1
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Park SJ, Park SJ, Kwon YW, Choi EH. Synergistic combination of RAD51-SCR7 improves CRISPR-Cas9 genome editing efficiency by preventing R-loop accumulation. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102274. [PMID: 39161621 PMCID: PMC11331969 DOI: 10.1016/j.omtn.2024.102274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/13/2024] [Indexed: 08/21/2024]
Abstract
CRISPR-Cas9 has emerged as a powerful tool for genome editing. However, Cas9 genome editing faces challenges, including low efficiency and off-target effects. Here, we report that combined treatment with RAD51, a key factor in homologous recombination, and SCR7, a DNA ligase IV small-molecule inhibitor, enhances CRISPR-Cas9-mediated genome-editing efficiency in human embryonic kidney 293T and human induced pluripotent stem cells, as confirmed by cyro- transmission electron microscopy and functional analyses. First, our findings reveal the crucial role of RAD51 in homologous recombination (HR)-mediated DNA repair process. Elevated levels of exogenous RAD51 promote a post-replication step via single-strand DNA gap repair process, ensuring the completion of DNA replication. Second, using the all-in-one CRISPR-Cas9-RAD51 system, highly expressed RAD51 improved the multiple endogenous gene knockin/knockout efficiency and insertion/deletion (InDel) mutation by activating the HR-based repair pathway in concert with SCR7. Sanger sequencing shows distinct outcomes for RAD51-SCR7 in the ratio of InDel mutations in multiple genome sites. Third, RAD51-SCR7 combination can induce efficient R-loop resolution and DNA repair by enhanced HR process, which leads to DNA replication stalling and thus is advantageous to CRISPR-Cas9-based stable genome editing. Our study suggests promising applications in genome editing by enhancing CRISPR-Cas9 efficiency through RAD51 and SCR7, offering potential advancements in biotechnology and therapeutics.
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Affiliation(s)
- Sun-Ji Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Deagu 41061, South Korea
| | - Seo Jung Park
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju 28160, South Korea
| | - Yang Woo Kwon
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Deagu 41061, South Korea
| | - Eui-Hwan Choi
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Deagu 41061, South Korea
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2
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Jin YY, Zhang P, Liu LL, Zhao X, Hu XQ, Liu SZ, Li ZK, Liu Q, Wang JQ, Hao DL, Zhang ZQ, Chen HZ, Liu DP. Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor. Nat Commun 2024; 15:6843. [PMID: 39122671 PMCID: PMC11315919 DOI: 10.1038/s41467-024-50788-x] [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: 10/02/2023] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Despite the potential of small molecules and recombinant proteins to enhance the efficiency of homology-directed repair (HDR), single-stranded DNA (ssDNA) donors, as currently designed and chemically modified, remain suboptimal for precise gene editing. Here, we screen the biased ssDNA binding sequences of DNA repair-related proteins and engineer RAD51-preferred sequences into HDR-boosting modules for ssDNA donors. Donors with these modules exhibit an augmented affinity for RAD51, thereby enhancing HDR efficiency across various genomic loci and cell types when cooperated with Cas9, nCas9, and Cas12a. By combining with an inhibitor of non-homologous end joining (NHEJ) or the HDRobust strategy, these modular ssDNA donors achieve up to 90.03% (median 74.81%) HDR efficiency. The HDR-boosting modules targeting an endogenous protein enable a chemical modification-free strategy to improve the efficacy of ssDNA donors for precise gene editing.
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Affiliation(s)
- Ying-Ying Jin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Peng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Le-Le Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiang Zhao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiao-Qing Hu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Si-Zhe Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Ze-Kun Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Qian Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Jian-Qiao Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - De-Long Hao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zhu-Qin Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Hou-Zao Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
- Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
| | - De-Pei Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
- Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300301, China.
