1
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Li P, Li X, Wang F, Gao M, Bai Y, Zhang Z, Wei Z. Enrichment of prime-edited mammalian cells with surrogate Puro R reporters. Int J Biol Macromol 2024; 271:132474. [PMID: 38777019 DOI: 10.1016/j.ijbiomac.2024.132474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/01/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Prime editing is a programmable genetic method that can precisely generate any desired small-scale variations in cells without requiring double-strand breaks and DNA donors. However, higher editing efficiency is greatly desirable for wide practical applications. In this study, we developed a target-specific prime editing reporter (tsPER) and a universal prime editing reporter (UPER) to facilitate rapid selection of desired edited cells through puromycin screening. The modification efficiency of HEK3_i1CTT_d5G in HEK293T cells improved from 36.37 % to 64.84 % with the incorporation of tsPER. The target sequence of interested genes could be custom inserted into a selection cassette in tsPER to establish personalized reporters. The UPER demonstrated PE3 editing efficiency up to 74.49 % on HEK3_i1CTT_d5G and 73.52 % on HEK3_i1His6, achieved through co-selection with an additional pegRNA (puro) to repair the mutant PuroR cassette. Overall, tsPER and UPER robustly improved the efficiency of prime editing. Both of these approaches expand enrichment strategies for genomically modified cells and accelerate the generation of genetically modified models.
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Affiliation(s)
- Pengcheng Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Yazhouwan National Laboratory, Sanya 572024, China
| | - Xinyi Li
- Division of Cardiovascular Medicine, Department of Medicin Solna(MedS), Karolinska institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Fang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Mengyu Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yichun Bai
- School of Public Health, Xinxiang Medical University, Xinxiang 453000, China
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Zehui Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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2
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Zou K, Wang F, Zhang Z, Zhou Y, Li P, Wang D, Zhu M, Jia C, Wei Z. Optimized CRISPR/Cas9 system for gene knockout in chicken DF1 cells. Poult Sci 2023; 102:102970. [PMID: 37562129 PMCID: PMC10432839 DOI: 10.1016/j.psj.2023.102970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/18/2023] [Accepted: 07/23/2023] [Indexed: 08/12/2023] Open
Abstract
The editing efficiency primarily hinders the utility of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology in poultry. For a better understanding of the factors that influence the efficiency of gene knockout mediated by CRISPR/Cas9 in chicken DF1 cells, the single or dual single guide RNA (sgRNA) targeted exon regions of genes (taking anti-Müllerian hormone, TGF-beta receptor type-2 and Peroxisome proliferator-activated receptor gamma as examples) were designed. The sgRNA-CRISPR/Cas9 vectors with corresponding reporter vectors were transfected into DF1 cells. T7 endonuclease 1 (T7E1) and amplicon sequencing assay were compared for evaluating genome editing efficiency and the indel profiles were analyzed based on the data of amplicon sequencing. Meanwhile, to evaluate the precision of Cas9 cleavage, we also analyzed the homology of small insertion with the nucleotides of upstream and downstream of cleave sties. The surrogate reporter systems showed strong enrichment function, and the indel percentages were increased after puromycin selection. The indel ratios of T7E1 assay were lower than amplicon sequencing assay, which indicated T7E1 isn't fit to be used as the sole evaluation criterion for the targeting efficiency of CRISPR/Cas9. Based on the amplicon sequencing analysis, the editing efficiency showed noticeable differences among cells treated with different sgRNAs. However, the variety of indel efficiencies was not related to the GC content of sgRNA or chromosome types of targeted genes. The results showed that the dual sgRNA might not raise the indel ratios compared with individual sgRNA, but they could increase the ratios of the fragment deletions. The present study suggested that the surrogate reporter was an effective method to promote the editing efficiencies of CRISPR/Cas9 in chicken cells. The dual sgRNA could increase the fragment deletions, and the sensitivity of amplicon sequencing to detect cleavage was higher than the T7 endonuclease 1 assay. These results are essential to improve the application of CRISPR/Cas9 technology in chicken cells.
