified a small molecule, farrerol, that promotes HR but does not affect NHEJ. Further mechanistic studies indicate that farrerol functions through stimulating the recruitment of RAD51 to DSB sites. Importantly, we demonstrated that farrerol effectively promotes precise targeted integration in human cells, mouse cells and mouse embryos at multiple genomic loci. In addition, treating cells with farrerol did not have any obvious negative effect on genomic stability. Moreover, farrerol significantly improved the knock-in efficiency in blastocysts, and the subsequently generated knock-in mice retained the capacity for germline transmission.
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Affiliation(s)
- Weina Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yu Chen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiaqing Yang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jing Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiayu Yu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaodong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ke Wei
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaoping Wan
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaojun Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ying Jiang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Tsingtao Advanced Research Institute, Tongji University, Qingdao, China
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64
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Park H, Shin J, Choi H, Cho B, Kim J. Valproic Acid Significantly Improves CRISPR/Cas9-Mediated Gene Editing. Cells 2020; 9:cells9061447. [PMID: 32532133 PMCID: PMC7349485 DOI: 10.3390/cells9061447] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has emerged as a powerful technology, with the potential to generate transgenic animals. Particularly, efficient and precise genetic editing with CRISPR/Cas9 offers immense prospects in various biotechnological applications. Here, we report that the histone deacetylase inhibitor valproic acid (VPA) significantly increases the efficiency of CRISPR/Cas9-mediated gene editing in mouse embryonic stem cells and embryos. This effect may be caused through globally enhanced chromatin accessibility, as indicate by histone hyperacetylation. Taken together, our results suggest that VPA can be used to increase the efficacy of CRISPR/Cas9 in generating transgenic systems.
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Affiliation(s)
- Hanseul Park
- Department of Biomedical Engineering (BK21 Plus), Dongguk University, Seoul 04620, Korea; (H.P.); (J.S.); (H.C.); (B.C.)
- Laboratory of Cell reprogramming and Gene editing, Department of Chemistry, Dongguk University, Seoul 04620, Korea
| | - Jaein Shin
- Department of Biomedical Engineering (BK21 Plus), Dongguk University, Seoul 04620, Korea; (H.P.); (J.S.); (H.C.); (B.C.)
- Laboratory of Cell reprogramming and Gene editing, Department of Chemistry, Dongguk University, Seoul 04620, Korea
| | - Hwan Choi
- Department of Biomedical Engineering (BK21 Plus), Dongguk University, Seoul 04620, Korea; (H.P.); (J.S.); (H.C.); (B.C.)
- Laboratory of Cell reprogramming and Gene editing, Department of Chemistry, Dongguk University, Seoul 04620, Korea
| | - Byounggook Cho
- Department of Biomedical Engineering (BK21 Plus), Dongguk University, Seoul 04620, Korea; (H.P.); (J.S.); (H.C.); (B.C.)
- Laboratory of Cell reprogramming and Gene editing, Department of Chemistry, Dongguk University, Seoul 04620, Korea
| | - Jongpil Kim
- Department of Biomedical Engineering (BK21 Plus), Dongguk University, Seoul 04620, Korea; (H.P.); (J.S.); (H.C.); (B.C.)
- Laboratory of Cell reprogramming and Gene editing, Department of Chemistry, Dongguk University, Seoul 04620, Korea
- Correspondence: ; Tel.: +82-031-961-5153
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65
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Maurissen TL, Woltjen K. Synergistic gene editing in human iPS cells via cell cycle and DNA repair modulation. Nat Commun 2020; 11:2876. [PMID: 32513994 PMCID: PMC7280248 DOI: 10.1038/s41467-020-16643-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/13/2020] [Indexed: 01/08/2023] Open
Abstract
Precise gene editing aims at generating single-nucleotide modifications to correct or model human disease. However, precision editing with nucleases such as CRIPSR-Cas9 has seen limited success due to poor efficiency and limited practicality. Here, we establish a fluorescent DNA repair assay in human induced pluripotent stem (iPS) cells to visualize and quantify the frequency of DNA repair outcomes during monoallelic and biallelic targeting. We found that modulating both DNA repair and cell cycle phase via defined culture conditions and small molecules synergistically enhanced the frequency of homology-directed repair (HDR). Notably, targeting in homozygous reporter cells results in high levels of editing with a vast majority of biallelic HDR outcomes. We then leverage efficient biallelic HDR with mixed ssODN repair templates to generate heterozygous mutations. Synergistic gene editing represents an effective strategy to generate precise genetic modifications in human iPS cells. Precision editing with CRISPR-Cas9 often suffers from poor efficiency. Here the authors identify culture conditions and small molecules that synergize to promote homology-directed repair (HDR) in induced pluripotent stem (iPS) cells.
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Affiliation(s)
- Thomas L Maurissen
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.,Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
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66
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Yun Y, Ha Y. CRISPR/Cas9-Mediated Gene Correction to Understand ALS. Int J Mol Sci 2020; 21:E3801. [PMID: 32471232 PMCID: PMC7312396 DOI: 10.3390/ijms21113801] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by the death of motor neurons in the spinal cord and brainstem. ALS has a diverse genetic origin; at least 20 genes have been shown to be related to ALS. Most familial and sporadic cases of ALS are caused by variants of the SOD1, C9orf72, FUS, and TARDBP genes. Genome editing using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9) can provide insights into the underlying genetics and pathophysiology of ALS. By correcting common mutations associated with ALS in animal models and patient-derived induced pluripotent stem cells (iPSCs), CRISPR/Cas9 has been used to verify the effects of ALS-associated mutations and observe phenotype differences between patient-derived and gene-corrected iPSCs. This technology has also been used to create mutations to investigate the pathophysiology of ALS. Here, we review recent studies that have used CRISPR/Cas9 to understand the genetic underpinnings of ALS.
