1
|
Matsuzaki S, Sakuma T, Yamamoto T. REMOVER-PITCh: microhomology-assisted long-range gene replacement with highly multiplexed CRISPR-Cas9. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00850-1. [PMID: 38334880 DOI: 10.1007/s11626-024-00850-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024]
Abstract
A variety of CRISPR-Cas9-based gene editing technologies have been developed, including gene insertion and gene replacement, and applied to the study and treatment of diseases. While numerous studies have been conducted to improve the efficiency of gene insertion and to expand the system in various ways, there have been relatively few reports on gene replacement technology; therefore, further improvements are still needed in this context. Here, we developed the REMOVER-PITCh system to establish an efficient long-range gene replacement method and demonstrated its utility at two genomic loci in human cultured cells. REMOVER-PITCh depends on microhomology-assisted gene insertion technology called PITCh with highly multiplexed CRISPR-Cas9. First, we achieved gene replacement of about 20-kb GUSB locus using this system. Second, by applying the previously established knock-in-enhancing platform, the LoAD system, along with REMOVER-PITCh, we achieved the replacement of a longer gene region of about 200 kb at the ARSB locus. Our REMOVER-PITCh system will make it possible to remove and incorporate a variety of sequences from and into the genome, respectively, which will facilitate the generation of various disease and humanized models.
Collapse
Affiliation(s)
- Shu Matsuzaki
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., 1624 Shimokotachi, Koda-Cho, Akitakata-Shi, Hiroshima, 739-1195, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| |
Collapse
|
2
|
Li J, Kong D, Ke Y, Zeng W, Miki D. Application of multiple sgRNAs boosts efficiency of CRISPR/Cas9-mediated gene targeting in Arabidopsis. BMC Biol 2024; 22:6. [PMID: 38233866 PMCID: PMC10795408 DOI: 10.1186/s12915-024-01810-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Precise gene targeting (GT) is a powerful tool for heritable precision genome engineering, enabling knock-in or replacement of the endogenous sequence via homologous recombination. We recently established a CRISPR/Cas9-mediated approach for heritable GT in Arabidopsis thaliana (Arabidopsis) and rice and reported that the double-strand breaks (DSBs) frequency of Cas9 influences the GT efficiency. However, the relationship between DSBs and GT at the same locus was not examined. Furthermore, it has never been investigated whether an increase in the number of copies of sgRNAs or the use of multiple sgRNAs would improve the efficiency of GT. RESULTS Here, we achieved precise GT at endogenous loci Embryo Defective 2410 (EMB2410) and Repressor of Silencing 1 (ROS1) using the sequential transformation strategy and the combination of sgRNAs. We show that increasing of sgRNAs copy number elevates both DSBs and GT efficiency. On the other hand, application of multiple sgRNAs does not always enhance GT efficiency. Our results also suggested that some inefficient sgRNAs would play a role as a helper to facilitate other sgRNAs DSBs activity. CONCLUSIONS The results of this study clearly show that DSB efficiency, rather than mutation pattern, is one of the most important key factors determining GT efficiency. This study provides new insights into the relationship between sgRNAs, DSBs, and GTs and the molecular mechanisms of CRISPR/Cas9-mediated GTs in plants.
Collapse
Affiliation(s)
- Jing Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongping Ke
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Zeng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| |
Collapse
|
3
|
Padula A, Spinelli M, Nusco E, Bujanda Cundin X, Capolongo F, Campione S, Perna C, Bastille A, Ericson M, Wang CC, Zhang S, Amoresano A, Nacht M, Piccolo P. Genome editing without nucleases confers proliferative advantage to edited hepatocytes and corrects Wilson disease. JCI Insight 2023; 8:e171281. [PMID: 37707949 PMCID: PMC10721260 DOI: 10.1172/jci.insight.171281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Application of classic liver-directed gene replacement strategies is limited in genetic diseases characterized by liver injury due to hepatocyte proliferation, resulting in decline of therapeutic transgene expression and potential genotoxic risk. Wilson disease (WD) is a life-threatening autosomal disorder of copper homeostasis caused by pathogenic variants in copper transporter ATP7B and characterized by toxic copper accumulation, resulting in severe liver and brain diseases. Genome editing holds promise for the treatment of WD; nevertheless, to rescue copper homeostasis, ATP7B function must be restored in at least 25% of the hepatocytes, which surpasses by far genome-editing correction rates. We applied a liver-directed, nuclease-free genome editing approach, based on adeno-associated viral vector-mediated (AAV-mediated) targeted integration of a promoterless mini-ATP7B cDNA into the albumin (Alb) locus. Administration of AAV-Alb-mini-ATP7B in 2 WD mouse models resulted in extensive liver repopulation by genome-edited hepatocytes holding a proliferative advantage over nonedited ones, and ameliorated liver injury and copper metabolism. Furthermore, combination of genome editing with a copper chelator, currently used for WD treatment, achieved greater disease improvement compared with chelation therapy alone. Nuclease-free genome editing provided therapeutic efficacy and may represent a safer and longer-lasting alternative to classic gene replacement strategies for WD.