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Affiliation(s)
- Kexin Zou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zechun Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengcheng Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengqi Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cunling Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zehui Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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3
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Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [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: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
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Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
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4
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Mikkelsen NS, Hernandez SS, Jensen TI, Schneller JL, Bak RO. Enrichment of transgene integrations by transient CRISPR activation of a silent reporter gene. Mol Ther Methods Clin Dev 2023; 29:1-16. [PMID: 36922985 PMCID: PMC10009645 DOI: 10.1016/j.omtm.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
CRISPR-Cas-mediated site-specific integration of transgenes by homology-directed repair (HDR) is challenging, especially in primary cells, where inferior editing efficiency may impede the development of gene- and cellular therapies. Various strategies for enrichment of cells with transgene integrations have been developed, but most strategies either generate unwanted genomic scars or rely on permanent integration and expression of a reporter gene used for selection. However, stable expression of a reporter gene may perturb cell homeostasis and function. Here we develop a broadly applicable and versatile enrichment strategy by harnessing the capability of CRISPR activation (CRISPRa) to transiently induce expression of a therapeutically relevant reporter gene used for immunomagnetic enrichment. This strategy is readily adaptable to primary human T cells and CD34+ hematopoietic stem and progenitor cells (HSPCs), where enrichment of 1.8- to 3.3-fold and 3.2- to 3.6-fold was achieved, respectively. Furthermore, chimeric antigen receptor (CAR) T cells were enriched 2.5-fold and demonstrated improved cytotoxicity over non-enriched CAR T cells. Analysis of HDR integrations showed a proportion of cells harboring deletions of the transgene cassette arising either from impartial HDR or truncated adeno-associated virus (AAV) vector genomes. Nonetheless, this novel enrichment strategy expands the possibility to enrich for transgene integrations in research settings and in gene and cellular therapies.
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Affiliation(s)
| | | | - Trine I Jensen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Jessica L Schneller
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.,RNA and Gene Therapies, Novo Nordisk A/S, Maaloev, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Aarhus C, Denmark
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5
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Tu CF, Peng SH, Chuang CK, Wong CH, Yang TS. - Invited Review - Reproductive technologies needed for the generation of precise gene-edited pigs in the pathways from laboratory to farm. Anim Biosci 2023; 36:339-349. [PMID: 36397683 PMCID: PMC9899582 DOI: 10.5713/ab.22.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022] Open
Abstract
Gene editing (GE) offers a new breeding technique (NBT) of sustainable value to animal agriculture. There are 3 GE working sites covering 5 feasible pathways to generate GE pigs along with the crucial intervals of GE/genotyping, microinjection/electroporation, induced pluripotent stem cells, somatic cell nuclear transfer, cryopreservation, and nonsurgical embryo transfer. The extension of NBT in the new era of pig breeding depends on the synergistic effect of GE and reproductive biotechnologies; the outcome relies not only on scientific due diligence and operational excellence but also on the feasibility of application on farms to improve sustainability.
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Affiliation(s)
- Ching-Fu Tu
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan,Corresponding Author: Ching-Fu Tu, Tel: +886-37-585815, E-mail:
| | - Shu-Hui Peng
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan
| | - Chin-kai Chuang
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan
| | - Chi-Hong Wong
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan
| | - Tien-Shuh Yang
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan,Department of Biotechnology and Animal Science, National Ilan University, Yilan 260007,
Taiwan
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6
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Challagulla A, Shi S, Nair K, O'Neil TE, Morris KR, Wise TG, Cahill DM, Tizard ML, Doran TJ, Jenkins KA. Marker counter-selection via CRISPR/Cas9 co-targeting for efficient generation of genome edited avian cell lines and germ cells. Anim Biotechnol 2022; 33:1235-1245. [PMID: 33650465 DOI: 10.1080/10495398.2021.1885428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Efficient isolation of genetically modified cells that are phenotypically indistinguishable from the unmodified cells remains a major technical barrier for the broader utilization of CRISPR/Cas9. Here, we report a novel enrichment approach to select the genome engineered cells by co-targeting a genomically integrated GFP gene along with the endogenous gene of interest (GOI). Using this co-targeting approach, multiple genomic loci were successfully targeted in chicken (DF1) and quail (CEC-32) fibroblast cell lines by transient transfection of Cas9 and guide RNAs (gRNAs). Clonal isolation of co-targeted DF1 cells showed 75% of cell clones had deletion of GFP and biallelic deletion of the GOI. To assess the utility of this approach to generate genome modified animals, we tested it on chicken primordial germ cells (PGCs) expressing GFP by co-targeting with gRNAs against GFP and endogenous ovomucoid (OVM) gene. PGCs enriched for loss of GFP and confirmed for OVM deletion, derived by co-targeting, were injected into Hamburger and Hamilton stage 14-15 chicken embryos, and their ability to migrate to the genital ridge was confirmed. This simple, efficient enrichment approach could easily be applied to the creation of knock-out or edited cell lines or animals.
