1
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Husser MC, Pham NP, Law C, Araujo FRB, Martin VJJ, Piekny A. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies. eLife 2024; 12:RP92819. [PMID: 38652106 PMCID: PMC11037917 DOI: 10.7554/elife.92819] [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] [Indexed: 04/25/2024] Open
Abstract
Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.
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Affiliation(s)
| | - Nhat P Pham
- Biology Department, Concordia University, Montreal, Canada
| | - Chris Law
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
| | - Flavia R B Araujo
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Biology Department, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Alisa Piekny
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
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2
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Chen X, Zhong S, Zhan Y, Zhang X. CRISPR-Cas9 applications in T cells and adoptive T cell therapies. Cell Mol Biol Lett 2024; 29:52. [PMID: 38609863 PMCID: PMC11010303 DOI: 10.1186/s11658-024-00561-1] [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: 12/04/2023] [Accepted: 03/15/2024] [Indexed: 04/14/2024] Open
Abstract
T cell immunity is central to contemporary cancer and autoimmune therapies, encompassing immune checkpoint blockade and adoptive T cell therapies. Their diverse characteristics can be reprogrammed by different immune challenges dependent on antigen stimulation levels, metabolic conditions, and the degree of inflammation. T cell-based therapeutic strategies are gaining widespread adoption in oncology and treating inflammatory conditions. Emerging researches reveal that clustered regularly interspaced palindromic repeats-associated protein 9 (CRISPR-Cas9) genome editing has enabled T cells to be more adaptable to specific microenvironments, opening the door to advanced T cell therapies in preclinical and clinical trials. CRISPR-Cas9 can edit both primary T cells and engineered T cells, including CAR-T and TCR-T, in vivo and in vitro to regulate T cell differentiation and activation states. This review first provides a comprehensive summary of the role of CRISPR-Cas9 in T cells and its applications in preclinical and clinical studies for T cell-based therapies. We also explore the application of CRISPR screen high-throughput technology in editing T cells and anticipate the current limitations of CRISPR-Cas9, including off-target effects and delivery challenges, and envisioned improvements in related technologies for disease screening, diagnosis, and treatment.
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Affiliation(s)
- Xiaoying Chen
- Department of Cardiology, Cardiovascular Institute of Zhengzhou University, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Shuhan Zhong
- Department of Hematology, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, 310003, China
| | - Yonghao Zhan
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450003, China.
| | - Xuepei Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450003, China.
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3
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Zhao JJ, Sun XY, Tian SN, Zhao ZZ, Yin MD, Zhao M, Zhang F, Li SA, Yang ZX, Wen W, Cheng T, Gong A, Zhang JP, Zhang XB. Decoding the complexity of on-target integration: characterizing DNA insertions at the CRISPR-Cas9 targeted locus using nanopore sequencing. BMC Genomics 2024; 25:189. [PMID: 38368357 PMCID: PMC10874558 DOI: 10.1186/s12864-024-10050-6] [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: 06/05/2023] [Accepted: 01/24/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND CRISPR-Cas9 technology has advanced in vivo gene therapy for disorders like hemophilia A, notably through the successful targeted incorporation of the F8 gene into the Alb locus in hepatocytes, effectively curing this disorder in mice. However, thoroughly evaluating the safety and specificity of this therapy is essential. Our study introduces a novel methodology to analyze complex insertion sequences at the on-target edited locus, utilizing barcoded long-range PCR, CRISPR RNP-mediated deletion of unedited alleles, magnetic bead-based long amplicon enrichment, and nanopore sequencing. RESULTS We identified the expected F8 insertions and various fragment combinations resulting from the in vivo linearization of the double-cut plasmid donor. Notably, our research is the first to document insertions exceeding ten kbp. We also found that a small proportion of these insertions were derived from sources other than donor plasmids, including Cas9-sgRNA plasmids, genomic DNA fragments, and LINE-1 elements. CONCLUSIONS Our study presents a robust method for analyzing the complexity of on-target editing, particularly for in vivo long insertions, where donor template integration can be challenging. This work offers a new tool for quality control in gene editing outcomes and underscores the importance of detailed characterization of edited genomic sequences. Our findings have significant implications for enhancing the safety and effectiveness of CRISPR-Cas9 gene therapy in treating various disorders, including hemophilia A.
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Affiliation(s)
- Juan-Juan Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xin-Yu Sun
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | | | - Zong-Ze Zhao
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266000, China
| | - Meng-Di Yin
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - An Gong
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266000, China.
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
- Tianjin Medical University, Tianjin, China.
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4
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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [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: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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5
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Baik R, Cromer MK, Glenn SE, Vakulskas CA, Chmielewski KO, Dudek AM, Feist WN, Klermund J, Shipp S, Cathomen T, Dever DP, Porteus MH. Transient inhibition of 53BP1 increases the frequency of targeted integration in human hematopoietic stem and progenitor cells. Nat Commun 2024; 15:111. [PMID: 38169468 PMCID: PMC10762240 DOI: 10.1038/s41467-023-43413-w] [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: 02/23/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named "i53") as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.
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Affiliation(s)
- Ron Baik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steve E Glenn
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Amanda M Dudek
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - William N Feist
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Suzette Shipp
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel P Dever
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Koller F, Cieslak M. A perspective from the EU: unintended genetic changes in plants caused by NGT-their relevance for a comprehensive molecular characterisation and risk assessment. Front Bioeng Biotechnol 2023; 11:1276226. [PMID: 37965049 PMCID: PMC10641861 DOI: 10.3389/fbioe.2023.1276226] [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: 08/11/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Several regions in the world are currently holding discussions in regard to the regulation of new genomic techniques (NGTs) and their application in agriculture. The European Commission, for instance, is proposing the introduction of specific regulation for NGT plants. Various questions need to be answered including e.g., the extent to which NGT-induced intended and unintended genetic modifications must be subjected to a mandatory risk assessment as part of an approval procedure. This review mostly focuses on findings in regard to unintended genetic changes that can be caused by the application of NGTs. More specifically, the review deals with the application of the nuclease CRISPR/Cas, which is currently the most important tool for developing NGT plants, and its potential to introduce double strand breaks (DSBs) at a targeted DNA sequence. For this purpose, we identified the differences in comparison to non-targeted mutagenesis methods used in conventional breeding. The review concludes that unintended genetic changes caused by NGT processes are relevant to risk assessment. Due to the technical characteristics of NGTs, the sites of the unintended changes, their genomic context and their frequency (in regard to specific sites) mean that the resulting gene combinations (intended or unintended) may be unlikely to occur with conventional methods. This, in turn, implies that the biological effects (phenotypes) can also be different and may cause risks to health and the environment. Therefore, we conclude that the assessment of intended as well as unintended genetic changes should be part of a mandatory comprehensive molecular characterisation and risk assessment of NGT plants that are meant for environmental releases or for market authorisation.
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Affiliation(s)
- Franziska Koller
- Fachstelle Gentechnik und Umwelt (FGU), Munich, Bavaria, Germany
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7
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Li B, Liu J, Huang Q. A Digital PCR Method Based on Highly Specific Taq for Detecting Gene Editing and Mutations. Int J Mol Sci 2023; 24:13405. [PMID: 37686219 PMCID: PMC10488114 DOI: 10.3390/ijms241713405] [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: 08/08/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Digital PCR (dPCR) has great potential for assessing gene editing or gene mutation due to its ability to independently inspect each DNA template in parallel. However, current dPCR methods use a fluorescence-labeled probe to detect gene variation events, and their ability to distinguish variated sequences from the wild-type sequence is limited by the probe's tolerance to mismatch. To address this, we have developed a novel dPCR method that uses a primer instead of a probe to sense gene variation. The enhanced Taq DNA polymerase in the PCR system has a high mismatch sensitivity, which enables our dPCR method to distinguish gene mutations from wild-type sequences. Compared to current dPCR methods, our method shows superior precision in assessing gene editing efficiency and single-base DNA mutation. This presents a promising opportunity to advance gene editing research and rare gene mutation detection.