Collapse
Affiliation(s)
- Agnese Padula
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Michele Spinelli
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | | | | | - Claudia Perna
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Amy Bastille
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | - Megan Ericson
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | | | | | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Mariana Nacht
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | | |
Collapse
|
4
|
Chen H, Neubauer M, Wang JP. Enhancing HR Frequency for Precise Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:883421. [PMID: 35592579 PMCID: PMC9113527 DOI: 10.3389/fpls.2022.883421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
Collapse
Affiliation(s)
- Hao Chen
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Matthew Neubauer
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| |
Collapse
|
5
|
Covello G, Ibrahim GH, Bacchi N, Casarosa S, Denti MA. Exon Skipping Through Chimeric Antisense U1 snRNAs to Correct Retinitis Pigmentosa GTPase-Regulator ( RPGR) Splice Defect. Nucleic Acid Ther 2022; 32:333-349. [PMID: 35166581 PMCID: PMC9416563 DOI: 10.1089/nat.2021.0053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal dystrophies are caused by mutations in more than 250 genes, each of them carrying several types of mutations that can lead to different clinical phenotypes. Mutations in Retinitis Pigmentosa GTPase-Regulator (RPGR) cause X-linked Retinitis pigmentosa (RP). A nucleotide substitution in intron 9 of RPGR causes the increase of an alternatively spliced isoform of the mature mRNA, bearing exon 9a (E9a). This introduces a stop codon, leading to truncation of the protein. Aiming at restoring impaired gene expression, we developed an antisense RNA-based therapeutic approach for the skipping of RPGR E9a. We designed a set of specific U1 antisense snRNAs (U1_asRNAs) and tested their efficacy in vitro, upon transient cotransfection with RPGR minigene reporter systems in HEK-293T, 661W, and PC-12 cell lines.
Collapse
Affiliation(s)
- Giuseppina Covello
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Gehan H Ibrahim
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Niccolò Bacchi
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Simona Casarosa
- Neural Development and Regeneration Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,Centre for Medical Science - CIS Med, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
| | - Michela Alessandra Denti
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
| |
Collapse
|
6
|
Yamagata M, Sanes JR. CRISPR-mediated Labeling of Cells in Chick Embryos Based on Selectively Expressed Genes. Bio Protoc 2021; 11:e4105. [PMID: 34458399 PMCID: PMC8376491 DOI: 10.21769/bioprotoc.4105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
The abilities to mark and manipulate specific cell types are essential for an increasing number of functional, structural, molecular, and developmental analyses in model organisms. In a few species, this can be accomplished by germline transgenesis; in other species, other methods are needed to selectively label somatic cells based on the genes that they express. Here, we describe a method for CRISPR-based somatic integration of reporters or Cre recombinase into specific genes in the chick genome, followed by visualization of cells in the retina and midbrain. Loci are chosen based on an RNA-seq-based cell atlas. Reporters can be soluble to visualize the morphology of individual cells or appended to the encoded protein to assess subcellular localization. We call the method eCHIKIN for electroporation- and CRISPR-mediated Homology-instructed Knock-IN.