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3
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Otarbayev D, Myung K. Exploring factors influencing choice of DNA double-strand break repair pathways. DNA Repair (Amst) 2024; 140:103696. [PMID: 38820807 DOI: 10.1016/j.dnarep.2024.103696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024]
Abstract
DNA double-strand breaks (DSBs) represent one of the most severe threats to genomic integrity, demanding intricate repair mechanisms within eukaryotic cells. A diverse array of factors orchestrates the complex choreography of DSB signaling and repair, encompassing repair pathways, such as non-homologous end-joining, homologous recombination, and polymerase-θ-mediated end-joining. This review looks into the intricate decision-making processes guiding eukaryotic cells towards a particular repair pathway, particularly emphasizing the processing of two-ended DSBs. Furthermore, we elucidate the transformative role of Cas9, a site-specific endonuclease, in revolutionizing our comprehension of DNA DSB repair dynamics. Additionally, we explore the burgeoning potential of Cas9's remarkable ability to induce sequence-specific DSBs, offering a promising avenue for precise targeting of tumor cells. Through this comprehensive exploration, we unravel the intricate molecular mechanisms of cellular responses to DSBs, shedding light on both fundamental repair processes and cutting-edge therapeutic strategies.
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Affiliation(s)
- Daniyar Otarbayev
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, South Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, South Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea.
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4
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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401797. [PMID: 38728624 PMCID: PMC11267366 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Mudi Meng Honors CollegeChina Pharmaceutical UniversityNanjing210009China
| | - Jianping Kong
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Gongyu Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Zhaoxing Li
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| | - Yibei Xiao
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
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5
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Moiani A, Letort G, Lizot S, Chalumeau A, Foray C, Felix T, Le Clerre D, Temburni-Blake S, Hong P, Leduc S, Pinard N, Marechal A, Seclen E, Boyne A, Mayer L, Hong R, Pulicani S, Galetto R, Gouble A, Cavazzana M, Juillerat A, Miccio A, Duclert A, Duchateau P, Valton J. Non-viral DNA delivery and TALEN editing correct the sickle cell mutation in hematopoietic stem cells. Nat Commun 2024; 15:4965. [PMID: 38862518 PMCID: PMC11166989 DOI: 10.1038/s41467-024-49353-3] [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] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
Sickle cell disease is a devastating blood disorder that originates from a single point mutation in the HBB gene coding for hemoglobin. Here, we develop a GMP-compatible TALEN-mediated gene editing process enabling efficient HBB correction via a DNA repair template while minimizing risks associated with HBB inactivation. Comparing viral versus non-viral DNA repair template delivery in hematopoietic stem and progenitor cells in vitro, both strategies achieve comparable HBB correction and result in over 50% expression of normal adult hemoglobin in red blood cells without inducing β-thalassemic phenotype. In an immunodeficient female mouse model, transplanted cells edited with the non-viral strategy exhibit higher engraftment and gene correction levels compared to those edited with the viral strategy. Transcriptomic analysis reveals that non-viral DNA repair template delivery mitigates P53-mediated toxicity and preserves high levels of long-term hematopoietic stem cells. This work paves the way for TALEN-based autologous gene therapy for sickle cell disease.
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Affiliation(s)
| | - Gil Letort
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Sabrina Lizot
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Anne Chalumeau
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Chloe Foray
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Tristan Felix
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | | | | | - Patrick Hong
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Sophie Leduc
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Noemie Pinard
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Alan Marechal
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | | | - Alex Boyne
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Louisa Mayer
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Robert Hong
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | | | - Roman Galetto
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Agnès Gouble
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Marina Cavazzana
- Biotherapy Clinical Investigation Center, Necker Children's Hospital, Assistance Publique Hopitaux de Paris, Paris, France
- Human Lymphohematopoiesis Laboratory, Imagine Institute, INSERM UMR1163, Paris Cité University, Paris, France
- Biotherapy Department, Necker Children's Hospital, Assistance Publique Hopitaux de Paris, Paris, France
| | | | - Annarita Miccio
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | | | | | - Julien Valton
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France.