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Affiliation(s)
- Arjun Challagulla
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Shunning Shi
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Kiran Nair
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Terri E O'Neil
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Kirsten R Morris
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Terry G Wise
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - David M Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Mark L Tizard
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Timothy J Doran
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Kristie A Jenkins
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
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7
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Marker-free co-selection for successive rounds of prime editing in human cells. Nat Commun 2022; 13:5909. [PMID: 36207338 PMCID: PMC9546848 DOI: 10.1038/s41467-022-33669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies. Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. Here the authors develop a co-selection strategy to facilitate prime editing in human cells and provide design principles to prevent the formation of undesired editing byproducts at the target site.
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8
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Ma S, Yang L, Zuo Q, Huang Q. GPI-anchored glutathione S-transferase as marker allows affinity sorting of transfection-positive cells. Front Mol Biosci 2022; 9:1016090. [PMID: 36250010 PMCID: PMC9558730 DOI: 10.3389/fmolb.2022.1016090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022] Open
Abstract
Cell transfection efficiency is still a limiting factor in gene function research. A method that allows isolation and enrichment of the transfection-positive cells is an effective solution. Here, we report a transfection-positive cell sorting system that utilizes GPI-anchored GST (Glutathione S-transferase) as a plasmid marker. The Glutathione S-transferase fusion protein will be expressed and displayed on the cell surface through GPI anchor, and hence permits the positive cells to be isolated using Glutathione (GSH) Magnetic Beads. We prove that the system works efficiently in both the adherent Lenti-X 293T cells and the suspension K-562 cells. The affinity cell sorting procedure efficiently enriched positive cells from 20% to 98% in K-562 cells. The applications in gene knockdown and overexpression experiments in K-562 cells dramatically enhanced the extent of gene alteration, with the gene knockdown efficiency increasing from 7% to 60% and the gene overexpression level rising from 47 to 253 times. This Glutathione S-transferase affinity transfection-positive cell sorting method is simple and fast to operate, large-instrument free, low cost, and hence possesses great potential in gene function study in vitro.
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9
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Ma L, Xing J, Li Q, Zhang Z, Xu K. Development of a universal antibiotic resistance screening reporter for improving efficiency of cytosine and adenine base-editing. J Biol Chem 2022; 298:102103. [PMID: 35671823 PMCID: PMC9287484 DOI: 10.1016/j.jbc.2022.102103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
Base editing has emerged as a revolutionary technology for single nucleotide modifications. The cytosine and adenine base editors (CBEs and ABEs) have demonstrated great potential in clinical and fundamental research. However, screening and isolating target-edited cells remains challenging. In the current study, we developed a universal Adenine and Cytosine Base-Editing Antibiotic Resistance Screening Reporter (ACBE-ARSR) for improving the editing efficiency. To develop the reporter, the CBE-ARSR was first constructed and shown to be capable of enriching cells for those that had undergone CBE editing activity. Then, the ACBE-ARSR was constructed and was further validated in the editing assays by four different CBEs and two versions of ABE at several different genomic loci. Our results demonstrated that ACBE-ARSR, compared to the reporter of transfection (RoT) screening strategy, improved the editing efficiency of CBE and ABE by 4.6- and 1.9-fold on average, respectively. We found the highest CBE and ABE editing efficiencies as enriched by ACBE-ARSR reached 90% and 88.7%. Moreover, we also demonstrated ACBE-ARSR could be employed for enhancing simultaneous multiplexed genome editing. In conclusion, both CBE and ABE activity can be improved significantly using our novel ACBE-ARSR screening strategy, which we believe will facilitate the development of base editors and their application in biomedical and fundamental research studies.
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Affiliation(s)
- Lixia Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; Changzhi Medical College, Changzhi 046000, Shanxi, China.
| | - Jiani Xing
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Qian Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, 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 712100, Shaanxi, China.
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10
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Heath NG, O’Geen H, Halmai NB, Corn JE, Segal DJ. Imaging Unique DNA Sequences in Individual Cells Using a CRISPR-Cas9-Based, Split Luciferase Biosensor. Front Genome Ed 2022; 4:867390. [PMID: 35403097 PMCID: PMC8990833 DOI: 10.3389/fgeed.2022.867390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
An extensive arsenal of biosensing tools has been developed based on the clustered regularly interspaced short palindromic repeat (CRISPR) platform, including those that detect specific DNA sequences both in vitro and in live cells. To date, DNA imaging approaches have traditionally used full fluorescent reporter-based fusion probes. Such “always-on” probes differentiate poorly between bound and unbound probe and are unable to sensitively detect unique copies of a target sequence in individual cells. Herein we describe a DNA biosensor that provides a sensitive readout for such low-copy DNA sequences through proximity-mediated reassembly of two independently optimized fragments of NanoLuc luciferase (NLuc), a small, bright luminescent reporter. Applying this “turn-on” probe in live cells, we demonstrate an application not easily achieved by fluorescent reporter-based probes, detection of individual endogenous genomic loci using standard epifluorescence microscopy. This approach could enable detection of gene edits during ex vivo editing procedures and should be a useful platform for many other live cell DNA biosensing applications.