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Affiliation(s)
- Yeomin Yun
- Department of Neurosurgery, Spine and Spinal Cord Institute, College of Medicine, Yonsei University, Seoul 03722, Korea;
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul 03722, Korea
| | - Yoon Ha
- Department of Neurosurgery, Spine and Spinal Cord Institute, College of Medicine, Yonsei University, Seoul 03722, Korea;
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul 03722, Korea
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67
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High Homology-Directed Repair Using Mitosis Phase and Nucleus Localizing Signal. Int J Mol Sci 2020; 21:ijms21113747. [PMID: 32466470 PMCID: PMC7312558 DOI: 10.3390/ijms21113747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/24/2020] [Indexed: 12/26/2022] Open
Abstract
In homology-directed repair, mediated knock-in single-stranded oligodeoxynucleotides (ssODNs) can be used as a homologous template and present high efficiency, but there is still a need to improve efficiency. Previous studies have mainly focused on controlling double-stranded break size, ssODN stability, and the DNA repair cycle. Nevertheless, there is a lack of research on the correlation between the cell cycle and single-strand template repair (SSTR) efficiency. Here, we investigated the relationship between cell cycle and SSTR efficiency. We found higher SSTR efficiency during mitosis, especially in the metaphase and anaphase. A Cas9 protein with a nuclear localization signal (NLS) readily migrated to the nucleus; however, the nuclear envelope inhibited the nuclear import of many nucleotide templates. This seemed to result in non-homologous end joining (NHEJ) before the arrival of the homologous template. Thus, we assessed whether NLS-tagged ssODNs and free NLS peptides could circumvent problems posed by the nuclear envelope. NLS-tagging ssODNs enhanced SSTR and indel efficiency by 4-fold compared to the control. Our results suggest the following: (1) mitosis is the optimal phase for SSTR, (2) the donor template needs to be delivered to the nucleus before nuclease delivery, and (3) NLS-tagging ssODNs improve SSTR efficiency, especially high in mitosis.
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68
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Improving Precise CRISPR Genome Editing by Small Molecules: Is there a Magic Potion? Cells 2020; 9:cells9051318. [PMID: 32466303 PMCID: PMC7291049 DOI: 10.3390/cells9051318] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/01/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome editing has become a standard method in molecular biology, for the establishment of genetically modified cellular and animal models, for the identification and validation of drug targets in animals, and is heavily tested for use in gene therapy of humans. While the efficiency of CRISPR mediated gene targeting is much higher than of classical targeted mutagenesis, the efficiency of CRISPR genome editing to introduce defined changes into the genome is still low. Overcoming this problem will have a great impact on the use of CRISPR genome editing in academic and industrial research and the clinic. This review will present efforts to achieve this goal by small molecules, which modify the DNA repair mechanisms to facilitate the precise alteration of the genome.
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69
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Zhou Q, Zhang Y, Zou Y, Yin T, Yang J. Human embryo gene editing: God's scalpel or Pandora's box? Brief Funct Genomics 2020; 19:154-163. [PMID: 32101273 DOI: 10.1093/bfgp/elz025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 12/26/2022] Open
Abstract
Gene editing refers to the site-specific modification of the genome, which mainly focuses on basic research, model organism construction and treatment and prevention of disease. Since the first application of CRISPR/Cas9 on the human embryo genome in 2015, the controversy over embryo gene editing (abbreviated as EGE in the following text) has never stopped. At present, the main contradictions focus on (1) ideal application prospects and immature technologies; (2) scientific progress and ethical supervision; and (3) definition of reasonable application scope. In fact, whether the EGE is 'God's scalpel' or 'Pandora's box' depends on the maturity of the technology and ethical supervision. This non-systematic review included English articles in NCBI, technical documents from the Human Fertilization and Embryology Authority as well as reports in the media, which performed from 1980 to 2018 with the following search terms: 'gene editing, human embryo, sequence-specific nuclease (SSN) (CRISPR/Cas, TALENT, ZFN), ethical consideration, gene therapy.' Based on the research status of EGE, this paper summarizes the technical defects and ethical controversies, enumerates the optimization measures and looks forward to the application prospect, aimed at providing some suggestions for the development trend. We should regard the research and development of EGE optimistically, improve and innovate the technology boldly and apply its clinical practice carefully.
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Affiliation(s)
- Qi Zhou
- Department of Reproductive Center, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang, Wuhan, Hubei 430060, P.R. China
| | - Yan Zhang
- Department of Reproductive Center, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang, Wuhan, Hubei 430060, P.R. China
| | - Yujie Zou
- Department of Reproductive Center, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang, Wuhan, Hubei 430060, P.R. China
| | - Tailang Yin
- Department of Reproductive Center, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang, Wuhan, Hubei 430060, P.R. China
| | - Jing Yang
- Department of Reproductive Center, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang, Wuhan, Hubei 430060, P.R. China
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70
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Lamas‐Toranzo I, Martínez‐Moro A, O´Callaghan E, Millán‐Blanca G, Sánchez J, Lonergan P, Bermejo‐Álvarez P. RS-1 enhances CRISPR-mediated targeted knock-in in bovine embryos. Mol Reprod Dev 2020; 87:542-549. [PMID: 32227559 PMCID: PMC7496720 DOI: 10.1002/mrd.23341] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/08/2020] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Targeted knock-in (KI) can be achieved in embryos by clustered regularly interspaced short palindromic repeats (CRISPR)-assisted homology directed repair (HDR). However, HDR efficiency is constrained by the competition of nonhomologous end joining. The objective of this study was to explore whether CRISPR-assisted targeted KI rates can be improved in bovine embryos by exposure to the HDR enhancer RS-1. In vitro produced zygotes were injected with CRISPR components (300 ng/µl Cas9 messenger RNA and 100 ng/µl single guide RNA against a noncoding region) and a single-stranded DNA (ssDNA) repair template (100 ng/µl). ssDNA template contained a 6 bp XbaI site insert, allowing targeted KI detection by restriction analysis, flanked by 50 bp homology arms. Following microinjection, zygotes were exposed to 0, 3.75, or 7.5 µM RS-1 for 24 hr. No differences were noted between groups in terms of development or genome edition rates. However, targeted KI rates were doubled in the group exposed to 7.5 µM RS-1 compared to the others (52.8% vs. 25% and 23.1%, for 7.5, 0, and 3.75 µM, respectively). In conclusion, transient exposure to 7.5 µM RS-1 enhances targeted KI rates resulting in approximately half of the embryos containing the intended mutation, hence allowing direct KI generation in embryos.