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6
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Bekaert B, Boel A, Rybouchkin A, Cosemans G, Declercq S, Chuva de Sousa Lopes SM, Parrington J, Stoop D, Coucke P, Menten B, Heindryckx B. Various repair events following CRISPR/Cas9-based mutational correction of an infertility-related mutation in mouse embryos. J Assist Reprod Genet 2024; 41:1605-1617. [PMID: 38557805 PMCID: PMC11224219 DOI: 10.1007/s10815-024-03095-9] [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: 11/24/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Unpredictable genetic modifications and chromosomal aberrations following CRISPR/Cas9 administration hamper the efficacy of germline editing. Repair events triggered by double-strand DNA breaks (DSBs) besides non-homologous end joining and repair template-driven homology-directed repair have been insufficiently investigated in mouse. In this work, we are the first to investigate the precise repair mechanisms triggered by parental-specific DSB induction in mouse for paternal mutational correction in the context of an infertility-related mutation. METHODS We aimed to correct a paternal 22-nucleotide deletion in Plcz1, associated with lack of fertilisation in vitro, by administrating CRISPR/Cas9 components during intracytoplasmic injection of Plcz1-null sperm in wild-type oocytes combined with assisted oocyte activation. Through targeted next-generation sequencing, 77 injected embryos and 26 blastomeres from seven injected embryos were investigated. In addition, low-pass whole genome sequencing was successfully performed on 17 injected embryo samples. RESULTS Repair mechanisms induced by two different CRISPR/Cas9 guide RNA (gRNA) designs were investigated. In 13.73% (7/51; gRNA 1) and 19.05% (4/21; gRNA 2) of the targeted embryos, only the wild-type allele was observed, of which the majority (85.71%; 6/7) showed integrity of the targeted chromosome. Remarkably, for both designs, only in one of these embryos (1/7; gRNA 1 and 1/4; gRNA2) could repair template use be detected. This suggests that alternative repair events have occurred. Next, various genetic events within the same embryo were detected after single-cell analysis of four embryos. CONCLUSION Our results suggest the occurrence of mosaicism and complex repair events after CRISPR/Cas9 DSB induction where chromosomal integrity is predominantly contained.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - A Boel
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - A Rybouchkin
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - S Declercq
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - S M Chuva de Sousa Lopes
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - J Parrington
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - D Stoop
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - P Coucke
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
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7
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Shi H, Li L, Mu S, Gou S, Liu X, Chen F, Chen M, Jin Q, Lai L, Wang K. Exonuclease editor promotes precision of gene editing in mammalian cells. BMC Biol 2024; 22:119. [PMID: 38769511 PMCID: PMC11107001 DOI: 10.1186/s12915-024-01918-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: 04/28/2023] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Many efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing byproducts, which proved to be challenging. RESULTS Here, we have developed a human exonuclease 1-based genome-editing tool, referred to as exonuclease editor. When compared to Cas9, the exonuclease editor gave rise to increased HDR efficiency, reduced NHEJ repair frequency, and significantly elevated HDR/indel ratio. Robust gene editing precision of exonuclease editor was even superior to the fusion of Cas9 with E1B or DN1S, two previously reported precision-enhancing domains. Notably, exonuclease editor inhibited NHEJ at double strand breaks locally rather than globally, reducing indel frequency without compromising genome integrity. The replacement of Cas9 with single-strand DNA break-creating Cas9 nickase further increased the HDR/indel ratio by 453-fold than the original Cas9. In addition, exonuclease editor resulted in high microhomology-mediated end joining efficiency, allowing accurate and flexible deletion of targeted sequences with extended lengths with the aid of paired sgRNAs. Exonuclease editor was further used for correction of DMD patient-derived induced pluripotent stem cells, where 30.0% of colonies were repaired by HDR versus 11.1% in the control. CONCLUSIONS Therefore, the exonuclease editor system provides a versatile and safe genome editing tool with high precision and holds promise for therapeutic gene correction.