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Affiliation(s)
| | | | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
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8
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Medert R, Thumberger T, Tavhelidse-Suck T, Hub T, Kellner T, Oguchi Y, Dlugosz S, Zimmermann F, Wittbrodt J, Freichel M. Efficient single copy integration via homology-directed repair (scHDR) by 5'modification of large DNA donor fragments in mice. Nucleic Acids Res 2023; 51:e14. [PMID: 36533445 PMCID: PMC10021492 DOI: 10.1093/nar/gkac1150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 09/22/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas-based approaches have largely replaced conventional gene targeting strategies. However, homology-directed repair (HDR) in the mouse genome is not very efficient, and precisely inserting longer sequences using HDR remains challenging given that donor constructs preferentially integrate as concatemers. Here, we showed that injecting 5' biotinylated donor DNA into mouse embryos at the two-cell stage led to efficient single-copy HDR (scHDR) allele generation. Our dedicated genotyping strategy showed that these alleles occurred with frequencies of 19%, 20%, and 26% at three independent gene loci, indicating that scHDR was dramatically increased by 5' biotinylation. Thus, we suggest that the combination of a 5' biotinylated donor and diligent analysis of concatemer integration are prerequisites for efficiently and reliably generating conditional alleles or other large fragment knock-ins in the mouse genome.
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Affiliation(s)
- Rebekka Medert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Tobias Hub
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yoko Oguchi
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Sascha Dlugosz
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Frank Zimmermann
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
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9
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Erbs V, Lorentz R, Eisenman B, Schaeffer L, Luppi L, Lindner L, Hérault Y, Pavlovic G, Wattenhofer-Donzé M, Birling MC. Increased On-Target Rate and Risk of Concatemerization after CRISPR-Enhanced Targeting in ES Cells. Genes (Basel) 2023; 14:genes14020401. [PMID: 36833328 PMCID: PMC9957269 DOI: 10.3390/genes14020401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The French mouse clinic (Institut Clinique de la Souris; ICS) has produced more than 2000 targeting vectors for 'à la carte' mutagenesis in C57BL/6N mice. Although most of the vectors were used successfully for homologous recombination in murine embryonic stem cells (ESCs), a few have failed to target a specific locus after several attempts. We show here that co-electroporation of a CRISPR plasmid with the same targeting construct as the one that failed previously allows the systematic achievement of positive clones. A careful validation of these clones is, however, necessary as a significant number of clones (but not all) show a concatemerization of the targeting plasmid at the locus. A detailed Southern blot analysis permitted characterization of the nature of these events as standard long-range 5' and 3' PCRs were not able to distinguish between correct and incorrect alleles. We show that a simple and inexpensive PCR performed prior to ESC amplification allows detection and elimination of those clones with concatemers. Finally, although we only tested murine ESCs, our results highlight the risk of mis-validation of any genetically modified cell line (such as established lines, induced pluripotent stem cells or those used for ex vivo gene therapy) that combines the use of CRISPR/Cas9 and a circular double-stranded donor. We strongly advise the CRISPR community to perform a Southern blot with internal probes when using CRISPR to enhance homologous recombination in any cell type, including fertilized oocytes.
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Affiliation(s)
- Valérie Erbs
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Romain Lorentz
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Benjamin Eisenman
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Laurence Schaeffer
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Laurence Luppi
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Loic Lindner
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Yann Hérault
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
- CNRS, INSERM, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Translational Medicine and Neurogenetics, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Guillaume Pavlovic
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Marie Wattenhofer-Donzé
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Marie-Christine Birling
- CNRS, INSERM, Université de Strasbourg, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
- Correspondence:
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10
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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11
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Cockey JR, Leifer CA. Racing CARs to veterinary immuno-oncology. Front Vet Sci 2023; 10:1130182. [PMID: 36876006 PMCID: PMC9982037 DOI: 10.3389/fvets.2023.1130182] [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: 12/22/2022] [Accepted: 01/31/2023] [Indexed: 02/19/2023] Open
Abstract
Chimeric antigen receptors (CARs) have demonstrated remarkable promise in human oncology over the past two decades, yet similar strategies in veterinary medicine are still in development. CARs are synthetically engineered proteins comprised of a specific antigen-binding single chain variable fragment (ScFv) fused to the signaling domain of a T cell receptor and co-receptors. Patient T cells engineered to express a CAR are directed to recognize and kill target cells, most commonly hematological malignancies. The U.S Food and Drug Administration (FDA) has approved multiple human CAR T therapies, but translation of these therapies into veterinary medicine faces many challenges. In this review, we discuss considerations for veterinary use including CAR design and cell carrier choice, and discuss the future promise of translating CAR therapy into veterinary oncology.
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Affiliation(s)
- James R Cockey
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Cynthia A Leifer
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
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12
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Vidalis T. Genome Editing in Human Gametes and Embryos: The Legal Dimension in Europe. BIOTECH (BASEL (SWITZERLAND)) 2022; 12:biotech12010001. [PMID: 36648827 PMCID: PMC9844473 DOI: 10.3390/biotech12010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
To date, the legal aspects of the ongoing debate on the application of genome editing in human gametes and early embryos have attracted little attention. In Europe, this seems to have changed with a recent official position that clarifies the meaning of the relevant provision of the common legal instrument on Human Rights and Biomedicine (Oviedo Convention). This provision explicitly prohibits modifications to the genome of future persons and adoptes a precautionary stance with regard to genetic interventions in the human reproductive material. In this article, we examine relevant interpretative options, following the new official clarifications, focusing on the research/clinical application distinctions that characterize their approach. From this viewpoint, we propose an approach that favors basic research activities involving genome editing, even for exploring potential clinical applications under conditions of safety, which may justify a future legislative amendment. Furthermore, we explore the patenting issue, based on the current approach of European case law, and give reasons that may justify patent rights in this ethically sensitive area.
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Affiliation(s)
- Takis Vidalis
- Hellenic National Commission for Bioethics & Technoethics, 10674 Athens, Greece
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13
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O'Reilly M, Sommerfeld LC, O'Shea C, Broadway-Stringer S, Andaleeb S, Reyat JS, Kabir SN, Stastny D, Malinova A, Delbue D, Fortmueller L, Gehmlich K, Pavlovic D, Skryabin BV, Holmes AP, Kirchhof P, Fabritz L. Familial atrial fibrillation mutation M1875T-SCN5A increases early sodium current and dampens the effect of flecainide. Europace 2022; 25:1152-1161. [PMID: 36504385 PMCID: PMC10062360 DOI: 10.1093/europace/euac218] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
AIMS Atrial fibrillation (AF) is the most common cardiac arrhythmia. Pathogenic variants in genes encoding ion channels are associated with familial AF. The point mutation M1875T in the SCN5A gene, which encodes the α-subunit of the cardiac sodium channel Nav1.5, has been associated with increased atrial excitability and familial AF in patients. METHODS AND RESULTS We designed a new murine model carrying the Scn5a-M1875T mutation enabling us to study the effects of the Nav1.5 mutation in detail in vivo and in vitro using patch clamp and microelectrode recording of atrial cardiomyocytes, optical mapping, electrocardiogram, echocardiography, gravimetry, histology, and biochemistry. Atrial cardiomyocytes from newly generated adult Scn5a-M1875T+/- mice showed a selective increase in the early (peak) cardiac sodium current, larger action potential amplitude, and a faster peak upstroke velocity. Conduction slowing caused by the sodium channel blocker flecainide was less pronounced in Scn5a-M1875T+/- compared to wildtype atria. Overt hypertrophy or heart failure in Scn5a-M1875T+/- mice could be excluded. CONCLUSION The Scn5a-M1875T point mutation causes gain-of-function of the cardiac sodium channel. Our results suggest increased atrial peak sodium current as a potential trigger for increased atrial excitability.