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Affiliation(s)
| | - A. Martínez‐Moro
- Animal Reproduction DepartmentINIAMadridSpain
- ProcreatecMadridSpain
| | - E. O´Callaghan
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | | | - J.M. Sánchez
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | - P. Lonergan
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
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71
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Abstract
PURPOSE OF REVIEW We review the ways in which stem cells are used in psychiatric disease research, including the related advances in gene editing and directed cell differentiation. RECENT FINDINGS The recent development of induced pluripotent stem cell (iPSC) technologies has created new possibilities for the study of psychiatric disease. iPSCs can be derived from patients or controls and differentiated to an array of neuronal and non-neuronal cell types. Their genomes can be edited as desired, and they can be assessed for a variety of phenotypes. This makes them especially interesting for studying genetic variation, which is particularly useful today now that our knowledge on the genetics of psychiatric disease is quickly expanding. The recent advances in cell engineering have led to powerful new methods for studying psychiatric illness including schizophrenia, bipolar disorder, and autism. There is a wide array of possible applications as illustrated by the many examples from the literature, most of which are cited here.
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Affiliation(s)
- Debamitra Das
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyra Feuer
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marah Wahbeh
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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72
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Generation of New Isogenic Models of Huntington's Disease Using CRISPR-Cas9 Technology. Int J Mol Sci 2020; 21:ijms21051854. [PMID: 32182692 PMCID: PMC7084361 DOI: 10.3390/ijms21051854] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/17/2020] [Accepted: 03/05/2020] [Indexed: 01/12/2023] Open
Abstract
Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by the expansion of CAG repeats in exon 1 of the huntingtin gene (HTT). Despite its monogenic nature, HD pathogenesis is still not fully understood, and no effective therapy is available to patients. The development of new techniques such as genome engineering has generated new opportunities in the field of disease modeling and enabled the generation of isogenic models with the same genetic background. These models are very valuable for studying the pathogenesis of a disease and for drug screening. Here, we report the generation of a series of homozygous HEK 293T cell lines with different numbers of CAG repeats at the HTT locus and demonstrate their usefulness for testing therapeutic reagents. In addition, using the CRISPR-Cas9 system, we corrected the mutation in HD human induced pluripotent stem cells and generated a knock-out of the HTT gene, thus providing a comprehensive set of isogenic cell lines for HD investigation.
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73
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Hirotsune S, Kiyonari H, Jin M, Kumamoto K, Yoshida K, Shinohara M, Watanabe H, Wynshaw-Boris A, Matsuzaki F. Enhanced homologous recombination by the modulation of targeting vector ends. Sci Rep 2020; 10:2518. [PMID: 32054870 PMCID: PMC7018964 DOI: 10.1038/s41598-020-58893-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/11/2019] [Indexed: 11/17/2022] Open
Abstract
The field of genome editing was founded on the establishment of methods, such as the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR/Cas) system, used to target DNA double-strand breaks (DSBs). However, the efficiency of genome editing also largely depends on the endogenous cellular repair machinery. Here, we report that the specific modulation of targeting vectors to provide 3' overhangs at both ends increased the efficiency of homology-directed repair (HDR) in embryonic stem cells. We applied the modulated targeting vectors to produce homologous recombinant mice directly by pronuclear injection, but the frequency of HDR was low. Furthermore, we combined our method with the CRISPR/Cas9 system, resulting in a significant increase in HDR frequency. Thus, our HDR-based method, enhanced homologous recombination for genome targeting (eHOT), is a new and powerful method for genome engineering.
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Affiliation(s)
- Shinji Hirotsune
- Department of Genetic Disease Research, Osaka City University, Graduate School of Medicine, Asahi-machi 1-4-3, Abeno, Osaka, 545-8585, Japan.
| | - Hiroshi Kiyonari
- Animal Resource Development Unit, Genetic Engineering Team, Division of Bio-Function Dynamics Imaging, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
| | - Mingyue Jin
- Department of Genetic Disease Research, Osaka City University, Graduate School of Medicine, Asahi-machi 1-4-3, Abeno, Osaka, 545-8585, Japan
| | - Kanako Kumamoto
- Department of Genetic Disease Research, Osaka City University, Graduate School of Medicine, Asahi-machi 1-4-3, Abeno, Osaka, 545-8585, Japan
| | - Kayo Yoshida
- Laboratory Animal Science, Osaka City University, Graduate School of Medicine, Asahi-machi 1-4-3, Abeno, Osaka, 545-8585, Japan
| | - Miki Shinohara
- Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Faculty of Agriculture, Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara-city, Nara, 631-8505, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Anthony Wynshaw-Boris
- Department of Genetics and Genome Sciences, Case Western Reserve University, School of Medicine, University Hospitals Case Medical Center 10900 Euclid Avenue, BRB731, Cleveland, Ohio, 44106-4955, USA
| | - Fumio Matsuzaki
- RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
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74
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Skryabin BV, Kummerfeld DM, Gubar L, Seeger B, Kaiser H, Stegemann A, Roth J, Meuth SG, Pavenstädt H, Sherwood J, Pap T, Wedlich-Söldner R, Sunderkötter C, Schwartz YB, Brosius J, Rozhdestvensky TS. Pervasive head-to-tail insertions of DNA templates mask desired CRISPR-Cas9-mediated genome editing events. SCIENCE ADVANCES 2020; 6:eaax2941. [PMID: 32095517 PMCID: PMC7015686 DOI: 10.1126/sciadv.aax2941] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 11/25/2019] [Indexed: 02/05/2023]
Abstract
CRISPR-Cas9-mediated homology-directed DNA repair is the method of choice for precise gene editing in a wide range of model organisms, including mouse and human. Broad use by the biomedical community refined the method, making it more efficient and sequence specific. Nevertheless, the rapidly evolving technique still contains pitfalls. During the generation of six different conditional knockout mouse models, we discovered that frequently (sometimes solely) homology-directed repair and/or nonhomologous end joining mechanisms caused multiple unwanted head-to-tail insertions of donor DNA templates. Disturbingly, conventionally applied PCR analysis, in most cases, failed to identify these multiple integration events, which led to a high rate of falsely claimed precisely edited alleles. We caution that comprehensive analysis of modified alleles is essential and offer practical solutions to correctly identify precisely edited chromosomes.