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Affiliation(s)
- Hui Shi
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Lei Li
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangshuang Mu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shixue Gou
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Xiaoyi Liu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Menglong Chen
- Department of Neurology and Stroke Centre, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qin Jin
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
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8
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Kato-Inui T, Takahashi G, Ono T, Miyaoka Y. Fusion of histone variants to Cas9 suppresses non-homologous end joining. PLoS One 2024; 19:e0288578. [PMID: 38739603 PMCID: PMC11090291 DOI: 10.1371/journal.pone.0288578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/11/2024] [Indexed: 05/16/2024] Open
Abstract
As a versatile genome editing tool, the CRISPR-Cas9 system induces DNA double-strand breaks at targeted sites to activate mainly two DNA repair pathways: HDR which allows precise editing via recombination with a homologous template DNA, and NHEJ which connects two ends of the broken DNA, which is often accompanied by random insertions and deletions. Therefore, how to enhance HDR while suppressing NHEJ is a key to successful applications that require precise genome editing. Histones are small proteins with a lot of basic amino acids that generate electrostatic affinity to DNA. Since H2A.X is involved in DNA repair processes, we fused H2A.X to Cas9 and found that this fusion protein could improve the HDR/NHEJ ratio by suppressing NHEJ. As various post-translational modifications of H2A.X play roles in the regulation of DNA repair, we also fused H2A.X mimicry variants to replicate these post-translational modifications including phosphorylation, methylation, and acetylation. However, none of them were effective to improve the HDR/NHEJ ratio. We further fused other histone variants to Cas9 and found that H2A.1 suppressed NHEJ better than H2A.X. Thus, the fusion of histone variants to Cas9 is a promising option to enhance precise genome editing.
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Affiliation(s)
- Tomoko Kato-Inui
- Tokyo Metropolitan Institute of Medical Science, Regenerative Medicine Project, Tokyo, Japan
| | - Gou Takahashi
- Tokyo Metropolitan Institute of Medical Science, Regenerative Medicine Project, Tokyo, Japan
| | - Terumi Ono
- Tokyo Metropolitan Institute of Medical Science, Regenerative Medicine Project, Tokyo, Japan
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuichiro Miyaoka
- Tokyo Metropolitan Institute of Medical Science, Regenerative Medicine Project, Tokyo, Japan
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
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9
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Lee BC, Gin A, Wu C, Singh K, Grice M, Mortlock R, Abraham D, Fan X, Zhou Y, AlJanahi A, Choi U, DeRavin SS, Shin T, Hong S, Dunbar CE. Impact of CRISPR/HDR editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques. Cell Stem Cell 2024; 31:455-466.e4. [PMID: 38508195 PMCID: PMC10997443 DOI: 10.1016/j.stem.2024.02.010] [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: 12/18/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) is required. The impact of HDR on true LT-HSC clonal dynamics in a relevant large animal model has not been studied. To track the output and clonality of HDR-edited cells and to provide a comparison to lentivirally transduced HSCs in vivo, we developed a competitive rhesus macaque (RM) autologous transplantation model, co-infusing HSCs transduced with a barcoded GFP-expressing lentiviral vector (LV) and HDR edited at the CD33 locus. CRISPR/HDR-edited cells showed a two-log decrease by 2 months following transplantation, with little improvement via p53 inhibition, in comparison to minimal loss of LV-transduced cells long term. HDR long-term clonality was oligoclonal in contrast to highly polyclonal LV-transduced HSCs. These results suggest marked clinically relevant differences in the impact of current genetic modification approaches on HSCs.
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Affiliation(s)
- Byung-Chul Lee
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Biological Sciences, Sookmyung Women's University, Seoul, Korea; Research Institute of Women's Health, Sookmyung Women's University, Seoul, Korea.
| | - Ashley Gin
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Komudi Singh
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Max Grice
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryland Mortlock
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diana Abraham
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Aisha AlJanahi
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Uimook Choi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Suk See DeRavin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Taehoon Shin
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Korea
| | - Sogun Hong
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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10
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Li Z, You L, Hermann A, Bier E. Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier. Nat Commun 2024; 15:2629. [PMID: 38521791 PMCID: PMC10960810 DOI: 10.1038/s41467-024-46479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
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Affiliation(s)
- Zhiqian Li
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lang You
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anita Hermann
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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11
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Singh S, Pugliano CM, Honaker Y, Laird A, DeGottardi MQ, Lopez E, Lachkar S, Stoffers C, Sommer K, Khan IF, Rawlings DJ. Efficient and sustained FOXP3 locus editing in hematopoietic stem cells as a therapeutic approach for IPEX syndrome. Mol Ther Methods Clin Dev 2024; 32:101183. [PMID: 38282895 PMCID: PMC10818254 DOI: 10.1016/j.omtm.2023.101183] [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: 06/14/2022] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a monogenic disorder caused by mutations in the FOXP3 gene, required for generation of regulatory T (Treg) cells. Loss of Treg cells leads to immune dysregulation characterized by multi-organ autoimmunity and early mortality. Hematopoietic stem cell (HSC) transplantation can be curative, but success is limited by autoimmune complications, donor availability and/or graft-vs.-host disease. Correction of FOXP3 in autologous HSC utilizing a homology-directed repair (HDR)-based platform may provide a safer alternative therapy. Here, we demonstrate efficient editing of FOXP3 utilizing co-delivery of Cas9 ribonucleoprotein complexes and adeno-associated viral vectors to achieve HDR rates of >40% in vitro using mobilized CD34+ cells from multiple donors. Using this approach to deliver either a GFP or a FOXP3 cDNA donor cassette, we demonstrate sustained bone marrow engraftment of approximately 10% of HDR-edited cells in immune-deficient recipient mice at 16 weeks post-transplant. Further, we show targeted integration of FOXP3 cDNA in CD34+ cells from an IPEX patient and expression of the introduced FOXP3 transcript in gene-edited primary T cells from both healthy individuals and IPEX patients. Our combined findings suggest that refinement of this approach is likely to provide future clinical benefit in IPEX.