Collapse
Affiliation(s)
- Masahito Yamagata
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138, USA
| |
Collapse
|
7
|
Čermák T. Sequence modification on demand: search and replace tools for precise gene editing in plants. Transgenic Res 2021; 30:353-379. [PMID: 34086167 DOI: 10.1007/s11248-021-00253-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022]
Abstract
Until recently, our ability to generate allelic diversity in plants was limited to introduction of variants from domesticated and wild species by breeding via uncontrolled recombination or the use of chemical and physical mutagens-processes that are lengthy and costly or lack specificity, respectively. Gene editing provides a faster and more precise way to create new variation, although its application in plants has been dominated by the creation of short insertion and deletion mutations leading to loss of gene function, mostly due to the dependence of editing outcomes on DNA repair pathway choices intrinsic to higher eukaryotes. Other types of edits such as point mutations and precise and pre-designed targeted sequence insertions have rarely been implemented, despite providing means to modulate the expression of target genes or to engineer the function and stability of their protein products. Several advancements have been developed in recent years to facilitate custom editing by regulation of repair pathway choices or by taking advantage of alternative types of DNA repair. We have seen the advent of novel gene editing tools that are independent of DNA double-strand break repair, and methods completely independent of host DNA repair processes are being increasingly explored. With the aim to provide a comprehensive review of the state-of-the-art methodology for allele replacement in plants, I discuss the adoption of these improvements for plant genome engineering.
Collapse
|
8
|
Hamaker NK, Lee KH. A Site-Specific Integration Reporter System That Enables Rapid Evaluation of CRISPR/Cas9-Mediated Genome Editing Strategies in CHO Cells. Biotechnol J 2020; 15:e2000057. [PMID: 32500600 DOI: 10.1002/biot.202000057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/09/2020] [Indexed: 12/12/2022]
Abstract
Targeted gene knockout and site-specific integration (SSI) are powerful genome editing techniques to improve the development of industrially relevant Chinese hamster ovary (CHO) cell lines. However, past efforts to perform SSI in CHO cells are characterized by low efficiencies. Moreover, numerous strategies proposed to boost SSI efficiency in mammalian cell types have yet to be evaluated head to head or in combination to appreciably boost efficiencies in CHO. To enable systematic and rapid optimization of genome editing methods, the SSIGNAL (site-specific integration and genome alteration) reporter system is developed. This tool can analyze CRISPR (clustered regularly interspaced palindromic repeats)/Cas9 (CRISPR-associated protein 9)-mediated disruption activity alone or in conjunction with SSI efficiency. The reporter system uses green and red dual-fluorescence signals to indicate genotype states within four days following transfection, facilitating rapid data acquisition via standard flow cytometry instrumentation. In addition to describing the design and development of the system, two of its applications are demonstrated by first comparing transfection conditions to maximize CRISPR/Cas9 activity and subsequently assessing the efficiency of several promising SSI strategies. Due to its sensitivity and versatility, the SSIGNAL reporter system may serve as a tool to advance genome editing technology.
Collapse
Affiliation(s)
- Nathaniel K Hamaker
- Biopharmaceutical Innovation Center, Newark, DE, 19713, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Kelvin H Lee
- Biopharmaceutical Innovation Center, Newark, DE, 19713, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| |
Collapse
|
9
|
Liu JT, Corbett JL, Heslop JA, Duncan SA. Enhanced genome editing in human iPSCs with CRISPR-CAS9 by co-targeting ATP1a1. PeerJ 2020; 8:e9060. [PMID: 32391204 PMCID: PMC7197401 DOI: 10.7717/peerj.9060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/04/2020] [Indexed: 12/11/2022] Open
Abstract
Genome editing in human induced pluripotent stem cells (iPSCs) provides the potential for disease modeling and cell therapy. By generating iPSCs with specific mutations, researchers can differentiate the modified cells to their lineage of interest for further investigation. However, the low efficiency of targeting in iPSCs has hampered the application of genome editing. In this study we used a CRISPR-Cas9 system that introduces a specific point substitution into the sequence of the Na+/K+-ATPase subunit ATP1A1. The introduced mutation confers resistance to cardiac glycosides, which can then be used to select successfully targeted cells. Using this system, we introduced different formats of donor DNA for homology-directed repair (HDR), including single-strand DNAs, double-strand DNAs, and plasmid donors. We achieved a 35-fold increase in HDR when using plasmid donor with a 400 bp repair template. We further co-targeted ATP1A1 and a second locus of interest to determine the enrichment of mutagenesis after cardiac glycoside selection. Through this approach, INDEL rate was increased after cardiac glycoside treatment, while HDR enrichment was only observed at certain loci. Collectively, these results suggest that a plasmid donor with a 400 bp repair template is an optimal donor DNA for targeted substitution and co-targeting ATP1A1 with the second locus enriches for mutagenesis events through cardiac glycoside selection in human iPSCs.
