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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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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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Wimmer T, Bonthu D, Moeschl V, Kleekamp P, Thiel C, Lytvynchuk L, Ellinwood M, Stieger K. A Bioluminescence Resonance Energy Transfer-Based Reporter System: Characterization and Applications. CRISPR J 2021; 4:884-895. [PMID: 34847743 DOI: 10.1089/crispr.2021.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome editing strategies and DNA repair research need powerful analytical tools. We generated a bioluminescence resonance energy transfer (BRET)-based reporter for the quantification of indel frequencies induced by DNA repair. The BRET reporter, expressed as a single molecule, consists of a mutated Renilla reniformis luciferase domain and a GFP2 domain separated by a shuttle-cloning box for the integration of any given endonuclease target sequence. The luciferase activity acts both as energy donor and as the internal standard, while the loss of GFP2 fluorescence acts as a reporter for the out-of-frame sequence alterations that result from the DNA repair via the non-homologous end joining/microhomology-mediated end joining DNA repair pathways of the endonuclease-mediated DNA double-strand break. This results in a decrease of the fluorescence/luminescence ratio. Employing this reporter in different experimental scenarios, using different cell lines and diseases targeted, we quantified the influence of both protein knockdown of DNA repair pathways as well as guide RNA mismatches on CRISPR-mediated nuclease activity and subsequent repair based on mutagenic repair on the reporter. In conclusion, we demonstrated this BRET-based reporter to be a robust and sensitive analytical tool for assessment of variety of different genome editing-based approaches.
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Affiliation(s)
- Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Dileep Bonthu
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Vincent Moeschl
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Philip Kleekamp
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christian Thiel
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Lyubomyr Lytvynchuk
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | | | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
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Jung SB, Lee CY, Lee KH, Heo K, Choi SH. A cleavage-based surrogate reporter for the evaluation of CRISPR-Cas9 cleavage efficiency. Nucleic Acids Res 2021; 49:e85. [PMID: 34086942 PMCID: PMC8421217 DOI: 10.1093/nar/gkab467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/30/2021] [Accepted: 05/17/2021] [Indexed: 12/03/2022] Open
Abstract
CRISPR-Cas9 is a powerful tool for genome engineering, but its efficiency largely depends on guide RNA (gRNA). There are multiple methods available to evaluate the efficiency of gRNAs, including the T7E1 assay, surveyor nuclease assay, deep sequencing, and surrogate reporter systems. In the present study, we developed a cleavage-based surrogate that we have named the LacI-reporter to evaluate gRNA cleavage efficiency. The LacI repressor, under the control of the EF-1α promoter, represses luciferase or EGFP reporter expression by binding to the lac operator. Upon CRISPR-Cas9 cleavage at a target site located between the EF-1α promoter and the lacI gene, repressor expression is disrupted, thereby triggering luciferase or EGFP expression. Using this system, we can quantitate gRNA cleavage efficiency by assessing luciferase activity or EGFP expression. We found a strong positive correlation between the cleavage efficiency of gRNAs measured using this reporter and mutation frequency, measured using surveyor and deep sequencing. The genome-editing efficiency of gRNAs was validated in human liver organoids. Our LacI-reporter system provides a useful tool to select efficient gRNAs for genome editing.
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Affiliation(s)
- Soo Bin Jung
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, 46033, Republic of Korea
| | - Chae young Lee
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, 46033, Republic of Korea
| | - Kwang-Ho Lee
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Kyu Heo
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, 46033, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, 46033, Republic of Korea
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Tang N, Zhang Y, Shen Z, Yao Y, Nair V. Application of CRISPR-Cas9 Editing for Virus Engineering and the Development of Recombinant Viral Vaccines. CRISPR J 2021; 4:477-490. [PMID: 34406035 DOI: 10.1089/crispr.2021.0017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technology, discovered originally as a bacterial defense system, has been extensively repurposed as a powerful tool for genome editing for multiple applications in biology. In the field of virology, CRISPR-Cas9 technology has been widely applied on genetic recombination and engineering of genomes of various viruses to ask some fundamental questions about virus-host interactions. Its high efficiency, specificity, versatility, and low cost have also provided great inspiration and hope in the field of vaccinology to solve a series of bottleneck problems in the development of recombinant viral vaccines. This review highlights the applications of CRISPR editing in the technological advances compared to the traditional approaches used for the construction of recombinant viral vaccines and vectors, the main factors affecting their application, and the challenges that need to be overcome for further streamlining their effective usage in the prevention and control of diseases. Factors affecting efficiency, target specificity, and fidelity of CRISPR-Cas editing in the context of viral genome editing and development of recombinant vaccines are also discussed.
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Affiliation(s)
- Na Tang
- Shandong Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, P.R. China; University of Oxford, Oxford, United Kingdom
| | - Yaoyao Zhang
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Zhiqiang Shen
- Shandong Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, P.R. China; University of Oxford, Oxford, United Kingdom
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom.,The Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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Jung H, Rim YA, Park N, Nam Y, Ju JH. Restoration of Osteogenesis by CRISPR/Cas9 Genome Editing of the Mutated COL1A1 Gene in Osteogenesis Imperfecta. J Clin Med 2021; 10:jcm10143141. [PMID: 34300306 PMCID: PMC8307903 DOI: 10.3390/jcm10143141] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 01/13/2023] Open
Abstract
Osteogenesis imperfecta (OI) is a genetic disease characterized by bone fragility and repeated fractures. The bone fragility associated with OI is caused by a defect in collagen formation due to mutation of COL1A1 or COL1A2. Current strategies for treating OI are not curative. In this study, we generated induced pluripotent stem cells (iPSCs) from OI patient-derived blood cells harboring a mutation in the COL1A1 gene. Osteoblast (OB) differentiated from OI-iPSCs showed abnormally decreased levels of type I collagen and osteogenic differentiation ability. Gene correction of the COL1A1 gene using CRISPR/Cas9 recovered the decreased type I collagen expression in OBs differentiated from OI-iPSCs. The osteogenic potential of OI-iPSCs was also recovered by the gene correction. This study suggests a new possibility of treatment and in vitro disease modeling using patient-derived iPSCs and gene editing with CRISPR/Cas9.
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Affiliation(s)
- Hyerin Jung
- CiSTEM Laboratory, Convergent Research Consortium for Immunologic Disease, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea; (H.J.); (Y.A.R.); (N.P.)
- Catholic iPSC Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea
| | - Yeri Alice Rim
- CiSTEM Laboratory, Convergent Research Consortium for Immunologic Disease, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea; (H.J.); (Y.A.R.); (N.P.)
- Catholic iPSC Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea
| | - Narae Park
- CiSTEM Laboratory, Convergent Research Consortium for Immunologic Disease, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea; (H.J.); (Y.A.R.); (N.P.)
- Catholic iPSC Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea
| | - Yoojun Nam
- YiPSCELL, Inc., 39 Banpo-daero, Seocho-gu, Seoul 06579, Korea;
| | - Ji Hyeon Ju
- CiSTEM Laboratory, Convergent Research Consortium for Immunologic Disease, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea; (H.J.); (Y.A.R.); (N.P.)
- Catholic iPSC Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea
- YiPSCELL, Inc., 39 Banpo-daero, Seocho-gu, Seoul 06579, Korea;
- Divison of Rheumatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06281, Korea
- Correspondence: ; Tel.: +82-2-2258-6013
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