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Affiliation(s)
- Molly O'Reilly
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK.,Department of Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Laura C Sommerfeld
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK.,University Center of Cardiovascular Science, University Heart and Vascular Center, UKE Hamburg, Martinistraße 52, Hamburg 20246, Germany.,DZHK Standort Hamburg/Kiel/Luebeck, Martinistraße 52, Hamburg 20246, Germany
| | - C O'Shea
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK
| | - S Broadway-Stringer
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK
| | - S Andaleeb
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK
| | - J S Reyat
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK
| | - S N Kabir
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK
| | - D Stastny
- University Center of Cardiovascular Science, University Heart and Vascular Center, UKE Hamburg, Martinistraße 52, Hamburg 20246, Germany
| | - A Malinova
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK
| | - D Delbue
- University Center of Cardiovascular Science, University Heart and Vascular Center, UKE Hamburg, Martinistraße 52, Hamburg 20246, Germany.,DZHK Standort Hamburg/Kiel/Luebeck, Martinistraße 52, Hamburg 20246, Germany
| | - L Fortmueller
- University Center of Cardiovascular Science, University Heart and Vascular Center, UKE Hamburg, Martinistraße 52, Hamburg 20246, Germany.,DZHK Standort Hamburg/Kiel/Luebeck, Martinistraße 52, Hamburg 20246, Germany
| | - K Gehmlich
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Oxford, UK
| | - D Pavlovic
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK
| | - B V Skryabin
- Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - A P Holmes
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK.,Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - P Kirchhof
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK.,DZHK Standort Hamburg/Kiel/Luebeck, Martinistraße 52, Hamburg 20246, Germany.,Department of Cardiology, University Heart and Vascular Center, UKE Hamburg, Martinistraße 52, Hamburg 20246, Germany
| | - L Fabritz
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Wolfson Drive, Birmingham B15 2TT, UK.,University Center of Cardiovascular Science, University Heart and Vascular Center, UKE Hamburg, Martinistraße 52, Hamburg 20246, Germany.,DZHK Standort Hamburg/Kiel/Luebeck, Martinistraße 52, Hamburg 20246, Germany.,Department of Cardiology, University Heart and Vascular Center, UKE Hamburg, Martinistraße 52, Hamburg 20246, Germany
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14
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Yoshida M, Saito T, Takayanagi Y, Totsuka Y, Onaka T. Necessity of integrated genomic analysis to establish a designed knock-in mouse from CRISPR-Cas9-induced mutants. Sci Rep 2022; 12:20390. [PMID: 36437283 PMCID: PMC9701781 DOI: 10.1038/s41598-022-24810-5] [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: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The CRISPR-Cas9 method for generation of knock-in mutations in rodent embryos yields many F0 generation candidates that may have the designed mutations. The first task for selection of promising F0 generations is to analyze genomic DNA which likely contains a mixture of designed and unexpected mutations. In our study, while generating Prlhr-Venus knock-in reporter mice, we found that genomic rearrangements near the targeted knock-in allele, tandem multicopies at a target allele locus, and mosaic genotypes for two different knock-in alleles occurred in addition to the designed knock-in mutation in the F0 generation. Conventional PCR and genomic sequencing were not able to detect mosaicism nor discriminate between the designed one-copy knock-in mutant and a multicopy-inserted mutant. However, by using a combination of Southern blotting and the next-generation sequencing-based RAISING method, these mutants were successfully detected in the F0 generation. In the F1 and F2 generations, droplet digital PCR assisted in establishing the strain, although a multicopy was falsely detected as one copy by analysis of the F0 generation. Thus, the combination of these methods allowed us to select promising F0 generations and facilitated establishment of the designed strain. We emphasize that focusing only on positive evidence of knock-in can lead to erroneous selection of undesirable strains.
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Affiliation(s)
- Masahide Yoshida
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Tomoko Saito
- Institute of Immunology Co., Ltd., 1198-4 Iwazo, Utsunomiya, Tochigi 321-0973 Japan
| | - Yuki Takayanagi
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Yoshikazu Totsuka
- Institute of Immunology Co., Ltd., 1198-4 Iwazo, Utsunomiya, Tochigi 321-0973 Japan
| | - Tatsushi Onaka
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
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15
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CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae. Nat Commun 2022; 13:7168. [PMID: 36418866 PMCID: PMC9684475 DOI: 10.1038/s41467-022-34736-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR-Cas mediated genome engineering has revolutionized functional genomics. However, understanding of DNA repair following Cas-mediated DNA cleavage remains incomplete. Using Cas12a ribonucleoprotein genome editing in the fungal pathogen, Magnaporthe oryzae, we detail non-canonical DNA repair outcomes from hundreds of transformants. Sanger and nanopore sequencing analysis reveals significant variation in DNA repair profiles, ranging from small INDELs to kilobase size deletions and insertions. Furthermore, we find the frequency of DNA repair outcomes varies between loci. The results are not specific to the Cas-nuclease or selection procedure. Through Ku80 deletion analysis, a key protein required for canonical non-homologous end joining, we demonstrate activity of an alternative end joining mechanism that creates larger DNA deletions, and uses longer microhomology compared to C-NHEJ. Together, our results suggest preferential DNA repair pathway activity in the genome that can create different mutation profiles following repair, which could create biased genome variation and impact genome engineering and genome evolution.
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16
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Wienert B, Cromer MK. CRISPR nuclease off-target activity and mitigation strategies. Front Genome Ed 2022; 4:1050507. [PMID: 36439866 PMCID: PMC9685173 DOI: 10.3389/fgeed.2022.1050507] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
The discovery of CRISPR has allowed site-specific genomic modification to become a reality and this technology is now being applied in a number of human clinical trials. While this technology has demonstrated impressive efficacy in the clinic to date, there remains the potential for unintended on- and off-target effects of CRISPR nuclease activity. A variety of in silico-based prediction tools and empirically derived experimental methods have been developed to identify the most common unintended effect-small insertions and deletions at genomic sites with homology to the guide RNA. However, large-scale aberrations have recently been reported such as translocations, inversions, deletions, and even chromothripsis. These are more difficult to detect using current workflows indicating a major unmet need in the field. In this review we summarize potential sequencing-based solutions that may be able to detect these large-scale effects even at low frequencies of occurrence. In addition, many of the current clinical trials using CRISPR involve ex vivo isolation of a patient's own stem cells, modification, and re-transplantation. However, there is growing interest in direct, in vivo delivery of genome editing tools. While this strategy has the potential to address disease in cell types that are not amenable to ex vivo manipulation, in vivo editing has only one desired outcome-on-target editing in the cell type of interest. CRISPR activity in unintended cell types (both on- and off-target) is therefore a major safety as well as ethical concern in tissues that could enable germline transmission. In this review, we have summarized the strengths and weaknesses of current editing and delivery tools and potential improvements to off-target and off-tissue CRISPR activity detection. We have also outlined potential mitigation strategies that will ensure that the safety of CRISPR keeps pace with efficacy, a necessary requirement if this technology is to realize its full translational potential.
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Affiliation(s)
- Beeke Wienert
- Graphite Bio, Inc., South San Francisco, CA, United States
| | - M. Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States,Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA, United States,*Correspondence: M. Kyle Cromer,
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17
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Almeida RS, Wisnieski F, Takao Real Karia B, Smith MAC. CRISPR/Cas9 Genome-Editing Technology and Potential Clinical Application in Gastric Cancer. Genes (Basel) 2022; 13:2029. [PMID: 36360266 PMCID: PMC9690943 DOI: 10.3390/genes13112029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 10/09/2023] Open
Abstract
Gastric cancer is the subject of clinical and basic studies due to its high incidence and mortality rates worldwide. Due to the diagnosis occurring in advanced stages and the classic treatment methodologies such as gastrectomy and chemotherapy, they are extremely aggressive and limit the quality of life of these patients. CRISPR/Cas9 is a tool that allows gene editing and has been used to explore the functions of genes related to gastric cancer, in addition to being used in the treatment of this neoplasm, greatly increasing our understanding of cancer genomics. In this mini-review, we seek the current status of the CRISPR/Cas9 gene-editing technology in gastric cancer research and clinical research.