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Affiliation(s)
- Swati Singh
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Cole M. Pugliano
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yuchi Honaker
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Aidan Laird
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - M. Quinn DeGottardi
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Ezra Lopez
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Stefan Lachkar
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Claire Stoffers
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Karen Sommer
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Iram F. Khan
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
- Department of Immunology, University of Washington, Seattle, WA 98101, USA
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12
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De Saeger J, Coulembier Vandelannoote E, Lee H, Park J, Blomme J. Genome editing in macroalgae: advances and challenges. Front Genome Ed 2024; 6:1380682. [PMID: 38516199 PMCID: PMC10955705 DOI: 10.3389/fgeed.2024.1380682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
This minireview examines the current state and challenges of genome editing in macroalgae. Despite the ecological and economic significance of this group of organisms, genome editing has seen limited applications. While CRISPR functionality has been established in two brown (Ectocarpus species 7 and Saccharina japonica) and one green seaweed (Ulva prolifera), these studies are limited to proof-of-concept demonstrations. All studies also (co)-targeted ADENINE PHOSPHORIBOSYL TRANSFERASE to enrich for mutants, due to the relatively low editing efficiencies. To advance the field, there should be a focus on advancing auxiliary technologies, particularly stable transformation, so that novel editing reagents can be screened for their efficiency. More work is also needed on understanding DNA repair in these organisms, as this is tightly linked with the editing outcomes. Developing efficient genome editing tools for macroalgae will unlock the ability to characterize their genes, which is largely uncharted terrain. Moreover, given their economic importance, genome editing will also impact breeding campaigns to develop strains that have better yields, produce more commercially valuable compounds, and show improved resilience to the impacts of global change.
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Affiliation(s)
- Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Emma Coulembier Vandelannoote
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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13
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Li S, Wang Y, van der Stoel M, Zhou X, Madhusudan S, Kanerva K, Nguyen VD, Eskici N, Olkkonen VM, Zhou Y, Raivio T, Ikonen E. HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells. Genome Biol 2024; 25:58. [PMID: 38409044 PMCID: PMC10895734 DOI: 10.1186/s13059-024-03187-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: 05/30/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of proteolysis. However, generation of human AID cell lines is challenging, especially in human embryonic stem cells (hESCs). Here, we develop HiHo-AID2, a streamlined procedure for rapid, one-step generation of human cancer and hESC lines with high homozygous degron-tagging efficiency based on an optimized AID2 system and homology-directed repair enhancers. We demonstrate its application for rapid and inducible functional inactivation of twelve endogenous target proteins in five cell lines, including targets with diverse expression levels and functions in hESCs and cells differentiated from hESCs.