Collapse
Affiliation(s)
- Jui-Tung Liu
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States of America
| | - James L Corbett
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States of America
| | - James A Heslop
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States of America
| |
Collapse
|
10
|
Abstract
A transgenic mouse carries within its genome an artificial DNA construct (transgene) that is deliberately introduced by an experimentalist. These animals are widely used to understand gene function and protein function. When addressing the history of transgenic mouse technology, it is apparent that a number of basic science research areas laid the groundwork for success. These include reproductive science, genetics and molecular biology, and micromanipulation and microscopy equipment. From reproductive physiology came applications on how to optimize mouse breeding, how to superovulate mice to produce zygotes for DNA microinjection or preimplantation embryos for combination with embryonic stem (ES) cells, and how to return zygotes and embryos to a pseudopregnant surrogate dam for gestation and birth. From developmental biology, it was learned how to micromanipulate embryos for morula aggregation and blastocyst microinjection and how to establish germline competent ES cells. From genetics came the foundational principles governing the inheritance of genes, the interactions of gene products, and an understanding of the phenotypic consequences of genetic mutations. From molecular biology came a panoply of tools and reagents that are used to clone DNA transgenes, to detect the presence of transgenes, to assess gene expression by measuring transcription, and to detect proteins in cells and tissues. Technical advances in light microscopes, micromanipulators, micropipette pullers, and ancillary equipment made it possible for experimentalists to insert thin glass needles into zygotes or embryos under controlled conditions to inject DNA solutions or ES cells. To fully discuss the breadth of contributions of these numerous scientific disciplines to a comprehensive history of transgenic science is beyond the scope of this work. Examples will be used to illustrate scientific developments central to the foundation of transgenic technology and that are in use today.
Collapse
Affiliation(s)
- Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan Medical School, Ann Arbor, MI, USA.
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
11
|
Yan N, Sun Y, Fang Y, Deng J, Mu L, Xu K, Mymryk JS, Zhang Z. A Universal Surrogate Reporter for Efficient Enrichment of CRISPR/Cas9-Mediated Homology-Directed Repair in Mammalian Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:775-789. [PMID: 31955009 PMCID: PMC6970138 DOI: 10.1016/j.omtn.2019.12.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022]
Abstract
CRISPR/Cas9-mediated homology-directed repair (HDR) can be leveraged to precisely engineer mammalian genomes. However, the inherently low efficiency of HDR often hampers to identify the desired modified cells. Here, we developed a novel universal surrogate reporter system that efficiently enriches for genetically modified cells arising from CRISPR/Cas9-induced HDR events (namely, the "HDR-USR" system). This episomally based reporter can be self-cleaved and self-repaired via HDR to create a functional puromycin selection cassette without compromising genome integrity. Co-transfection of the HDR-USR system into host cells and transient puromycin selection efficiently achieves enrichment of HDR-modified cells. We tested the system for precision point mutation at 16 loci in different human cell lines and one locus in two rodent cell lines. This system exhibited dramatic improvements in HDR efficiency at a single locus (up to 20.7-fold) and two loci at once (42% editing efficiency compared to zero in the control), as well as greatly improved knockin efficiency (8.9-fold) and biallelic deletion (35.9-fold) at test loci. Further increases were achieved by co-expression of yeast Rad52 and linear single-/double-stranded DNA donors. Taken together, our HDR-USR system provides a simple, robust and efficient surrogate reporter for the enrichment of CRISPR/Cas9-induced HDR-based precision genome editing across various targeting loci in different cell lines.