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Affiliation(s)
- Renata Sanches Almeida
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
| | - Fernanda Wisnieski
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
- Discipline of Gastroenterology, Department of Medicine, Federal University of São Paulo, Rua Loefgreen, 1726, São Paulo 04040002, Brazil
| | - Bruno Takao Real Karia
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
| | - Marilia Arruda Cardoso Smith
- Discipline of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, Rua Botucatu, 740, São Paulo 04023900, Brazil
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18
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Zech ATL, Prondzynski M, Singh SR, Pietsch N, Orthey E, Alizoti E, Busch J, Madsen A, Behrens CS, Meyer-Jens M, Mearini G, Lemoine MD, Krämer E, Mosqueira D, Virdi S, Indenbirken D, Depke M, Salazar MG, Völker U, Braren I, Pu WT, Eschenhagen T, Hammer E, Schlossarek S, Carrier L. ACTN2 Mutant Causes Proteopathy in Human iPSC-Derived Cardiomyocytes. Cells 2022; 11:cells11172745. [PMID: 36078153 PMCID: PMC9454684 DOI: 10.3390/cells11172745] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variants in α-actinin-2 (ACTN2) are associated with several forms of (cardio)myopathy. We previously reported a heterozygous missense (c.740C>T) ACTN2 gene variant, associated with hypertrophic cardiomyopathy, and characterized by an electro-mechanical phenotype in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Here, we created with CRISPR/Cas9 genetic tools two heterozygous functional knock-out hiPSC lines with a second wild-type (ACTN2wt) and missense ACTN2 (ACTN2mut) allele, respectively. We evaluated their impact on cardiomyocyte structure and function, using a combination of different technologies, including immunofluorescence and live cell imaging, RNA-seq, and mass spectrometry. This study showed that ACTN2mut presents a higher percentage of multinucleation, protein aggregation, hypertrophy, myofibrillar disarray, and activation of both the ubiquitin-proteasome system and the autophagy-lysosomal pathway as compared to ACTN2wt in 2D-cultured hiPSC-CMs. Furthermore, the expression of ACTN2mut was associated with a marked reduction of sarcomere-associated protein levels in 2D-cultured hiPSC-CMs and force impairment in engineered heart tissues. In conclusion, our study highlights the activation of proteolytic systems in ACTN2mut hiPSC-CMs likely to cope with ACTN2 aggregation and therefore directs towards proteopathy as an additional cellular pathology caused by this ACTN2 variant, which may contribute to human ACTN2-associated cardiomyopathies.
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Affiliation(s)
- Antonia T. L. Zech
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Maksymilian Prondzynski
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia R. Singh
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Niels Pietsch
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Ellen Orthey
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Erda Alizoti
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Josefine Busch
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Alexandra Madsen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Charlotta S. Behrens
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Moritz Meyer-Jens
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Giulia Mearini
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Marc D. Lemoine
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
- Department of Cardiology, University Heart and Vascular Center, 20246 Hamburg, Germany
| | - Elisabeth Krämer
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Diogo Mosqueira
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Sanamjeet Virdi
- Heinrich-Pette-Institute, Leibniz Institute of Virology, 20246 Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute of Virology, 20246 Hamburg, Germany
| | - Maren Depke
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Manuela Gesell Salazar
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Ingke Braren
- Vector Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Elke Hammer
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Saskia Schlossarek
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Lucie Carrier
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
- Correspondence: ; Tel.: +49-40-7410-57208
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19
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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20
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Tao J, Wang Q, Mendez-Dorantes C, Burns KH, Chiarle R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat Commun 2022; 13:3685. [PMID: 35760782 PMCID: PMC9237045 DOI: 10.1038/s41467-022-31322-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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21
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Huang YY, Zhang XY, Zhu P, Ji L. Development of clustered regularly interspaced short palindromic repeats/CRISPR-associated technology for potential clinical applications. World J Clin Cases 2022; 10:5934-5945. [PMID: 35949837 PMCID: PMC9254185 DOI: 10.12998/wjcc.v10.i18.5934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 04/24/2022] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) proteins constitute the innate adaptive immune system in several bacteria and archaea. This immune system helps them in resisting the invasion of phages and foreign DNA by providing sequence-specific acquired immunity. Owing to the numerous advantages such as ease of use, low cost, high efficiency, good accuracy, and a diverse range of applications, the CRISPR-Cas system has become the most widely used genome editing technology. Hence, the advent of the CRISPR/Cas technology highlights a tremendous potential in clinical diagnosis and could become a powerful asset for modern medicine. This study reviews the recently reported application platforms for screening, diagnosis, and treatment of different diseases based on CRISPR/Cas systems. The limitations, current challenges, and future prospectus are summarized; this article would be a valuable reference for future genome-editing practices.
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Affiliation(s)
- Yue-Ying Huang
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Xiao-Yu Zhang
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Ping Zhu
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Ling Ji
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen 518035, Guangdong Province, China
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22
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Huang Y, Shang M, Liu T, Wang K. High-throughput methods for genome editing: the more the better. PLANT PHYSIOLOGY 2022; 188:1731-1745. [PMID: 35134245 PMCID: PMC8968257 DOI: 10.1093/plphys/kiac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 05/04/2023]
Abstract
During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.
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Affiliation(s)
- Yong Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Meiqi Shang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Tingting Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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23
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Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
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Affiliation(s)
- Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada.
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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24
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Kuno A, Ikeda Y, Ayabe S, Kato K, Sakamoto K, Suzuki SR, Morimoto K, Wakimoto A, Mikami N, Ishida M, Iki N, Hamada Y, Takemura M, Daitoku Y, Tanimoto Y, Dinh TTH, Murata K, Hamada M, Muratani M, Yoshiki A, Sugiyama F, Takahashi S, Mizuno S. DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. PLoS Biol 2022; 20:e3001507. [PMID: 35041655 PMCID: PMC8765641 DOI: 10.1371/journal.pbio.3001507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.
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Affiliation(s)
- Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Ikeda
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kotaro Sakamoto
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Sayaka R. Suzuki
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Arata Wakimoto
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Natsuki Mikami
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Miyuki Ishida
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Natsumi Iki
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuko Hamada
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Megumi Takemura
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tra Thi Huong Dinh
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuya Murata
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Michito Hamada
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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25
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Smirnov A, Battulin N. Concatenation of Transgenic DNA: Random or Orchestrated? Genes (Basel) 2021; 12:genes12121969. [PMID: 34946918 PMCID: PMC8701086 DOI: 10.3390/genes12121969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Generation of transgenic organisms by pronuclear microinjection has become a routine procedure. However, while the process of DNA integration in the genome is well understood, we still do not know much about the recombination between transgene molecules that happens in the first moments after DNA injection. Most of the time, injected molecules are joined together in head-to-tail tandem repeats-the so-called concatemers. In this review, we focused on the possible concatenation mechanisms and how they could be studied with genetic reporters tracking individual copies in concatemers. We also discuss various features of concatemers, including palindromic junctions and repeat-induced gene silencing (RIGS). Finally, we speculate how cooperation of DNA repair pathways creates a multicopy concatenated insert.