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Affiliation(s)
- Boris V Skryabin
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Delf-Magnus Kummerfeld
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Leonid Gubar
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Birte Seeger
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Helena Kaiser
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Anja Stegemann
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Johannes Roth
- Institute of Immunology, University Hospital Muenster, Muenster, Germany
| | - Sven G Meuth
- Clinic of Neurology with Institute of Translational Neurology, University Hospital Muenster, Muenster, Germany
| | | | - Joanna Sherwood
- Institute of Experimental Musculoskeletal Medicine (IMM), University Hospital Muenster, Muenster, Germany
| | - Thomas Pap
- Institute of Experimental Musculoskeletal Medicine (IMM), University Hospital Muenster, Muenster, Germany
| | | | - Cord Sunderkötter
- Department of Dermatology and Venereology, University Hospital Halle, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Juergen Brosius
- Institute of Experimental Pathology (ZMBE), University of Muenster, Muenster, Germany.,Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Timofey S Rozhdestvensky
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Muenster, Germany
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75
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TIRR: a potential front runner in HDR race−hypotheses and perspectives. Mol Biol Rep 2020; 47:2371-2379. [DOI: 10.1007/s11033-020-05285-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/27/2020] [Indexed: 01/01/2023]
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76
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Embryo-Based Large Fragment Knock-in in Mammals: Why, How and What's Next. Genes (Basel) 2020; 11:genes11020140. [PMID: 32013077 PMCID: PMC7073597 DOI: 10.3390/genes11020140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 02/08/2023] Open
Abstract
Endonuclease-mediated genome editing technologies, most notably CRISPR/Cas9, have revolutionized animal genetics by allowing for precise genome editing directly through embryo manipulations. As endonuclease-mediated model generation became commonplace, large fragment knock-in remained one of the most challenging types of genetic modification. Due to their unique value in biological and biomedical research, however, a diverse range of technological innovations have been developed to achieve efficient large fragment knock-in in mammalian animal model generation, with a particular focus on mice. Here, we first discuss some examples that illustrate the importance of large fragment knock-in animal models and then detail a subset of the recent technological advancements that have allowed for efficient large fragment knock-in. Finally, we envision the future development of even larger fragment knock-ins performed in even larger animal models, the next step in expanding the potential of large fragment knock-in in animal models.
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77
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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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78
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Viner-Breuer R, Yilmaz A, Benvenisty N, Goldberg M. The essentiality landscape of cell cycle related genes in human pluripotent and cancer cells. Cell Div 2020; 14:15. [PMID: 31889988 PMCID: PMC6927170 DOI: 10.1186/s13008-019-0058-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022] Open
Abstract
Background Cell cycle regulation is a complex system consisting of growth-promoting and growth-restricting mechanisms, whose coordinated activity is vital for proper division and propagation. Alterations in this regulation may lead to uncontrolled proliferation and genomic instability, triggering carcinogenesis. Here, we conducted a comprehensive bioinformatic analysis of cell cycle-related genes using data from CRISPR/Cas9 loss-of-function screens performed in four cancer cell lines and in human embryonic stem cells (hESCs). Results Cell cycle genes, and in particular S phase and checkpoint genes, are highly essential for the growth of cancer and pluripotent cells. However, checkpoint genes are also found to underlie the differences between the cell cycle features of these cell types. Interestingly, while growth-promoting cell cycle genes overlap considerably between cancer and stem cells, growth-restricting cell cycle genes are completely distinct. Moreover, growth-restricting genes are consistently less frequent in cancer cells than in hESCs. Here we show that most of these genes are regulated by the tumor suppressor gene TP53, which is mutated in most cancer cells. Therefore, the growth-restriction system in cancer cells lacks important factors and does not function properly. Intriguingly, M phase genes are specifically essential for the growth of hESCs and are highly abundant among hESC-enriched genes. Conclusions Our results highlight the differences in cell cycle regulation between cell types and emphasize the importance of conducting cell cycle studies in cells with intact genomes, in order to obtain an authentic representation of the genetic features of the cell cycle.
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Affiliation(s)
- Ruth Viner-Breuer
- 1The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Givat-Ram, 9190401 Jerusalem, Israel.,2Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, 9190401 Jerusalem, Israel
| | - Atilgan Yilmaz
- 1The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Givat-Ram, 9190401 Jerusalem, Israel.,2Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, 9190401 Jerusalem, Israel
| | - Nissim Benvenisty
- 1The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Givat-Ram, 9190401 Jerusalem, Israel.,2Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, 9190401 Jerusalem, Israel
| | - Michal Goldberg
- 2Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, 9190401 Jerusalem, Israel
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79
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Banan M. Recent advances in CRISPR/Cas9-mediated knock-ins in mammalian cells. J Biotechnol 2020; 308:1-9. [DOI: 10.1016/j.jbiotec.2019.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 12/16/2022]
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80
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Li Z, Cai Z, Fu W, Liu Y, Tian C, Wang H, Fu T, Wu Z, Wu D, Jin Y, Cheng Z, Terada N, Liu L, Wu W, Jin S, Bai F. High-efficiency protein delivery into transfection-recalcitrant cell types. Biotechnol Bioeng 2019; 117:816-831. [PMID: 31814110 DOI: 10.1002/bit.27245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/14/2019] [Accepted: 11/30/2019] [Indexed: 12/15/2022]
Abstract
Intracellular delivery of functional proteins is of great interest for basic biological research as well as for clinical applications. Transfection is the most commonly used method, however, it is not applicable to large-scale manipulation and inefficient in important cell types implicated in biomedical applications, such as epithelial, immune and pluripotent stem cells. In this study, we explored a bacterial type III secretion system (Bac-T3SS)-mediated proteofection method to overcome these limitations. An attenuated Pseudomonas aeruginosa vector was constructed, which has features of low toxicity, high T3SS activity, and self-limiting growth. Compared to the method of transfection, the Bac-T3SS showed significantly higher efficiencies of Cre recombinase translocation and target site recombination for hard-to-transfect human cell lines. Furthermore, through the delivery of β-lactamase in live animals, we demonstrated the feasibility and biosafety of in vivo application of the Bac-T3SS. This study provided an efficient and low-cost proteofection strategy for laboratory use as well as for application in large-scale cell manipulations.