Collapse
Affiliation(s)
- Nana Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongsen Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanyuan Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingrong Deng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Mu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Joe S Mymryk
- Department of Microbiology & Immunology, Oncology and Otolaryngology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
12
|
Abstract
Recombineering inserts PCR products into DNA using homologous recombination. A pair of short homology arms (50 base pairs) on the ends of a PCR cassette target the cassette to its intended location. These homology arms can be easily introduced as 5' primer overhangs during the PCR reaction. The flexibility to choose almost any pair of homology arms enables the precise modification of virtually any DNA for purposes of sequence deletion, replacement, insertion, or point mutation. Recombineering often offers significant advantages relative to previous homologous recombination methods that require the construction of cassettes with large homology arms, and relative to traditional cloning methods that become intractable for large plasmids or DNA sequences. However, the tremendous number of variables, options, and pitfalls that can be encountered when designing and performing a recombineering protocol for the first time introduce barriers that can make recombineering a challenging technique for new users to adopt. This article focuses on three recombineering protocols we have found to be particularly robust, providing a detailed guide for choosing the simplest recombineering method for a given application and for performing and troubleshooting experiments. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Louis J Papa
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts
| | - Matthew D Shoulders
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts
| |
Collapse
|
13
|
Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
Collapse
Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| |
Collapse
|
14
|
Spiegel A, Bachmann M, Jurado Jiménez G, Sarov M. CRISPR/Cas9-based knockout pipeline for reverse genetics in mammalian cell culture. Methods 2019; 164-165:49-58. [PMID: 31051255 DOI: 10.1016/j.ymeth.2019.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/04/2019] [Accepted: 04/24/2019] [Indexed: 12/14/2022] Open
Abstract
We present a straightforward protocol for reverse genetics in cultured mammalian cells, using CRISPR/Cas9-mediated homology-dependent repair (HDR) based insertion of a protein trap cassette, resulting in a termination of the endogenous gene expression. Complete loss of function can be achieved with monoallelic trap cassette insertion, as the second allele is frequently disrupted by an error-prone non-homologous end joining (NHEJ) mechanism. The method should be applicable to any expressed gene in most cell lines, including those with low HDR efficiency, as the knockout alleles can be directly selected for.
Collapse
Affiliation(s)
- Aleksandra Spiegel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mandy Bachmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Gabriel Jurado Jiménez
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
| |
Collapse
|
15
|
Zhou ZP, Yang LL, Cao H, Chen ZR, Zhang Y, Wen XY, Hu J. In Vitro Validation of a CRISPR-Mediated CFTR Correction Strategy for Preclinical Translation in Pigs. Hum Gene Ther 2019; 30:1101-1116. [PMID: 31099266 DOI: 10.1089/hum.2019.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Early efforts in cystic fibrosis (CF) gene therapy faced major challenges in delivery efficiency and sustained therapeutic gene expression. Recent advancements in engineered site-specific endonucleases such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 make permanent CF transmembrane conductance regulator (CFTR) gene correction possible. However, because of safety concerns of the CRISPR/Cas9 system and challenges in in vivo delivery to inflamed CF airway, CRISPR-based gene correction strategies need to be tested in proper animal models. In this study, we aimed at creating vectors for testing CFTR gene correction in pig models. We constructed helper-dependent adenoviral (HD-Ad) vectors to deliver CRISPR/Cas9 and a donor template (a 6 kb LacZ or 8.7 kb human CFTR expression cassette) into cultured pig cells. We demonstrated precise integration of each donor into the GGTA1 safe harbor through Cas9-induced homology directed repair with 3 kb homology arms. In addition, we showed that both LacZ and hCFTR were persistently expressed in transduced cells. Furthermore, we created a CFTR-deficient cell line for testing CFTR correction. We detected hCFTR mRNA and protein expression in cells transduced with the hCFTR vector. We also demonstrated CFTR function in the CF cells transduced with the HD-Ad delivering the CRISPR-Cas9 system and hCFTR donor at late cellular passages using the membrane potential sensitive dye-based assay (FLIPR®). Combined with our previous report on gene delivery to pig airway basal cells, these data provide the feasibility of testing CRISPR/Cas9-mediated permanent human CFTR correction through HD-Ad vector delivery in pigs.
Collapse
Affiliation(s)
- Zhichang Peter Zhou
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada.,Zebrafish Centre for Advanced Drug Discovery and Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Liang Leo Yang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Huibi Cao
- Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Ziyan Rachel Chen
- Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Yiqian Zhang
- Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Xiao-Yan Wen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Zebrafish Centre for Advanced Drug Discovery and Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada.,Department of Medicine, Physiology and Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Jim Hu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| |
Collapse
|
16
|
Zhu F, Nair RR, Fisher EMC, Cunningham TJ. Humanising the mouse genome piece by piece. Nat Commun 2019; 10:1845. [PMID: 31015419 PMCID: PMC6478830 DOI: 10.1038/s41467-019-09716-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/23/2019] [Indexed: 12/14/2022] Open
Abstract
To better understand human health and disease, researchers create a wide variety of mouse models that carry human DNA. With recent advances in genome engineering, the targeted replacement of mouse genomic regions with orthologous human sequences has become increasingly viable, ranging from finely tuned humanisation of individual nucleotides and amino acids to the incorporation of many megabases of human DNA. Here, we examine emerging technologies for targeted genomic humanisation, we review the spectrum of existing genomically humanised mouse models and the insights such models have provided, and consider the lessons learned for designing such models in the future. Generation of transgenic mice has become routine in studying gene function and disease mechanisms, but often this is not enough to fully understand human biology. Here, the authors review the current state of the art of targeted genomic humanisation strategies and their advantages over classic approaches.