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Affiliation(s)
- Nicholas G. Heath
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Nicole B. Halmai
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Biology, ETH, Zürich, Switzerland
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: David J. Segal,
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11
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Feng S, Wang Z, Li A, Xie X, Liu J, Li S, Li Y, Wang B, Hu L, Yang L, Guo T. Strategies for High-Efficiency Mutation Using the CRISPR/Cas System. Front Cell Dev Biol 2022; 9:803252. [PMID: 35198566 PMCID: PMC8860194 DOI: 10.3389/fcell.2021.803252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated systems have revolutionized traditional gene-editing tools and are a significant tool for ameliorating gene defects. Characterized by high target specificity, extraordinary efficiency, and cost-effectiveness, CRISPR/Cas systems have displayed tremendous potential for genetic manipulation in almost any organism and cell type. Despite their numerous advantages, however, CRISPR/Cas systems have some inherent limitations, such as off-target effects, unsatisfactory efficiency of delivery, and unwanted adverse effects, thereby resulting in a desire to explore approaches to address these issues. Strategies for improving the efficiency of CRISPR/Cas-induced mutations, such as reducing off-target effects, improving the design and modification of sgRNA, optimizing the editing time and the temperature, choice of delivery system, and enrichment of sgRNA, are comprehensively described in this review. Additionally, several newly emerging approaches, including the use of Cas variants, anti-CRISPR proteins, and mutant enrichment, are discussed in detail. Furthermore, the authors provide a deep analysis of the current challenges in the utilization of CRISPR/Cas systems and the future applications of CRISPR/Cas systems in various scenarios. This review not only serves as a reference for improving the maturity of CRISPR/Cas systems but also supplies practical guidance for expanding the applicability of this technology.
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Affiliation(s)
- Shuying Feng
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zilong Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Aifang Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xin Xie
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Junjie Liu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuxuan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yalan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Baiyan Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lina Hu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lianhe Yang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tao Guo
- Department of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
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12
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Kojima C, Kanetsuki A, Nakajima Y, Kawano T, Takatsuka K, Tanaka S, Haraguchi Y, Matsuura K, Shimizu T. Cell detachment from monolayer- and bilayer-type gold nanoparticle-containing collagen coatings by visible laser irradiation for cell sorting applications. Polym J 2021. [DOI: 10.1038/s41428-021-00527-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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A reporter system for enriching CRISPR/Cas9 knockout cells in technically challenging settings like patient models. Sci Rep 2021; 11:12649. [PMID: 34135367 PMCID: PMC8209181 DOI: 10.1038/s41598-021-91760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas9 represents a valuable tool to determine protein function, but technical hurdles limit its use in challenging settings such as cells unable to grow in vitro like primary leukemia cells and xenografts derived thereof (PDX). To enrich CRISPR/Cas9-edited cells, we improved a dual-reporter system and cloned the genomic target sequences of the gene of interest (GOI) upstream of an out-of-frame fluorochrome which was expressed only upon successful gene editing. To reduce rounds of in vivo passaging required for PDX leukemia growth, targets of 17 GOI were cloned in a row, flanked by an improved linker, and PDX cells were lentivirally transduced for stable expression. The reporter enriched scarce, successfully gene-edited PDX cells as high as 80%. Using the reporter, we show that KO of the SRC-family kinase LYN increased the response of PDX cells of B precursor cell ALL towards Vincristine, even upon heterozygous KO, indicating haploinsufficiency. In summary, our reporter system enables enriching KO cells in technically challenging settings and extends the use of gene editing to highly patient-related model systems.