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Affiliation(s)
- Zhenpeng Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Zeqiong Cai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Weixin Fu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenglei Tian
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - He Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Tongtong Fu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhenzhou Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Donghai Wu
- Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Naohiro Terada
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Shouguang Jin
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
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81
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Advances in genome editing through control of DNA repair pathways. Nat Cell Biol 2019; 21:1468-1478. [PMID: 31792376 DOI: 10.1038/s41556-019-0425-z] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
Eukaryotic cells deploy overlapping repair pathways to resolve DNA damage. Advancements in genome editing take advantage of these pathways to produce permanent genetic changes. Despite recent improvements, genome editing can produce diverse outcomes that can introduce risks in clinical applications. Although homology-directed repair is attractive for its ability to encode precise edits, it is particularly difficult in human cells. Here we discuss the DNA repair pathways that underlie genome editing and strategies to favour various outcomes.
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82
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Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM, Reddy ST. Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells. MAbs 2019; 11:1367-1380. [PMID: 31478465 PMCID: PMC6816377 DOI: 10.1080/19420862.2019.1662691] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in cellular engineering enabled by CRISPR-Cas9 genome editing have made it possible to expand the use of mammalian cells in biotechnological applications. Here, we describe an antibody engineering and screening approach where complete variable light (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, we are able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, we could isolate a diverse panel of >40 unique antigen-binding variants. Additionally, we successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | | | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
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83
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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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84
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Abstract
The evolution of genome editing technology based on CRISPR (clustered regularly interspaced short palindromic repeats) system has led to a paradigm shift in biological research. CRISPR/Cas9-guide RNA complexes enable rapid and efficient genome editing in mammalian cells. This system induces double-stranded DNA breaks (DSBs) at target sites and most DNA breakages induce mutations as small insertions or deletions (indels) by non-homologous end joining (NHEJ) repair pathway. However, for more precise correction as knock-in or replacement of DNA base pairs, using the homology-directed repair (HDR) pathway is essential. Until now, many trials have greatly enhanced knock-in or substitution efficiency by increasing HDR efficiency, or newly developed methods such as Base Editors (BEs). However, accuracy remains unsatisfactory. In this review, we summarize studies to overcome the limitations of HDR using the CRISPR system and discuss future direction.
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Affiliation(s)
- Seuk-Min Ryu
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Junseok W Hur
- Department of Neurosurgery, Korea University College of Medicine, Seoul 02841, Korea
| | - Kyoungmi Kim
- Department of Biomedical Sciences and Department of Physiology, Korea University College of Medicine, Seoul 02841, Korea
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85
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Bollen Y, Post J, Koo BK, Snippert HJG. How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing. Nucleic Acids Res 2019; 46:6435-6454. [PMID: 29955892 PMCID: PMC6061873 DOI: 10.1093/nar/gky571] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022] Open
Abstract
Model systems with defined genetic modifications are powerful tools for basic research and translational disease modelling. Fortunately, generating state-of-the-art genetic model systems is becoming more accessible to non-geneticists due to advances in genome editing technologies. As a consequence, solely relying on (transient) overexpression of (mutant) effector proteins is no longer recommended since scientific standards increasingly demand genetic modification of endogenous loci. In this review, we provide up-to-date guidelines with respect to homology-directed repair (HDR)-mediated editing of mammalian model systems, aimed at assisting researchers in designing an efficient genome editing strategy.
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Affiliation(s)
- Yannik Bollen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands.,Medical Cell BioPhysics, MIRA Institute, University of Twente, Enschede, The Netherlands
| | - Jasmin Post
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
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86
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Rozov SM, Permyakova NV, Deineko EV. The Problem of the Low Rates of CRISPR/Cas9-Mediated Knock-ins in Plants: Approaches and Solutions. Int J Mol Sci 2019; 20:E3371. [PMID: 31323994 PMCID: PMC6651222 DOI: 10.3390/ijms20133371] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
The main number of genome editing events in plant objects obtained during the last decade with the help of specific nucleases zinc finger (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas are the microindels causing frameshift and subsequent gene knock-out. The knock-ins of genes or their parts, i.e., the insertion of them into a target genome region, are between one and two orders of magnitude less frequent. First and foremost, this is associated with the specific features of the repair systems of higher eukaryotes and the availability of the donor template in accessible proximity during double-strand break (DSB) repair. This review briefs the main repair pathways in plants according to the aspect of their involvement in genome editing. The main methods for increasing the frequency of knock-ins are summarized both along the homologous recombination pathway and non-homologous end joining, which can be used for plant objects.