Collapse
Affiliation(s)
- Fei Zhu
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Remya R Nair
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK.
| | | |
Collapse
|
17
|
Chen Z, Cai X, Li M, Yan L, Wu L, Wang X, Tang N. CRISPR/Cas9-based liver-derived reporter cells for screening of mPGES-1 inhibitors. J Enzyme Inhib Med Chem 2019; 34:799-807. [PMID: 30879343 PMCID: PMC6427568 DOI: 10.1080/14756366.2019.1587416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
mPGES-1 is a terminal rate-limiting enzyme responsible for inflammation-induced PGE2 production. The inhibition of mPGES-1 has been considered as a safe and effective target for the treatment of inflammation and cancer. However, a specific, efficient, and simple method for high-throughput screening of mPGES-1 inhibitors is still lacking. In this study, we developed a fluorescence imaging strategy to monitor the expression of mPGES-1 via CRISPR/Cas9 knock-in system. Immunofluorescence colocalisation, Sanger sequencing, RNAi, and IL-1β treatment all confirmed the successful construction of mPGES-1 reporter cells. The fluorescence signal intensity of the reporter cells treated with four conventional mPGES-1 inhibitors was considerably attenuated via flow cytometry and fluorescent microplate reader, demonstrating that the reporter cells can be used as an efficient and convenient means for screening and optimising mPGES-1 inhibitors. Moreover, it provides a new technical support for the development of targeted small molecule compounds for anti-inflammatory and tumour therapy.
Collapse
Affiliation(s)
- Zhanfei Chen
- a Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital , Fuzhou , China
| | - Xiaoling Cai
- a Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital , Fuzhou , China
| | - Man Li
- a Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital , Fuzhou , China
| | - LinLin Yan
- a Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital , Fuzhou , China
| | - Luxi Wu
- a Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital , Fuzhou , China
| | - Xiaoqian Wang
- a Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital , Fuzhou , China
| | - Nanhong Tang
- a Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital , Fuzhou , China.,b Key Laboratory of Ministry of Education for Gastrointestinal Cancer , Research Center for Molecular Medicine, Fujian Medical University , Fuzhou , China
| |
Collapse
|
18
|
Hamaker NK, Lee KH. Site-specific Integration Ushers in a New Era of Precise CHO Cell Line Engineering. Curr Opin Chem Eng 2018; 22:152-160. [PMID: 31086757 DOI: 10.1016/j.coche.2018.09.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chinese hamster ovary (CHO) cells are widely used for the production of therapeutic proteins. Customarily, CHO production cell lines are established through random integration, which requires laborious screening of many clones to isolate suitable producers. In contrast, site-specific integration (SSI) accelerates cell line development by targeting integration of transgenes to pre-validated genomic loci capable of supporting high and stable expression. To date, a relatively small number of these so called 'hot spots' have been identified, mainly through empirical methods. Nevertheless, nuclease-mediated and recombinase-mediated SSI have revolutionized cell line engineering by enabling rational and reproducible transgene targeting.