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14
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Ramachandran H, Martins S, Kontarakis Z, Krutmann J, Rossi A. Fast but not furious: a streamlined selection method for genome-edited cells. Life Sci Alliance 2021; 4:4/6/e202101051. [PMID: 33903218 PMCID: PMC8127327 DOI: 10.26508/lsa.202101051] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 11/24/2022] Open
Abstract
Magnetic-activated genome-edited cell sorting (MAGECS) allows a fast and easy generation of genetically modified cells. In the last decade, transcription activator-like effector nucleases and CRISPR-based genome engineering have revolutionized our approach to biology. Because of their high efficiency and ease of use, the development of custom knock-out and knock-in animal or cell models is now within reach for almost every laboratory. Nonetheless, the generation of genetically modified cells often requires a selection step, usually achieved by antibiotics or fluorescent markers. The choice of the selection marker is based on the available laboratory resources, such as cell types, and parameters such as time and cost should also be taken into consideration. Here, we present a new and fast strategy called magnetic-activated genome-edited cell sorting, to select genetically modified cells based on the ability to magnetically sort surface antigens (i.e., tCD19) present in Cas9-positive cells. By using magnetic-activated genome-edited cell sorting, we successfully generated and isolated genetically modified human-induced pluripotent stem cells, primary human fibroblasts, SH-SY5Y neuroblast-like cells, HaCaT and HEK 293T cells. Our strategy expands the genome editing toolbox by offering a fast, cheap, and an easy to use alternative to the available selection methods.
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Affiliation(s)
- Haribaskar Ramachandran
- IUF-Leibniz Research Institute for Environmental Medicine, Core Unit Model Development, Düsseldorf, Germany
| | - Soraia Martins
- IUF-Leibniz Research Institute for Environmental Medicine, Core Unit Model Development, Düsseldorf, Germany
| | - Zacharias Kontarakis
- Genome Engineering and Measurement Laboratory, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.,Functional Genomics Center Zurich of ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Jean Krutmann
- IUF-Leibniz Research Institute for Environmental Medicine, Core Unit Model Development, Düsseldorf, Germany.,Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Andrea Rossi
- IUF-Leibniz Research Institute for Environmental Medicine, Core Unit Model Development, Düsseldorf, Germany
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15
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Shen MJ, Olsthoorn RC, Zeng Y, Bakkum T, Kros A, Boyle AL. Magnetic-Activated Cell Sorting Using Coiled-Coil Peptides: An Alternative Strategy for Isolating Cells with High Efficiency and Specificity. ACS APPLIED MATERIALS & INTERFACES 2021; 13:11621-11630. [PMID: 33656313 PMCID: PMC7975280 DOI: 10.1021/acsami.0c22185] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Magnetic-activated cell sorting (MACS) is an affinity-based technique used to separate cells according to the presence of specific markers. Current MACS systems generally require an antigen to be expressed at the cell surface; these antigen-presenting cells subsequently interact with antibody-labeled magnetic particles, facilitating separation. Here, we present an alternative MACS method based on coiled-coil peptide interactions. We demonstrate that HeLa, CHO, and NIH3T3 cells can either incorporate a lipid-modified coiled-coil-forming peptide into their membrane, or that the cells can be transfected with a plasmid containing a gene encoding a coiled-coil-forming peptide. Iron oxide particles are functionalized with the complementary peptide and, upon incubation with the cells, labeled cells are facilely separated from nonlabeled populations. In addition, the resulting cells and particles can be treated with trypsin to facilitate detachment of the cells from the particles. Therefore, our new MACS method promotes efficient cell sorting of different cell lines, without the need for antigen presentation, and enables simple detachment of the magnetic particles from cells after the sorting process. Such a system can be applied to rapidly developing, sensitive research areas, such as the separation of genetically modified cells from their unmodified counterparts.
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Affiliation(s)
- Meng-Jie Shen
- Department
of Supramolecular & Biomaterials Chemistry, Leiden Institute of
Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - René C.L. Olsthoorn
- Department
of Supramolecular & Biomaterials Chemistry, Leiden Institute of
Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Ye Zeng
- Department
of Supramolecular & Biomaterials Chemistry, Leiden Institute of
Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Thomas Bakkum
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Alexander Kros
- Department
of Supramolecular & Biomaterials Chemistry, Leiden Institute of
Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Aimee L. Boyle
- Department
of Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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16
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Ratner LD, La Motta GE, Briski O, Salamone DF, Fernandez-Martin R. Practical Approaches for Knock-Out Gene Editing in Pigs. Front Genet 2021; 11:617850. [PMID: 33747029 PMCID: PMC7973260 DOI: 10.3389/fgene.2020.617850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022] Open
Abstract
Pigs are an important resource for meat production and serve as a model for human diseases. Due to their physiological and anatomical similarities to humans, these animals can recapitulate symptoms of human diseases, becoming an effective model for biomedical research. Although, in the past pig have not been widely used partially because of the difficulty in genetic modification; nowadays, with the new revolutionary technology of programmable nucleases, and fundamentally of the CRISPR-Cas9 systems, it is possible for the first time to precisely modify the porcine genome as never before. To this purpose, it is necessary to introduce the system into early stage zygotes or to edit cells followed by somatic cell nuclear transfer. In this review, several strategies for pig knock-out gene editing, using the CRISPR-Cas9 system, will be summarized, as well as genotyping methods and different delivery techniques to introduce these tools into the embryos. Finally, the best approaches to produce homogeneous, biallelic edited animals will be discussed.