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Affiliation(s)
- Serge M Rozov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Natalya V Permyakova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Deineko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Plant Physiology and Biotechnology, Tomsk State University, Tomsk 634050, Russia
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87
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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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88
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Aksoy YA, Nguyen DT, Chow S, Chung RS, Guillemin GJ, Cole NJ, Hesselson D. Chemical reprogramming enhances homology-directed genome editing in zebrafish embryos. Commun Biol 2019; 2:198. [PMID: 31149642 PMCID: PMC6533270 DOI: 10.1038/s42003-019-0444-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/15/2019] [Indexed: 12/26/2022] Open
Abstract
Precise genome editing is limited by the inefficiency of homology-directed repair (HDR) compared to the non-homologous end-joining (NHEJ) of double strand breaks (DSBs). The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 system generates precise, locus-specific DSBs that can serve as substrates for HDR. We developed an in vivo visual reporter assay to quantify HDR-mediated events at single-cell resolution in zebrafish and used this system to identify small-molecule modulators that shift the DNA repair equilibrium in favor of HDR. By further optimizing the reaction environment and repair template, we achieved dramatic enhancement of HDR-mediated repair efficiency in zebrafish. Accordingly, under optimized conditions, inhibition of NHEJ with NU7441 enhanced HDR-mediated repair up to 13.4-fold. Importantly, we demonstrate that the increase in somatic HDR events correlates directly with germline transmission, permitting the efficient recovery of large seamlessly integrated DNA fragments in zebrafish.
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Affiliation(s)
- Yagiz A. Aksoy
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW Australia
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - David T. Nguyen
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Sharron Chow
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Roger S. Chung
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Gilles J. Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Nicholas J. Cole
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Daniel Hesselson
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW Australia
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89
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Tran NT, Bashir S, Li X, Rossius J, Chu VT, Rajewsky K, Kühn R. Enhancement of Precise Gene Editing by the Association of Cas9 With Homologous Recombination Factors. Front Genet 2019; 10:365. [PMID: 31114605 PMCID: PMC6503098 DOI: 10.3389/fgene.2019.00365] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/05/2019] [Indexed: 12/27/2022] Open
Abstract
The CRISPR-Cas9 system is used for genome editing in mammalian cells by introducing double-strand breaks (DSBs) which are predominantly repaired via non-homologous end joining (NHEJ) or to lesser extent by homology-directed repair (HDR). To enhance HDR for improving the introduction of precise genetic modifications, we tested fusion proteins of Cas9 nuclease with HDR effectors to enforce their localization at DSBs. Using a traffic-light DSB repair reporter (TLR) system for the quantitative detection of HDR and NHEJ events in human HEK cells we found that Cas9 fusions with CtIP, Rad52, and Mre11, but not Rad51C promote HDR up to twofold in human cells and significantly reduce NHEJ events. We further compared, as an alternative to the direct fusion with Cas9, two components configurations that associate CtIP fusion proteins with a Cas9-SunTag fusion or with guide RNA that includes MS2 binding loops. We found that the Cas9-CtIP fusion and the MS2-CtIP system, but not the SunTag approach increase the ratio of HDR/NHEJ 4.5-6-fold. Optimal results are obtained by the combined use of Cas9-CtIP and MS2-CtIP, shifting the HDR/NHEJ ratio by a factor of 14.9. Thus, our findings provide a simple and effective tool to promote precise gene modifications in mammalian cells.
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Affiliation(s)
- Ngoc-Tung Tran
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Sanum Bashir
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Xun Li
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Jana Rossius
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Van Trung Chu
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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90
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Mani C, Reddy PH, Palle K. DNA repair fidelity in stem cell maintenance, health, and disease. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165444. [PMID: 30953688 DOI: 10.1016/j.bbadis.2019.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/13/2022]
Abstract
Stem cells are a sub population of cell types that form the foundation of our body, and have the potential to replicate, replenish and repair limitlessly to maintain the tissue and organ homeostasis. Increased lifetime and frequent replication set them vulnerable for both exogenous and endogenous agents-induced DNA damage compared to normal cells. To counter these damages and preserve genetic information, stem cells have evolved with various DNA damage response and repair mechanisms. Furthermore, upon experiencing irreparable DNA damage, stem cells mostly prefer early senescence or apoptosis to avoid the accumulation of damages. However, the failure of these mechanisms leads to various diseases, including cancer. Especially, given the importance of stem cells in early development, DNA repair deficiency in stem cells leads to various disabilities like developmental delay, premature aging, sensitivity to DNA damaging agents, degenerative diseases, etc. In this review, we have summarized the recent update about how DNA repair mechanisms are regulated in stem cells and their association with disease progression and pathogenesis.
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Affiliation(s)
- Chinnadurai Mani
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, TX 79430, United States of America
| | - P Hemachandra Reddy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, TX 79430, United States of America
| | - Komaraiah Palle
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, TX 79430, United States of America.
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91
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Huang TK, Puchta H. CRISPR/Cas-mediated gene targeting in plants: finally a turn for the better for homologous recombination. PLANT CELL REPORTS 2019; 38:443-453. [PMID: 30673818 DOI: 10.1007/s00299-019-02379-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/09/2019] [Indexed: 05/22/2023]
Abstract
We summarize recent progress of CRISPR/Cas9-mediated gene targeting in plants, provide recommendations for designing gene-targeting vectors and highlight the potential of new technologies applicable to plants. Gene targeting (GT) is a tool of urgent need for plant biotechnology and breeding. It is based on homologous recombination that is able to precisely introduce desired modifications within a target locus. However, its low efficiency in higher plants is a major barrier for its application. Using site-specific nucleases, such as the recent CRISPR/Cas system, GT has become applicable in plants, via the induction of double-strand breaks, although still at a too low efficiency for most practical applications in crops. Recently, a variety of promising new improvements regarding the efficiency of GT has been reported by several groups. It turns out that GT can be enhanced by cell-type-specific expression of Cas nucleases, by the use of self-amplified GT-vector DNA or by manipulation of DNA repair pathways. Here, we highlight the most recent progress of GT in plants. Moreover, we provide suggestions on how to use the technology efficiently, based on the mechanisms of DNA repair, and highlight several of the newest GT strategies in yeast or mammals that are potentially applicable to plants. Using the full potential of GT technology will definitely help us pave the way in enhancing crop yields and food safety for an ecologically friendly agriculture.
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Affiliation(s)
- Teng-Kuei Huang
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany.