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Affiliation(s)
- Alexander Smirnov
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Institute of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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26
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Knockout of Anopheles stephensi immune gene LRIM1 by CRISPR-Cas9 reveals its unexpected role in reproduction and vector competence. PLoS Pathog 2021; 17:e1009770. [PMID: 34784388 PMCID: PMC8631644 DOI: 10.1371/journal.ppat.1009770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/30/2021] [Accepted: 11/01/2021] [Indexed: 12/27/2022] Open
Abstract
PfSPZ Vaccine against malaria is composed of Plasmodium falciparum (Pf) sporozoites (SPZ) manufactured using aseptically reared Anopheles stephensi mosquitoes. Immune response genes of Anopheles mosquitoes such as Leucin-Rich protein (LRIM1), inhibit Plasmodium SPZ development (sporogony) in mosquitoes by supporting melanization and phagocytosis of ookinetes. With the aim of increasing PfSPZ infection intensities, we generated an A. stephensi LRIM1 knockout line, Δaslrim1, by embryonic genome editing using CRISPR-Cas9. Δaslrim1 mosquitoes had a significantly increased midgut bacterial load and an altered microbiome composition, including elimination of commensal acetic acid bacteria. The alterations in the microbiome caused increased mosquito mortality and unexpectedly, significantly reduced sporogony. The survival rate of Δaslrim1 mosquitoes and their ability to support PfSPZ development, were partially restored by antibiotic treatment of the mosquitoes, and fully restored to baseline when Δaslrim1 mosquitoes were produced aseptically. Deletion of LRIM1 also affected reproductive capacity: oviposition, fecundity and male fertility were significantly compromised. Attenuation in fecundity was not associated with the altered microbiome. This work demonstrates that LRIM1's regulation of the microbiome has a major impact on vector competence and longevity of A. stephensi. Additionally, LRIM1 deletion identified an unexpected role for this gene in fecundity and reduction of sperm transfer by males.
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27
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Bork NI, Kuret A, Cruz Santos M, Molina CE, Reiter B, Reichenspurner H, Friebe A, Skryabin BV, Rozhdestvensky TS, Kuhn M, Lukowski R, Nikolaev VO. Rise of cGMP by partial phosphodiesterase-3A degradation enhances cardioprotection during hypoxia. Redox Biol 2021; 48:102179. [PMID: 34763298 PMCID: PMC8590074 DOI: 10.1016/j.redox.2021.102179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
3',5'-cyclic guanosine monophosphate (cGMP) is a druggable second messenger regulating cell growth and survival in a plethora of cells and disease states, many of which are associated with hypoxia. For example, in myocardial infarction and heart failure (HF), clinical use of cGMP-elevating drugs improves disease outcomes. Although they protect mice from ischemia/reperfusion (I/R) injury, the exact mechanism how cardiac cGMP signaling is regulated in response to hypoxia is still largely unknown. By monitoring real-time cGMP dynamics in murine and human cardiomyocytes using in vitro and in vivo models of hypoxia/reoxygenation (H/R) and I/R injury combined with biochemical methods, we show that hypoxia causes rapid but partial degradation of cGMP-hydrolyzing phosphodiesterase-3A (PDE3A) protein via the autophagosomal-lysosomal pathway. While increasing cGMP in hypoxia prevents cell death, partially reduced PDE3A does not change the pro-apoptotic second messenger 3',5'-cyclic adenosine monophosphate (cAMP). However, it leads to significantly enhanced protective effects of clinically relevant activators of nitric oxide-sensitive guanylyl cyclase (NO-GC). Collectively, our mouse and human data unravel a new mechanism by which cardiac cGMP improves hypoxia-associated disease conditions.
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Affiliation(s)
- Nadja I Bork
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Anna Kuret
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Tübingen, Germany
| | - Melanie Cruz Santos
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Tübingen, Germany
| | - Cristina E Molina
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Beate Reiter
- Department of Cardiovascular Surgery, University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Hermann Reichenspurner
- Department of Cardiovascular Surgery, University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Andreas Friebe
- Physiologisches Institut, University of Würzburg, Würzburg, Germany
| | - Boris V Skryabin
- Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Münster, Münster, Germany
| | - Timofey S Rozhdestvensky
- Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Münster, Münster, Germany
| | - Michaela Kuhn
- Physiologisches Institut, University of Würzburg, Würzburg, Germany
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Tübingen, Germany
| | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany.
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28
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Kawall K. The Generic Risks and the Potential of SDN-1 Applications in Crop Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:2259. [PMID: 34834620 PMCID: PMC8622673 DOI: 10.3390/plants10112259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
The use of site-directed nucleases (SDNs) in crop plants to alter market-oriented traits is expanding rapidly. At the same time, there is an on-going debate around the safety and regulation of crops altered with the site-directed nuclease 1 (SDN-1) technology. SDN-1 applications can be used to induce a variety of genetic alterations ranging from fairly 'simple' genetic alterations to complex changes in plant genomes using, for example, multiplexing approaches. The resulting plants can contain modified alleles and associated traits, which are either known or unknown in conventionally bred plants. The European Commission recently published a study on new genomic techniques suggesting an adaption of the current GMO legislation by emphasizing that targeted mutagenesis techniques can produce genomic alterations that can also be obtained by natural mutations or conventional breeding techniques. This review highlights the need for a case-specific risk assessment of crop plants derived from SDN-1 applications considering both the characteristics of the product and the process to ensure a high level of protection of human and animal health and the environment. The published literature on so-called market-oriented traits in crop plants altered with SDN-1 applications is analyzed here to determine the types of SDN-1 application in plants, and to reflect upon the complexity and the naturalness of such products. Furthermore, it demonstrates the potential of SDN-1 applications to induce complex alterations in plant genomes that are relevant to generic SDN-associated risks. In summary, it was found that nearly half of plants with so-called market-oriented traits contain complex genomic alterations induced by SDN-1 applications, which may also pose new types of risks. It further underscores the need for data on both the process and the end-product for a case-by-case risk assessment of plants derived from SDN-1 applications.
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Affiliation(s)
- Katharina Kawall
- Fachstelle Gentechnik und Umwelt, Frohschammerstr. 14, 80807 Munich, Germany
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29
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Oz MT, Altpeter A, Karan R, Merotto A, Altpeter F. CRISPR/Cas9-Mediated Multi-Allelic Gene Targeting in Sugarcane Confers Herbicide Tolerance. Front Genome Ed 2021; 3:673566. [PMID: 34713261 PMCID: PMC8525412 DOI: 10.3389/fgeed.2021.673566] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/28/2021] [Indexed: 12/27/2022] Open
Abstract
Sugarcane is the source of 80% of the sugar and 26% of the bioethanol produced globally. However, its complex, highly polyploid genome (2n = 100 - 120) impedes crop improvement. Here, we report efficient and reproducible gene targeting (GT) in sugarcane, enabling precise co-editing of multiple alleles via template-mediated and homology-directed repair (HDR) of DNA double strand breaks induced by the programmable nuclease CRISPR/Cas9. The evaluation of 146 independently transformed plants from five independent experiments revealed a targeted nucleotide replacement that resulted in both targeted amino acid substitutions W574L and S653I in the acetolactate synthase (ALS) in 11 lines in addition to single, targeted amino acid substitutions W574L or S653I in 25 or 18 lines, respectively. Co-editing of up to three ALS copies/alleles that confer herbicide tolerance was confirmed by Sanger sequencing of cloned long polymerase chain reaction (PCR) amplicons. This work will enable crop improvement by conversion of inferior alleles to superior alleles through targeted nucleotide substitutions.
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Affiliation(s)
- Mehmet Tufan Oz
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, United States
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
| | - Angelika Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, United States
| | - Ratna Karan
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, United States
| | - Aldo Merotto
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, United States
| | - Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, United States
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, United States
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30
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Abstract
The emergence of an array of genome-editing tools in recent years has facilitated the introduction of genetic modifications directly into the embryo, increasing the ease, efficiency and catalogue of alleles accessible to researchers across a range of species. Bypassing the requirement for a selection cassette and resulting in a broad range of outcomes besides the desired allele, genome editing has altered the allele validation process both temporally and technically. Whereas traditional gene targeting relies upon selection and allows allele validation at the embryonic stem cell modification stage, screening for the presence of the intended allele now occurs in the (frequently mosaic) founder animals. Final confirmation of the edited allele can only take place at the subsequent G1 generation and the validation strategy must differentiate the desired allele from a range of unintended outcomes. Here we present some of the challenges posed by gene editing, strategies for validation and considerations for animal colony management.