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Affiliation(s)
- Laura Daniela Ratner
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gaston Emilio La Motta
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Olinda Briski
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Felipe Salamone
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Fernandez-Martin
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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17
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Genetic glycoengineering in mammalian cells. J Biol Chem 2021; 296:100448. [PMID: 33617880 PMCID: PMC8042171 DOI: 10.1016/j.jbc.2021.100448] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in nuclease-based gene-editing technologies have enabled precise, stable, and systematic genetic engineering of glycosylation capacities in mammalian cells, opening up a plethora of opportunities for studying the glycome and exploiting glycans in biomedicine. Glycoengineering using chemical, enzymatic, and genetic approaches has a long history, and precise gene editing provides a nearly unlimited playground for stable engineering of glycosylation in mammalian cells to explore and dissect the glycome and its many biological functions. Genetic engineering of glycosylation in cells also brings studies of the glycome to the single cell level and opens up wider use and integration of data in traditional omics workflows in cell biology. The last few years have seen new applications of glycoengineering in mammalian cells with perspectives for wider use in basic and applied glycosciences, and these have already led to discoveries of functions of glycans and improved designs of glycoprotein therapeutics. Here, we review the current state of the art of genetic glycoengineering in mammalian cells and highlight emerging opportunities.
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18
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Li S, Akrap N, Cerboni S, Porritt MJ, Wimberger S, Lundin A, Möller C, Firth M, Gordon E, Lazovic B, Sieńska A, Pane LS, Coelho MA, Ciotta G, Pellegrini G, Sini M, Xu X, Mitra S, Bohlooly-Y M, Taylor BJM, Sienski G, Maresca M. Universal toxin-based selection for precise genome engineering in human cells. Nat Commun 2021; 12:497. [PMID: 33479216 PMCID: PMC7820243 DOI: 10.1038/s41467-020-20810-z] [Citation(s) in RCA: 19] [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: 04/21/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Prokaryotic restriction enzymes, recombinases and Cas proteins are powerful DNA engineering and genome editing tools. However, in many primary cell types, the efficiency of genome editing remains low, impeding the development of gene- and cell-based therapeutic applications. A safe strategy for robust and efficient enrichment of precisely genetically engineered cells is urgently required. Here, we screen for mutations in the receptor for Diphtheria Toxin (DT) which protect human cells from DT. Selection for cells with an edited DT receptor variant enriches for simultaneously introduced, precisely targeted gene modifications at a second independent locus, such as nucleotide substitutions and DNA insertions. Our method enables the rapid generation of a homogenous cell population with bi-allelic integration of a DNA cassette at the selection locus, without clonal isolation. Toxin-based selection works in both cancer-transformed and non-transformed cells, including human induced pluripotent stem cells and human primary T-lymphocytes, as well as it is applicable also in vivo, in mice with humanized liver. This work represents a flexible, precise, and efficient selection strategy to engineer cells using CRISPR-Cas and base editing systems.