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92
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Li G, Zhang X, Ou H, Wang H, Liu D, Yang H, Wu Z. PIK-75 promotes homology-directed DNA repair. J Genet Genomics 2019; 46:141-144. [PMID: 30935856 DOI: 10.1016/j.jgg.2019.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/19/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Guoling Li
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xianwei Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Ou
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Haoqiang Wang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Huaqiang Yang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhenfang Wu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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93
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Nasri M, Mir P, Dannenmann B, Amend D, Skroblyn T, Xu Y, Schulze-Osthoff K, Klimiankou M, Welte K, Skokowa J. Fluorescent labeling of CRISPR/Cas9 RNP for gene knockout in HSPCs and iPSCs reveals an essential role for GADD45b in stress response. Blood Adv 2019; 3:63-71. [PMID: 30622144 PMCID: PMC6325296 DOI: 10.1182/bloodadvances.2017015511] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
CRISPR/Cas9-mediated gene editing of stem cells and primary cell types has several limitations for clinical applications. The direct delivery of ribonucleoprotein (RNP) complexes consisting of Cas9 nuclease and guide RNA (gRNA) has improved DNA- and virus-free gene modifications, but it does not enable the essential enrichment of the gene-edited cells. Here, we established a protocol for the fluorescent labeling and delivery of CRISPR/Cas9-gRNA RNP in primary human hematopoietic stem and progenitor cells (HSPCs) and induced pluripotent stem cells (iPSCs). As a proof of principle for genes with low-abundance transcripts and context-dependent inducible expression, we successfully deleted growth arrest and DNA-damage-inducible β (GADD45B). We found that GADD45B is indispensable for DNA damage protection and survival in stem cells. Thus, we describe an easy and efficient protocol of DNA-free gene editing of hard-to-target transcripts and enrichment of gene-modified cells that are generally difficult to transfect.
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Affiliation(s)
- Masoud Nasri
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
| | - Perihan Mir
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Benjamin Dannenmann
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
| | - Diana Amend
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
| | - Tessa Skroblyn
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Yun Xu
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
| | - Klaus Schulze-Osthoff
- German Cancer Research Center, Heidelberg, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, Tübingen, Germany; and
| | - Maksim Klimiankou
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
| | - Karl Welte
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
- University Children's Hospital Tübingen, Tübingen, Germany
| | - Julia Skokowa
- Department of Oncology, Hematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
- German Cancer Research Center, Heidelberg, Germany
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94
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Liu M, Rehman S, Tang X, Gu K, Fan Q, Chen D, Ma W. Methodologies for Improving HDR Efficiency. Front Genet 2019; 9:691. [PMID: 30687381 PMCID: PMC6338032 DOI: 10.3389/fgene.2018.00691] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/11/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is a precise genome manipulating technology that can be programmed to induce double-strand break (DSB) in the genome wherever needed. After nuclease cleavage, DSBs can be repaired by non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathway. For producing targeted gene knock-in or other specific mutations, DSBs should be repaired by the HDR pathway. While NHEJ can cause various length insertions/deletion mutations (indels), which can lead the targeted gene to lose its function by shifting the open reading frame (ORF). Furthermore, HDR has low efficiency compared with the NHEJ pathway. In order to modify the gene precisely, numerous methods arose by inhibiting NHEJ or enhancing HDR, such as chemical modulation, synchronized expression, and overlapping homology arm. Here we focus on the efficiency and other considerations of these methodologies.
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Affiliation(s)
- Mingjie Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Saad Rehman
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xidian Tang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Kui Gu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Qinlei Fan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Wentao Ma
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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95
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Gridina ММ. Improvement of the knock-in effciency in the genome of human induced pluripotent stem cells using the CRISPR/Cas9 system. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj18.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human induced pluripotent stem (hiPS) cells are a powerful tool for biomedical research. The ability to create patient-specifc pluripotent cells and their subsequent differentiation into any somatic cell type makes hiPS cells a valuable object for creating in vitro models of human diseases, screening drugs and a future source of cells for regenerative medicine. To realize entirely a potential of hiPScells, effective and precise methods for their genome editing are needed. The CRISPR/Cas9 system is the most widely used method for introducing site-specifc double-stranded breaks into DNA. It allows genes of interest to be knocked out with high efciency. However, knock-in into the target site of the genome is a much more difcult task. Moreover, many researchers have noted a low efciency of introducing target constructs into the hiPS cells’ genome. In this review, I attempt to describe the currently known information regarding the matter of increasing efciency of targeted insertions into hiPS cells’ genome. Here I will describe the most effective strategies for designing the donor template for homology-directed repair, methods to manipulate the double-strand break repair pathways introduced by a nuclease, including control of CRISPR/Cas9 delivery time. A low survival rate of hiPS cells following genome editing experiments is another difculty on the way towards successful knock-in, and here several highly effective approaches addressing it are proposed. Finally, I describe the most promising strategies, one-step reprogramming and genome editing, which allows gene-modifed integration-free hiPS cells to be efciently generated directly from somatic cells.
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96
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Yumlu S, Bashir S, Stumm J, Kühn R. Efficient Gene Editing of Human Induced Pluripotent Stem Cells Using CRISPR/Cas9. Methods Mol Biol 2019; 1961:137-151. [PMID: 30912045 DOI: 10.1007/978-1-4939-9170-9_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The generation of targeted mutants is a crucial step toward studying the biomedical effect of genes of interest. The generation of such mutants in human induced pluripotent stem cells (iPSCs) is of an utmost importance as these cells carry the potential to be differentiated into any cell lineage. Using the CRISPR/Cas9 nuclease system for induction of targeted double-strand breaks, gene editing of target loci in iPSCs can be achieved with high efficiency. This chapter covers protocols for the preparation of reagents to target loci of interest, the transfection, and for the genotyping of single cell-derived iPSC clones. Furthermore, we provide a protocol for the convenient generation of plasmids enabling multiplex gene targeting.
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Affiliation(s)
- Saniye Yumlu
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Sanum Bashir
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Jürgen Stumm
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany.