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Affiliation(s)
| | - Gemma F Codner
- The Mary Lyon Centre, Medical Research Council Harwell Institute, UK
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, UK
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31
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Epstein LR, Lee SS, Miller MF, Lombardi HA. CRISPR, animals, and FDA oversight: Building a path to success. Proc Natl Acad Sci U S A 2021; 118:e2004831117. [PMID: 34050010 PMCID: PMC8179205 DOI: 10.1073/pnas.2004831117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Technological advances, such as genome editing and specifically CRISPR, offer exciting promise for the creation of products that address public health concerns, such as disease transmission and a sustainable food supply and enable production of human therapeutics, such as organs and tissues for xenotransplantation or recombinant human proteins to treat disease. The Food and Drug Administration recognizes the need for such innovative solutions and plays a key role in bringing safe and effective animal biotechnology products to the marketplace. In this article, we (the Food and Drug Administration/Center for Veterinary Medicine) describe the current state of the science, including advances in technology as well as scientific limitations and considerations for how researchers and commercial developers working to create intentional genomic alterations in animals can work within these limitations. We also describe our risk-based approach and how it strikes a balance between our regulatory responsibilities and the need to get innovative products to market efficiently. We continue to seek input from our stakeholders and hope to use this feedback to improve the transparency, predictability, and efficiency of our process. We think that working together, using appropriate science- and risk-based oversight, is the foundation to a successful path forward.
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Affiliation(s)
- Laura R Epstein
- Office of the Director, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855
| | - Stella S Lee
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855
| | - Mayumi F Miller
- Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD 20708
| | - Heather A Lombardi
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855;
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32
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Bandyopadhyay S, Douglass J, Kapell S, Khan N, Feitosa-Suntheimer F, Klein JA, Temple J, Brown-Culbertson J, Tavares AH, Saeed M, Lau NC. DNA templates with blocked long 3' end single-stranded overhangs (BL3SSO) promote bona fide Cas9-stimulated homology-directed repair of long transgenes into endogenous gene loci. G3-GENES GENOMES GENETICS 2021; 11:6275753. [PMID: 33989385 PMCID: PMC8496256 DOI: 10.1093/g3journal/jkab169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022]
Abstract
Knock-in of large transgenes by Cas9-mediated homology-directed repair (HDR) is an extremely inefficient process. Although the use of single-stranded oligonucleotides (ssODN) as an HDR donor has improved the integration of smaller transgenes, they do not support efficient insertion of large DNA sequences. In an effort to gain insights into the mechanism(s) governing the HDR-mediated integration of larger transgenes and to improve the technology, we conducted knock-in experiments targeting the human EMX1 locus and applied rigorous genomic PCR analyses in the human HEK293 cell line. This exercise revealed an unexpected molecular complication arising from the transgene HDR being initiated at the single homology arm and the subsequent genomic integration of plasmid backbone sequences. To pivot around this problem, we devised a novel PCR-constructed template containing blocked long 3' single-stranded overhangs (BL3SSO) that greatly improved the efficiency of bona fide Cas9-stimulated HDR at the EMX1 locus. We further refined BL3SSO technology and successfully used it to insert GFP transgenes into two important interferon-stimulated genes (ISGs) loci, Viperin/RSAD2, and ISG15. This study demonstrates the utility of the BL3SSO platform for inserting long DNA sequences into both constitutive and inducible endogenous loci to generate novel human cell lines for the study of important biological processes.
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Affiliation(s)
- Saptaparni Bandyopadhyay
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Joseph Douglass
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Sebastian Kapell
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | | | - Jenny A Klein
- Department of Biology, Brandeis University, Waltham, MA 02453, USA.,Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Jasmine Temple
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Jayce Brown-Culbertson
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Nelson C Lau
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.,Genome Science Institute, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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Kummerfeld DM, Raabe CA, Brosius J, Mo D, Skryabin BV, Rozhdestvensky TS. A Comprehensive Review of Genetically Engineered Mouse Models for Prader-Willi Syndrome Research. Int J Mol Sci 2021; 22:3613. [PMID: 33807162 PMCID: PMC8037846 DOI: 10.3390/ijms22073613] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 02/05/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a neurogenetic multifactorial disorder caused by the deletion or inactivation of paternally imprinted genes on human chromosome 15q11-q13. The affected homologous locus is on mouse chromosome 7C. The positional conservation and organization of genes including the imprinting pattern between mice and men implies similar physiological functions of this locus. Therefore, considerable efforts to recreate the pathogenesis of PWS have been accomplished in mouse models. We provide a summary of different mouse models that were generated for the analysis of PWS and discuss their impact on our current understanding of corresponding genes, their putative functions and the pathogenesis of PWS. Murine models of PWS unveiled the contribution of each affected gene to this multi-facetted disease, and also enabled the establishment of the minimal critical genomic region (PWScr) responsible for core symptoms, highlighting the importance of non-protein coding genes in the PWS locus. Although the underlying disease-causing mechanisms of PWS remain widely unresolved and existing mouse models do not fully capture the entire spectrum of the human PWS disorder, continuous improvements of genetically engineered mouse models have proven to be very powerful and valuable tools in PWS research.
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Affiliation(s)
- Delf-Magnus Kummerfeld
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Carsten A. Raabe
- Research Group Regulatory Mechanisms of Inflammation, Institute of Medical Biochemistry (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Juergen Brosius
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dingding Mo
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;
| | - Boris V. Skryabin
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Timofey S. Rozhdestvensky
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
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34
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Bai T, Wang T, Li Y, Gao NL, Zhang L, Chen WH, Yin X. Optimization of scleroglucan production by Sclerotium rolfsii by lowering pH during fermentation via oxalate metabolic pathway manipulation using CRISPR/Cas9. Fungal Biol Biotechnol 2021; 8:1. [PMID: 33602329 PMCID: PMC7893912 DOI: 10.1186/s40694-021-00108-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/29/2021] [Indexed: 12/27/2022] Open
Abstract
Background Sclerotium rolfsii is a potent producer of many secondary metabolites, one of which like scleroglucan is an exopolysaccharide (EPS) appreciated as a multipurpose compound applicable in many industrial fields. Results Aspartate transaminase (AAT1) catalyzes the interconversion of aspartate and α-ketoglutarate to glutamate and oxaloacetate. We selected AAT1 in the oxalate metabolic pathway as a target of CRISPR/Cas9. Disruption of AAT1 leads to the accumulation of oxalate, rather than its conversion to α-ketoglutarate (AKG). Therefore, AAT1-mutant serves to lower the pH (pH 3–4) so as to increase the production of the pH-sensitive metabolite scleroglucan to 21.03 g L−1 with a productivity of up to 0.25 g L−1·h−1. Conclusions We established a platform for gene editing that could rapidly generate and select mutants to provide a new beneficial strain of S. rolfsii as a scleroglucan hyper-producer, which is expected to reduce the cost of controlling the optimum pH condition in the fermentation industry.
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Affiliation(s)
- Tianlong Bai
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, 110142, China.,Liaoning Province Key Laboratory of Green Functional Molecule Design and Development, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Teng Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yan Li
- Liaoning Province Key Laboratory of Green Functional Molecule Design and Development, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Na L Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lixin Zhang
- Liaoning Province Key Laboratory of Green Functional Molecule Design and Development, Shenyang University of Chemical Technology, Shenyang, 110142, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China. .,College of Life Science, HeNan Normal University, Xinxiang, 453007, Henan, China.
| | - Xiushan Yin
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, 110142, China.