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Affiliation(s)
- Songyuan Li
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Nina Akrap
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science and Experimental Medicine, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Michelle J Porritt
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Lundin
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Carl Möller
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- R&D Data Infrastructure & Tools, AstraZeneca, Cambridge, UK
| | - Euan Gordon
- Discovery Biology SWE, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bojana Lazovic
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Aleksandra Sieńska
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Luna Simona Pane
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Giovanni Ciotta
- Discovery Biology UK, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Giovanni Pellegrini
- CVRM pathology, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Marcella Sini
- CVRM pathology, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Xiufeng Xu
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Suman Mitra
- Inserm UMR1277 CNRS UMR9020 - CANTHER, Institut pour la Recherche sur le Cancer de Lille, Lille, France
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Benjamin J M Taylor
- Discovery Biology UK, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Grzegorz Sienski
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Marcello Maresca
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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19
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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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20
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21
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Xu W, Yang Y, Liu Y, Kang G, Wang F, Li L, Lv X, Zhao S, Yuan S, Song J, Wu Y, Feng F, He X, Zhang C, Song W, Zhao J, Yang J. Discriminated sgRNAs-Based SurroGate System Greatly Enhances the Screening Efficiency of Plant Base-Edited Cells. MOLECULAR PLANT 2020; 13:169-180. [PMID: 31634585 DOI: 10.1016/j.molp.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/27/2019] [Accepted: 10/13/2019] [Indexed: 05/13/2023]
Abstract
The development of CRISPR/Cas9-mediated base editing has made genomic modification more efficient. However, selection of genetically modified cells from millions of treated cells, especially plant cells, is still challenging. In this study, an efficient surrogate reporter system based on a defective hygromycin resistance gene was established in rice to enrich base-edited cells. After step-by-step optimization, the Discriminated sgRNAs-based SurroGate system (DisSUGs) was established by artificially differentiating the editing abilities of a wild-type single guide RNA (sgRNA) targeting the surrogate reporter gene and an enhanced sgRNA targeting endogenous sites. The DisSUGs enhanced the efficiency of screening base-edited cells by 3- to 5-fold for a PmCDA1-based cytosine-to-tyrosine base editor (PCBE), and 2.5- to 6.5-fold for an adenine base editor (ABE) at endogenous targets. These targets showed editing efficiencies of <25% in the conventional systems. The DisSUGs greatly enhanced the frequency of homozygous substitutions and expanded the activity window slightly for both a PCBE and an ABE. Analyses of the total number of single-nucleotide variants from whole-genome sequencing revealed that, compared with the no-enrichment PCBE strategy, the DisSUGs did not alter the frequency of genome-wide sgRNA-independent off-target mutations, but slightly increased the frequency of target-dependent off-target mutations. Collectively, the DisSUGs developed in this study greatly enhances the efficiency of screening plant base-edited cells and will be a useful system in future applications.
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Affiliation(s)
- Wen Xu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Yongxing Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Ya Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Guiting Kang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Feipeng Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Lu Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Xinxin Lv
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Si Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Shuang Yuan
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Jinling Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Ying Wu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Feng Feng
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Xiaoqing He
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China.
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China.
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China.
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22
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Yan N, Sun Y, Fang Y, Deng J, Mu L, Xu K, Mymryk JS, Zhang Z. A Universal Surrogate Reporter for Efficient Enrichment of CRISPR/Cas9-Mediated Homology-Directed Repair in Mammalian Cells. 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.
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Affiliation(s)
- Nana Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongsen Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanyuan Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingrong Deng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Mu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Joe S Mymryk
- Department of Microbiology & Immunology, Oncology and Otolaryngology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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23
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Ohtsuka M, Sato M. i-GONAD: A method for generating genome-edited animals without ex vivo handling of embryos. Dev Growth Differ 2019; 61:306-315. [PMID: 31198998 DOI: 10.1111/dgd.12620] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/05/2019] [Indexed: 01/01/2023]
Abstract
The recent development of genome editing technologies has enabled the creation of genome-edited animals, with alterations at the desired target locus. The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for this purpose because it is simpler and more efficient than other genome editing technologies. The conventional methods for creation of genome-edited animals involve ex vivo handling of embryos (zygotes) for microinjection or in vitro electroporation. However, this process is laborious and time-consuming, and relatively large numbers of animals are used. Furthermore, these methods require specialized skills for handling embryos. In 2015, we reported a novel method for the creation of genome-edited animals without ex vivo handling of embryos. The technology known as Genome-editing via Oviductal Nucleic Acids Delivery (GONAD) involved intraoviductal instillation of genome editing components into a pregnant female and subsequent in vivo electroporation of an entire oviduct. The genome editing components present in the oviductal lumen are transferred to preimplantation embryos in situ for introducing insertion or deletion (indel) mutations at the desired loci. This technology was further improved by optimizing several parameters to develop improved GONAD (i-GONAD) for the efficient generation of mutant or knock-in animals. In this review, we discuss the historical background, potential applications, advantages, and future challenges of GONAD/i-GONAD technology.