Collapse
Affiliation(s)
- Nathaniel K Hamaker
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Kelvin H Lee
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| |
Collapse
|
19
|
Leidy-Davis T, Cheng K, Goodwin LO, Morgan JL, Juan WC, Roca X, Ong ST, Bergstrom DE. Viable Mice with Extensive Gene Humanization (25-kbp) Created Using Embryonic Stem Cell/Blastocyst and CRISPR/Zygote Injection Approaches. Sci Rep 2018; 8:15028. [PMID: 30301924 PMCID: PMC6177426 DOI: 10.1038/s41598-018-33408-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
Here, we describe an expansion of the typical DNA size limitations associated with CRISPR knock-in technology, more specifically, the physical extent to which mouse genomic DNA can be replaced with donor (in this case, human) DNA at an orthologous locus by zygotic injection. Driving our efforts was the desire to create a whole animal model that would replace 17 kilobase pairs (kbp) of the mouse Bcl2l11 gene with the corresponding 25-kbp segment of human BCL2L11, including a conditionally removable segment (2.9-kbp) of intron 2, a cryptic human exon immediately 3' of this, and a native human exon some 20 kbp downstream. Using two methods, we first carried out the replacement by employing a combination of bacterial artificial chromosome recombineering, classic embryonic stem cell (ESC) targeting, dual selection, and recombinase-driven cassette removal (ESC/Blastocyst Approach). Using a unique second method, we employed the same vector (devoid of its selectable marker cassettes), microinjecting it along with redundant single guide RNAs (sgRNAs) and Cas9 mRNA into mouse zygotes (CRISPR/Zygote Approach). In both instances, we were able to achieve humanization of Bcl2l11 to the extent designed, remove all selection cassettes, and demonstrate the functionality of the conditionally removable, loxP-flanked, 2.9-kbp intronic segment.
Collapse
Affiliation(s)
| | - Kai Cheng
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
- Genetically Engineered Models and Services, Charles River Laboratories, Wilmington, USA
| | - Leslie O Goodwin
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Judith L Morgan
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
- Center for Biometric Analysis, The Jackson Laboratory, Bar Harbor, USA
| | - Wen Chun Juan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- MSD Pharma (Singapore) Private Limited, Singapore, Republic of Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - S Tiong Ong
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
- Department of Haematology, Singapore General Hospital, Singapore, Republic of Singapore
- Department of Medical Oncology, National Cancer Centre, Singapore, Republic of Singapore
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - David E Bergstrom
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA.
- Cancer Center, The Jackson Laboratory, Bar Harbor, ME, USA.
| |
Collapse
|
20
|
Lu W, Chao T, Ruiqi C, Juan S, Zhihong L. Patient-derived xenograft models in musculoskeletal malignancies. J Transl Med 2018; 16:107. [PMID: 29688859 PMCID: PMC5913806 DOI: 10.1186/s12967-018-1487-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/17/2018] [Indexed: 12/17/2022] Open
Abstract
Successful oncological drug development for bone and soft tissue sarcoma is grossly stagnating. A major obstacle in this process is the lack of appropriate animal models recapitulating the complexity and heterogeneity of musculoskeletal malignancies, resulting in poor efficiency in translating the findings of basic research to clinical applications. In recent years, patient-derived xenograft (PDX) models generated by directly engrafting patient-derived tumor fragments into immunocompromised mice have recaptured the attention of many researchers due to their properties of retaining the principle histopathology, biological behaviors, and molecular and genetic characteristics of the original tumor, showing promising future in both basic and clinical studies of bone and soft tissue sarcoma. Despite several limitations including low take rate and long take time in PDX generation, deficient immune system and heterologous tumor microenvironment of the host, PDXs offer a more advantageous platform for preclinical drug screening, biomarker identification and clinical therapeutic decision guiding. Here, we provide a timely review of the establishment and applications of PDX models for musculoskeletal malignancies and discuss current challenges and future directions of this approach.
Collapse
Affiliation(s)
- Wan Lu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410010, Hunan, People's Republic of China
| | - Tu Chao
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410010, Hunan, People's Republic of China
| | - Chen Ruiqi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410010, Hunan, People's Republic of China
| | - Su Juan
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410010, Hunan, People's Republic of China
| | - Li Zhihong
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, 410010, Hunan, People's Republic of China.