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35
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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36
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Ranawakage DC, Okada K, Sugio K, Kawaguchi Y, Kuninobu-Bonkohara Y, Takada T, Kamachi Y. Efficient CRISPR-Cas9-Mediated Knock-In of Composite Tags in Zebrafish Using Long ssDNA as a Donor. Front Cell Dev Biol 2021; 8:598634. [PMID: 33681181 PMCID: PMC7928300 DOI: 10.3389/fcell.2020.598634] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the unprecedented gene editing capability of CRISPR-Cas9-mediated targeted knock-in, the efficiency and precision of this technology still require further optimization, particularly for multicellular model organisms, such as the zebrafish (Danio rerio). Our study demonstrated that an ∼200 base-pair sequence encoding a composite tag can be efficiently "knocked-in" into the zebrafish genome using a combination of the CRISPR-Cas9 ribonucleoprotein complex and a long single-stranded DNA (lssDNA) as a donor template. Here, we targeted the sox3, sox11a, and pax6a genes to evaluate the knock-in efficiency of lssDNA donors with different structures in somatic cells of injected embryos and for their germline transmission. The structures and sequence characteristics of the lssDNA donor templates were found to be crucial to achieve a high rate of precise and heritable knock-ins. The following were our key findings: (1) lssDNA donor strand selection is important; however, strand preference and its dependency appear to vary among the target loci or their sequences. (2) The length of the 3' homology arm of the lssDNA donor affects knock-in efficiency in a site-specific manner; particularly, a shorter 50-nt arm length leads to a higher knock-in efficiency than a longer 300-nt arm for the sox3 and pax6a knock-ins. (3) Some DNA sequence characteristics of the knock-in donors and the distance between the CRISPR-Cas9 cleavage site and the tag insertion site appear to adversely affect the repair process, resulting in imprecise editing. By implementing the proposed method, we successfully obtained precisely edited sox3, sox11a, and pax6a knock-in alleles that contained a composite tag composed of FLAGx3 (or PAx3), Bio tag, and HiBiT tag (or His tag) with moderate to high germline transmission rates as high as 21%. Furthermore, the knock-in allele-specific quantitative polymerase chain reaction (qPCR) for both the 5' and 3' junctions indicated that knock-in allele frequencies were higher at the 3' side of the lssDNAs, suggesting that the lssDNA-templated knock-in was mediated by unidirectional single-strand template repair (SSTR) in zebrafish embryos.
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Affiliation(s)
| | | | | | | | | | | | - Yusuke Kamachi
- School of Environmental Science and Engineering, Kochi University of Technology, Kochi, Japan
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37
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DGK and DZHK position paper on genome editing: basic science applications and future perspective. Basic Res Cardiol 2021; 116:2. [PMID: 33449167 PMCID: PMC7810637 DOI: 10.1007/s00395-020-00839-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]
Abstract
For a long time, gene editing had been a scientific concept, which was limited to a few applications. With recent developments, following the discovery of TALEN zinc-finger endonucleases and in particular the CRISPR/Cas system, gene editing has become a technique applicable in most laboratories. The current gain- and loss-of function models in basic science are revolutionary as they allow unbiased screens of unprecedented depth and complexity and rapid development of transgenic animals. Modifications of CRISPR/Cas have been developed to precisely interrogate epigenetic regulation or to visualize DNA complexes. Moreover, gene editing as a clinical treatment option is rapidly developing with first trials on the way. This article reviews the most recent progress in the field, covering expert opinions gathered during joint conferences on genome editing of the German Cardiac Society (DGK) and the German Center for Cardiovascular Research (DZHK). Particularly focusing on the translational aspect and the combination of cellular and animal applications, the authors aim to provide direction for the development of the field and the most frequent applications with their problems.
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38
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Long Y, Cech TR. Targeted mutagenesis in human iPSCs using CRISPR genome-editing tools. Methods 2021; 191:44-58. [PMID: 33444739 DOI: 10.1016/j.ymeth.2021.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/27/2020] [Accepted: 01/02/2021] [Indexed: 12/27/2022] Open
Abstract
Mutagenesis studies have rapidly evolved in the era of CRISPR genome editing. Precise manipulation of genes in human induced pluripotent stem cells (iPSCs) allows biomedical researchers to study the physiological functions of individual genes during development. Furthermore, such genetic manipulation applied to patient-specific iPSCs allows disease modeling, drug screening and development of therapeutics. Although various genome-editing methods have been developed to introduce or remove mutations in human iPSCs, comprehensive strategic designs taking account of the potential side effects of CRISPR editing are needed. Here we present several novel and highly efficient strategies to introduce point mutations, insertions and deletions in human iPSCs, including step-by-step experimental protocols. These approaches involve the application of drug selection for effortless clone screening and the generation of a wild type control strain along with the mutant. We also present several examples of application of these strategies in human iPSCs and show that they are highly efficient and could be applied to other cell types.
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Affiliation(s)
- Yicheng Long
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, United States
| | - Thomas R Cech
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, United States; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, United States.
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39
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Bosch JA, Birchak G, Perrimon N. Precise genome engineering in Drosophila using prime editing. Proc Natl Acad Sci U S A 2021; 118:e2021996118. [PMID: 33443210 PMCID: PMC7817132 DOI: 10.1073/pnas.2021996118] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double-strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organism Drosophila melanogaster and developed conditions for optimal editing. By expressing prime editing components in cultured cells or somatic cells of transgenic flies, we precisely introduce premature stop codons in three classical visible marker genes, ebony, white, and forked Furthermore, by restricting editing to germ cells, we demonstrate efficient germ-line transmission of a precise edit in ebony to 36% of progeny. Our results suggest that prime editing is a useful system in Drosophila to study gene function, such as engineering precise point mutations, deletions, or epitope tags.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
| | - Gabriel Birchak
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- HHMI, Harvard Medical School, Boston, MA 02115
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40
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Lau CH, Tin C, Suh Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Fac Rev 2020; 9:20. [PMID: 33659952 PMCID: PMC7886068 DOI: 10.12703/r/9-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
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41
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Burgio G, Teboul L. Anticipating and Identifying Collateral Damage in Genome Editing. Trends Genet 2020; 36:905-914. [PMID: 33039248 PMCID: PMC7658041 DOI: 10.1016/j.tig.2020.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023]
Abstract
Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion article discusses how to anticipate and detect those editing events by a combination of assays to capture all possible genomic changes. It also discusses strategies for preventing unwanted effects, critical to appraise the benefit or risk associated with the use of the technology. Anticipating and verifying the result of genome editing are essential for the success for all applications.
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Affiliation(s)
- Gaëtan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, ACT 2603, Australia.
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK.
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42
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Aida T, Feng G. The dawn of non-human primate models for neurodevelopmental disorders. Curr Opin Genet Dev 2020; 65:160-168. [PMID: 32693220 PMCID: PMC7955645 DOI: 10.1016/j.gde.2020.05.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/31/2020] [Indexed: 12/12/2022]
Abstract
Non-human primates (NHPs) have been proposed as good models for neurodevelopmental disorders due to close similarities to humans in terms of brain structure and cognitive function. The recent development of genome editing technologies has opened new avenues to generate and investigate genetically modified NHPs as models for human disorders. Here, we review the early successes of genetic NHP models for neurodevelopmental disorders and further discuss the technological challenges and opportunities to create next generation NHP models with more sophisticated genetic manipulation and faithful representations of the human genetic mutations. Taken together, the field is now poised to usher in a new era of research using genetically modified NHP models to empower a more rapid translation of basic research and maximize the preclinical potential for biomarker discovery and therapeutic development.