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Affiliation(s)
- Masato Ohtsuka
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa, Japan.,Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa, Japan.,The Institute of Medical Sciences, Tokai University, Kanagawa, Japan
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Japan
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24
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Chen M, Chen L, Zeng AP. CRISPR/Cas9-facilitated engineering with growth-coupled and sensor-guided in vivo screening of enzyme variants for a more efficient chorismate pathway in E. coli. Metab Eng Commun 2019; 9:e00094. [PMID: 31193188 PMCID: PMC6520568 DOI: 10.1016/j.mec.2019.e00094] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/01/2019] [Accepted: 05/01/2019] [Indexed: 01/24/2023] Open
Abstract
Protein engineering plays an increasingly important role in developing new and optimizing existing metabolic pathways for biosynthesis. Conventional screening approach of libraries of gene and enzyme variants is often done using a host strain under conditions not relevant to the cultivation or intracellular conditions of the later production strain. This does not necessarily result in the identification of the best enzyme variant for in vivo use in the production strain. In this work, we propose a method which integrates CRISPR/Cas9-facilitated engineering of the target gene(s) with growth-coupled and sensor-guided in vivo screening (CGSS) for protein engineering and pathway optimization. The efficiency of the method is demonstrated for engineering 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase AroG, a key enzyme in the chorismate pathway for the synthesis of aromatic amino acids (AAAs), to obtain variants of AroG (AroGfbr) with increased resistance to feedback inhibition of Phe. Starting from a tryptophan (Trp)-producing E. coli strain (harboring a reported Phe-resistant AroG variant AroGS180F), the removal of all the endogenous DAHP synthases makes the growth of this strain dependent on the activity of an introduced AroG variant. The different catalytic efficiencies of AroG variants lead to different intracellular concentration of Trp which is sensed by a Trp biosensor (TnaC-eGFP). Using the growth rate and the signal strength of the biosensor as criteria, we successfully identified several novel Phe-resistant AroG variants (including the best one AroGD6G−D7A) which exhibited higher specific enzyme activity than that of the reference variant AroGS180F at the presence of 40 mM Phe. The replacement of AroGS180F with the newly identified AroGD6G−D7A in the Trp-producing strain significantly improved the Trp production by 38.5% (24.03 ± 1.02 g/L at 36 h) in a simple fed-batch fermentation. A novel approach for phenotype-focused and product-targeted in vivo screening of enzyme variants. AroG variant with high resistance to feedback inhibition of phenylalanine. Tryptophan production in E. coli improved by 38.5% with the new variant AroGD6G−D7A.
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Affiliation(s)
- Minliang Chen
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
| | - Lin Chen
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, 100029, Beijing, China
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25
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Sun Y, Yan N, Mu L, Sun B, Deng J, Fang Y, Shao S, Yan Q, Han F, Zhang Z, Xu K. sgRNA-shRNA Structure Mediated SNP Site Editing on Porcine IGF2 Gene by CRISPR/StCas9. Front Genet 2019; 10:347. [PMID: 31057603 PMCID: PMC6482158 DOI: 10.3389/fgene.2019.00347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/01/2019] [Indexed: 12/26/2022] Open
Abstract
The SNP within intron 3 of the porcine IGF2 gene (G3072A) plays an important role for muscle growth and fat deposition in pigs. In this study, the StCas9 derived from Streptococcus thermophilus together with the Drosha-mediated sgRNA-shRNA structure were combined to boost the G to A base editing on the IGF2 SNP site, which we called “SNP editing.” The codon-humanized StCas9 as we previously reported was firstly compared with the prevalently used SpCas9 derived from Streptococcus pyogenes using our idiomatic surrogate report assay, and the StCas9 demonstrated a comparable targeting activity. On the other hand, by combining shRNA with sgRNA, simultaneous gene silencing and genome targeting can be achieved. Thus, the novel IGF2.sgRNA-LIG4.shRNA-IGF2.sgRNA structure was constructed to enhance the sgRNA/Cas9-mediated HDR-based IGF2 SNP editing by silencing the LIG4 gene, which is a key molecule of the HDR’s competitive NHEJ pathway. The sgRNA-shRNA/StCas9 all-in-one expression vector and the IGF2.sgRNA/StCas9 as control were separately used to transfect porcine PK15 cells together with an ssODNs donor for the IGF2 SNP editing. The editing events were detected by the RFLP assay, Sanger sequencing as well as Deep-sequencing, and the Deep-sequencing results finally demonstrated a significant higher HDR-based editing efficiency (16.38%) for our sgRNA-shRNA/StCas9 strategy. In short, we achieved effective IGF2 SNP editing by using the combined sgRNA-shRNA/StCas9 strategy, which will facilitate the further production of base-edited animals and perhaps extend for the gene therapy for the base correction of some genetic diseases.
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Affiliation(s)
- Yongsen Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Nana Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 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, China
| | - Bing Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 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, 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, China
| | - Simin Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiang Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Furong Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 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, China
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