| |
Collapse
|
21
|
Stephens CJ, Kashentseva E, Everett W, Kaliberova L, Curiel DT. Targeted in vivo knock-in of human alpha-1-antitrypsin cDNA using adenoviral delivery of CRISPR/Cas9. Gene Ther 2018; 25:139-156. [PMID: 29588497 PMCID: PMC5919923 DOI: 10.1038/s41434-018-0003-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 12/17/2022]
Abstract
Serum deficiency diseases such as alpha-1-antitrypsin deficiency are characterized by reduced function of serum proteins, caused by deleterious genetic mutations. These diseases are promising targets for genetic interventions. Gene therapies using viral vectors have been used to introduce correct copies of the disease-causing gene in preclinical and clinical studies. However, these studies highlighted that disease-alleviating gene expression is lost over time. Integration into a specific chromosomal site could provide lasting therapeutic expression to overcome this major limitation. Additionally, targeted integration could avoid detrimental mutagenesis associated with integrative vectors, such as tumorigenesis or functional gene perturbation. To test if adenoviral vectors can facilitate long-term gene expression through targeted integration, we somatically incorporated the human alpha-1-antitrypsin gene into the ROSA26 "safe harbor" locus in murine livers, using CRISPR/Cas9. We found adenoviral-mediated delivery of CRISPR/Cas9 achieved gene editing outcomes persisting over 200 days. Furthermore, gene knock-in maintained greater levels of the serum protein than provided by episomal expression. Importantly, our "knock-in" approach is generalizable to other serum proteins and supports in vivo cDNA replacement therapy to achieve stable gene expression.
Collapse
Affiliation(s)
- Calvin J Stephens
- Department of Radiation Oncology, Cancer Biology Division, School of Medicine, Washington University in Saint Louis, 660 South Euclid Avenue, Campus Box 8224, St. Louis, MO, 63110, USA
- Molecular Genetics and Genomics Program, Division of Biology and Biomedical Sciences, School of Medicine, Washington University in Saint Louis, 660 South Euclid Avenue, Campus Box 8226, St. Louis, MO, 63110, USA
| | - Elena Kashentseva
- Department of Radiation Oncology, Cancer Biology Division, School of Medicine, Washington University in Saint Louis, 660 South Euclid Avenue, Campus Box 8224, St. Louis, MO, 63110, USA
| | - William Everett
- Department of Radiation Oncology, Cancer Biology Division, School of Medicine, Washington University in Saint Louis, 660 South Euclid Avenue, Campus Box 8224, St. Louis, MO, 63110, USA
| | - Lyudmila Kaliberova
- Department of Radiation Oncology, Cancer Biology Division, School of Medicine, Washington University in Saint Louis, 660 South Euclid Avenue, Campus Box 8224, St. Louis, MO, 63110, USA
| | - David T Curiel
- Department of Radiation Oncology, Cancer Biology Division, School of Medicine, Washington University in Saint Louis, 660 South Euclid Avenue, Campus Box 8224, St. Louis, MO, 63110, USA.
- Department of Radiation Oncology, Biologic Therapeutics Center, School of Medicine, Washington University in Saint Louis, 660 South Euclid Avenue, Campus Box 8224, St. Louis, MO, 63110, USA.
| |
Collapse
|
22
|
Pawelczak KS, Gavande NS, VanderVere-Carozza PS, Turchi JJ. Modulating DNA Repair Pathways to Improve Precision Genome Engineering. ACS Chem Biol 2018; 13:389-396. [PMID: 29210569 DOI: 10.1021/acschembio.7b00777] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Programmable nucleases like the popular CRISPR/Cas9 system allow for precision genome engineering by inducing a site-specific DNA double strand break (DSB) within a genome. The DSB is repaired by endogenous DNA repair pathways, either nonhomologous end joining (NHEJ) or homology directed repair (HDR). The predominant and error-prone NHEJ pathway often results in small nucleotide insertions or deletions that can be used to construct knockout alleles. Alternatively, HDR activity can result in precise modification incorporating exogenous DNA fragments into the cut site. However, genetic recombination in mammalian systems through the HDR pathway is an inefficient process and requires cumbersome laboratory methods to identify the desired accurate insertion events. This is further compromised by the activity of the competing DNA repair pathway, NHEJ, which repairs the majority of nuclease induced DNA DSBs and also is responsible for mutagenic insertion and deletion events at off-target locations throughout the genome. Various methodologies have been developed to increase the efficiency of designer nuclease-based HDR mediated gene editing. Here, we review these advances toward modulating the activities of the two critical DNA repair pathways, HDR and NHEJ, to enhance precision genome engineering.
Collapse
Affiliation(s)
- Katherine S. Pawelczak
- NERx Biosciences, 212 W 10th
Street, Suite A480, Indianapolis, Indiana 46202, United States
| | | | | | - John J. Turchi
- NERx Biosciences, 212 W 10th
Street, Suite A480, Indianapolis, Indiana 46202, United States
| |
Collapse
|