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Affiliation(s)
- Tomomi Aida
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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43
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Blayney J, Foster EM, Jagielowicz M, Kreuzer M, Morotti M, Reglinski K, Xiao JH, Hublitz P. Unexpectedly High Levels of Inverted Re-Insertions Using Paired sgRNAs for Genomic Deletions. Methods Protoc 2020; 3:mps3030053. [PMID: 32751356 PMCID: PMC7565582 DOI: 10.3390/mps3030053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Use of dual sgRNAs is a common CRISPR/Cas9-based strategy for the creation of genetic deletions. The ease of screening combined with a rather high rate of success makes this approach a reliable genome engineering procedure. Recently, a number of studies using CRISPR/Cas9 have revealed unwanted large-scale rearrangements, duplications, inversions or larger-than-expected deletions. Strict quality control measures are required to validate the model system, and this crucially depends on knowing which potential experimental outcomes to expect. Using the dual sgRNA deletion approach, our team discovered high levels of excision, inversion and re-insertion at the site of targeting. We detected those at a variety of genomic loci and in several immortalized cell lines, demonstrating that inverted re-insertions are a common by-product with an overall frequency between 3% and 20%. Our findings imply an inherent danger in the misinterpretation of screening data when using only a single PCR screening. While amplification of the region of interest might classify clones as wild type (WT) based on amplicon size, secondary analyses can discover heterozygous (HET) clones among presumptive WTs, and events deemed as HET clones could potentially be full KO. As such, screening for inverted re-insertions helps in decreasing the number of clones required to obtain a full KO. With this technical note, we want to raise awareness of this phenomenon and suggest implementing a standard secondary PCR while screening for deletions.
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Affiliation(s)
- Joseph Blayney
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK;
| | - Evangeline M. Foster
- Translational Neuroscience and Dementia Research Group, Department of Psychiatry, University of Oxford, Warneford Hospital, Warneford Lane, Oxford OX3 7JX, UK;
| | - Marta Jagielowicz
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; (M.J.); (K.R.); (J.H.X.)
| | - Mira Kreuzer
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; (M.K.); (M.M.)
| | - Matteo Morotti
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; (M.K.); (M.M.)
- Department of Oncology, University of Lausanne, Ludwig Cancer Research Centre, HiTIDE group, Rue du Bugnon 25A, CH-1005 Lausanne, Switzerland
| | - Katharina Reglinski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; (M.J.); (K.R.); (J.H.X.)
- Leibniz-Institute of Photonic Technologies & Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Max-Wien-Platz 1, D-07743 Jena, Germany
| | - Julie Huiyuan Xiao
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; (M.J.); (K.R.); (J.H.X.)
| | - Philip Hublitz
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK;
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; (M.J.); (K.R.); (J.H.X.)
- MRC Weatherall Institute of Molecular Medicine, Genome Engineering Facility, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
- Correspondence: ; Tel.: +44-1865-222339
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44
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Liu Q, Jiao X, Meng X, Wang C, Xu C, Tian Z, Xie C, Li G, Li J, Yu H, Wang K. FED: a web tool for foreign element detection of genome-edited organism. SCIENCE CHINA-LIFE SCIENCES 2020; 64:167-170. [PMID: 32504339 DOI: 10.1007/s11427-020-1731-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/20/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Qing Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Xiaozhen Jiao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chun Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Cao Xu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuanxiao Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
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On-Target CRISPR/Cas9 Activity Can Cause Undesigned Large Deletion in Mouse Zygotes. Int J Mol Sci 2020; 21:ijms21103604. [PMID: 32443745 PMCID: PMC7279260 DOI: 10.3390/ijms21103604] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering has been tremendously affected by the appearance of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-based approach. Initially discovered as an adaptive immune system for prokaryotes, the method has rapidly evolved over the last decade, overtaking multiple technical challenges and scientific tasks and becoming one of the most effective, reliable, and easy-to-use technologies for precise genomic manipulations. Despite its undoubtable advantages, CRISPR/Cas9 technology cannot ensure absolute accuracy and predictability of genomic editing results. One of the major concerns, especially for clinical applications, is mutations resulting from error-prone repairs of CRISPR/Cas9-induced double-strand DNA breaks. In some cases, such error-prone repairs can cause unpredicted and unplanned large genomic modifications within the CRISPR/Cas9 on-target site. Here we describe the largest, to the best of our knowledge, undesigned on-target deletion with a size of ~293 kb that occurred after the cytoplasmic injection of CRISPR/Cas9 system components into mouse zygotes and speculate about its origin. We suppose that deletion occurred as a result of the truncation of one of the ends of a double-strand break during the repair.
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Fleischer A, Vallejo-Díez S, Martín-Fernández JM, Sánchez-Gilabert A, Castresana M, Del Pozo A, Esquisabel A, Ávila S, Castrillo JL, Gaínza E, Pedraz JL, Viñas M, Bachiller D. iPSC-Derived Intestinal Organoids from Cystic Fibrosis Patients Acquire CFTR Activity upon TALEN-Mediated Repair of the p.F508del Mutation. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:858-870. [PMID: 32373648 PMCID: PMC7195499 DOI: 10.1016/j.omtm.2020.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis (CF) is the main genetic cause of death among the Caucasian population. The disease is characterized by abnormal fluid and electrolyte mobility across secretory epithelia. The first manifestations occur within hours of birth (meconium ileus), later extending to other organs, generally affecting the respiratory tract. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR encodes a cyclic adenosine monophosphate (cAMP)-dependent, phosphorylation-regulated chloride channel required for transport of chloride and other ions through cell membranes. There are more than 2,000 mutations described in the CFTR gene, but one of them, phenylalanine residue at amino acid position 508 (p.F508del), a recessive allele, is responsible for the vast majority of CF cases worldwide. Here, we present the results of the application of genome-editing techniques to the restoration of CFTR activity in p.F508del patient-derived induced pluripotent stem cells (iPSCs). Gene-edited iPSCs were subsequently used to produce intestinal organoids on which the physiological activity of the restored gene was tested in forskolin-induced swelling tests. The seamless restoration of the p.F508del mutation resulted in normal expression of the mature CFTR glycoprotein, full recovery of CFTR activity, and a normal response of the repaired organoids to treatment with two approved CF therapies: VX-770 and VX-809.
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Affiliation(s)
- Aarne Fleischer
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | - Sara Vallejo-Díez
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
| | | | | | - Mónica Castresana
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | | | - Amaia Esquisabel
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Silvia Ávila
- Genetadi Biotech S.L., Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | | | - José Luis Pedraz
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Miguel Viñas
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, University of Barcelona, 08097 Barcelona, Spain
| | - Daniel Bachiller
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
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Smirnov A, Fishman V, Yunusova A, Korablev A, Serova I, Skryabin BV, Rozhdestvensky TS, Battulin N. DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote. Nucleic Acids Res 2020; 48:719-735. [PMID: 31740957 PMCID: PMC7145541 DOI: 10.1093/nar/gkz1085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
Mechanisms that ensure repair of double-strand DNA breaks (DSBs) are instrumental in the integration of foreign DNA into the genome of transgenic organisms. After pronuclear microinjection, exogenous DNA is usually found as a concatemer comprising multiple co-integrated transgene copies. Here, we investigated the contribution of various DSB repair pathways to the concatemer formation. We injected mouse zygotes with a pool of linear DNA molecules carrying unique barcodes at both ends and obtained 10 transgenic embryos with 1–300 transgene copies. Sequencing the barcodes allowed us to assign relative positions to the copies in concatemers and detect recombination events that occurred during integration. Cumulative analysis of approximately 1,000 integrated copies reveals that over 80% of them underwent recombination when their linear ends were processed by synthesis-dependent strand annealing (SDSA) or double-strand break repair (DSBR). We also observed evidence of double Holliday junction (dHJ) formation and crossing over during the concatemer formations. Sequencing indels at the junctions between copies shows that at least 10% of DNA molecules introduced into the zygotes are ligated by non-homologous end joining (NHEJ). Our barcoding approach, verified with Pacific Biosciences Single Molecule Real-Time (SMRT) long-range sequencing, documents high activity of homologous recombination after DNA microinjection.
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Affiliation(s)
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | - Alexey Korablev
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Irina Serova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Boris V Skryabin
- Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Timofey S Rozhdestvensky
- Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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