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97
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Yiangou L, Grandy RA, Morell CM, Tomaz RA, Osnato A, Kadiwala J, Muraro D, Garcia-Bernardo J, Nakanoh S, Bernard WG, Ortmann D, McCarthy DJ, Simonic I, Sinha S, Vallier L. Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics. Stem Cell Reports 2018; 12:165-179. [PMID: 30595546 PMCID: PMC6335580 DOI: 10.1016/j.stemcr.2018.11.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/08/2023] Open
Abstract
Cell cycle progression and cell fate decisions are closely linked in human pluripotent stem cells (hPSCs). However, the study of these interplays at the molecular level remains challenging due to the lack of efficient methods allowing cell cycle synchronization of large quantities of cells. Here, we screened inhibitors of cell cycle progression and identified nocodazole as the most efficient small molecule to synchronize hPSCs in the G2/M phase. Following nocodazole treatment, hPSCs remain pluripotent, retain a normal karyotype and can successfully differentiate into the three germ layers and functional cell types. Moreover, genome-wide transcriptomic analyses on single cells synchronized for their cell cycle and differentiated toward the endoderm lineage validated our findings and showed that nocodazole treatment has no effect on gene expression during the differentiation process. Thus, our synchronization method provides a robust approach to study cell cycle mechanisms in hPSCs. Nocodazole can enrich cells in the G2/M, G1, and S phases of the cell cycle Treatment with nocodazole does not affect pluripotency maintenance hPSCs can efficiently form functional cell types after nocodazole treatment Nocodazole treatment allows genome-wide analyses of synchronous populations
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Affiliation(s)
- Loukia Yiangou
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Rodrigo A Grandy
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Carola M Morell
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rute A Tomaz
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Anna Osnato
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Juned Kadiwala
- Cambridge NIHR Biomedical Research Centre hIPSC Core Facility, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Daniele Muraro
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Shota Nakanoh
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Division of Embryology, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - William G Bernard
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Daniel Ortmann
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Davis J McCarthy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK; St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Ingrid Simonic
- Medical Genetics Laboratories, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK
| | - Sanjay Sinha
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
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98
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Devkota S. The road less traveled: strategies to enhance the frequency of homology-directed repair (HDR) for increased efficiency of CRISPR/Cas-mediated transgenesis. BMB Rep 2018. [PMID: 30103848 PMCID: PMC6177507 DOI: 10.5483/bmbrep.2018.51.9.187] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Non-homologous end joining (NHEJ), and to a lesser extent, the error-free pathway known as homology-directed repair (HDR) are cellular mechanisms for recovery from double-strand DNA breaks (DSB) induced by RNA-guided programmable nuclease CRISPR/Cas. Since NHEJ is equivalent to using a duck tape to stick two pieces of metals together, the outcome of this repair mechanism is prone to error. Any out-of-frame mutations or premature stop codons resulting from NHEJ repair mechanism are extremely handy for loss-of-function studies. Substitution of a mutation on the genome with the correct exogenous repair DNA requires coordination via an error-free HDR, for targeted transgenesis. However, several practical limitations exist in harnessing the potential of HDR to replace a faulty mutation for therapeutic purposes in all cell types and more so in somatic cells. In germ cells after the DSB, copying occurs from the homologous chromosome, which increases the chances of incorporation of exogenous DNA with some degree of homology into the genome compared with somatic cells where copying from the identical sister chromatid is always preferred. This review summarizes several strategies that have been implemented to increase the frequency of HDR with a focus on somatic cells. It also highlights the limitations of this technology in gene therapy and suggests specific solutions to circumvent those barriers.
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Affiliation(s)
- Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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99
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Lomova A, Clark DN, Campo-Fernandez B, Flores-Bjurström C, Kaufman ML, Fitz-Gibbon S, Wang X, Miyahira EY, Brown D, DeWitt MA, Corn JE, Hollis RP, Romero Z, Kohn DB. Improving Gene Editing Outcomes in Human Hematopoietic Stem and Progenitor Cells by Temporal Control of DNA Repair. Stem Cells 2018; 37:284-294. [PMID: 30372555 DOI: 10.1002/stem.2935] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated system (Cas9)-mediated gene editing of human hematopoietic stem cells (hHSCs) is a promising strategy for the treatment of genetic blood diseases through site-specific correction of identified causal mutations. However, clinical translation is hindered by low ratio of precise gene modification using the corrective donor template (homology-directed repair, HDR) to gene disruption (nonhomologous end joining, NHEJ) in hHSCs. By using a modified version of Cas9 with reduced nuclease activity in G1 phase of cell cycle when HDR cannot occur, and transiently increasing the proportion of cells in HDR-preferred phases (S/G2), we achieved a four-fold improvement in HDR/NHEJ ratio over the control condition in vitro, and a significant improvement after xenotransplantation of edited hHSCs into immunodeficient mice. This strategy for improving gene editing outcomes in hHSCs has important implications for the field of gene therapy, and can be applied to diseases where increased HDR/NHEJ ratio is critical for therapeutic success. Stem Cells 2019;37:284-294.
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Affiliation(s)
- Anastasia Lomova
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Danielle N Clark
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Beatriz Campo-Fernandez
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Carmen Flores-Bjurström
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Michael L Kaufman
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Sorel Fitz-Gibbon
- Institute of Genomics and Proteomics, UCLA, Los Angeles, California, USA
| | - Xiaoyan Wang
- Department of General Internal Medicine and Health Services Research, UCLA, Los Angeles, California, USA
| | - Eric Y Miyahira
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Devin Brown
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Mark A DeWitt
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Roger P Hollis
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Zulema Romero
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Donald B Kohn
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA.,Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, UCLA, Los Angeles, California, USA
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100
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Smirnikhina SA, Anuchina AA, Lavrov AV. Ways of improving precise knock-in by genome-editing technologies. Hum Genet 2018; 138:1-19. [DOI: 10.1007/s00439-018-1953-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023]
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