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Affiliation(s)
- Shiqian Li
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
| | - Yafei Wang
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Miesje van der Stoel
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Xin Zhou
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Shrinidhi Madhusudan
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Kristiina Kanerva
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Van Dien Nguyen
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Nazli Eskici
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Vesa M Olkkonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - You Zhou
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Taneli Raivio
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00290, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
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14
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Leal AF, Herreno-Pachón AM, Benincore-Flórez E, Karunathilaka A, Tomatsu S. Current Strategies for Increasing Knock-In Efficiency in CRISPR/Cas9-Based Approaches. Int J Mol Sci 2024; 25:2456. [PMID: 38473704 PMCID: PMC10931195 DOI: 10.3390/ijms25052456] [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: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a promising panorama for developing novel and highly precise genome editing-based gene therapy (GT) alternatives, leading to overcoming the challenges associated with classical GT. Classical GT aims to deliver transgenes to the cells via their random integration in the genome or episomal persistence into the nucleus through lentivirus (LV) or adeno-associated virus (AAV), respectively. Although high transgene expression efficiency is achieved by using either LV or AAV, their nature can result in severe side effects in humans. For instance, an LV (NCT03852498)- and AAV9 (NCT05514249)-based GT clinical trials for treating X-linked adrenoleukodystrophy and Duchenne Muscular Dystrophy showed the development of myelodysplastic syndrome and patient's death, respectively. In contrast with classical GT, the CRISPR/Cas9-based genome editing requires the homologous direct repair (HDR) machinery of the cells for inserting the transgene in specific regions of the genome. This sophisticated and well-regulated process is limited in the cell cycle of mammalian cells, and in turn, the nonhomologous end-joining (NHEJ) predominates. Consequently, seeking approaches to increase HDR efficiency over NHEJ is crucial. This manuscript comprehensively reviews the current alternatives for improving the HDR for CRISPR/Cas9-based GTs.
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Affiliation(s)
- Andrés Felipe Leal
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Angelica María Herreno-Pachón
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Eliana Benincore-Flórez
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
| | - Amali Karunathilaka
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shunji Tomatsu
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19144, USA
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15
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Lee BC, Gin A, Wu C, Singh K, Grice M, Mortlock R, Abraham D, Fan X, Zhou Y, AlJanahi A, Choi U, de Ravin SS, Shin T, Hong S, Dunbar CE. Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571396. [PMID: 38168153 PMCID: PMC10760194 DOI: 10.1101/2023.12.13.571396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34 + cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34 + cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively. CD33 knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction in CD33 KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP + cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.
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16
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Tanwar N, Arya SS, Rookes JE, Cahill DM, Lenka SK, Bansal KC. Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops. Crit Rev Biotechnol 2023; 43:1001-1018. [PMID: 35815847 DOI: 10.1080/07388551.2022.2092717] [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: 01/31/2022] [Accepted: 05/29/2022] [Indexed: 11/03/2022]
Abstract
Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.
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Affiliation(s)
- Neha Tanwar
- TERI-Deakin Nano-Biotechnology Centre, The Energy Resources Institute (TERI), New Delhi, India
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - Sagar S Arya
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - James E Rookes
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - David M Cahill
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, Australia
| | - Sangram K Lenka
- TERI-Deakin Nano-Biotechnology Centre, The Energy Resources Institute (TERI), New Delhi, India
- Gujarat Biotechnology University, Gujarat, India
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17
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Shell DJ, Foley CA, Wang Q, Smith CM, Guduru SKR, Zeng H, Dong A, Norris-Drouin JL, Axtman M, Hardy PB, Gupta G, Halabelian L, Frye SV, James LI, Pearce KH. Discovery of a 53BP1 Small Molecule Antagonist Using a Focused DNA-Encoded Library Screen. J Med Chem 2023; 66:14133-14149. [PMID: 37782247 PMCID: PMC10630848 DOI: 10.1021/acs.jmedchem.3c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Methyl-lysine reader p53 binding protein 1 (53BP1) is a central mediator of DNA break repair and is associated with various human diseases, including cancer. Thus, high-quality 53BP1 chemical probes can aid in further understanding the role of 53BP1 in genome repair pathways. Herein, we utilized focused DNA-encoded library screening to identify the novel hit compound UNC8531, which binds the 53BP1 tandem Tudor domain (TTD) with an IC50 of 0.47 ± 0.09 μM in a TR-FRET assay and Kd values of 0.85 ± 0.17 and 0.79 ± 0.52 μM in ITC and SPR, respectively. UNC8531 was cocrystallized with the 53BP1 TTD to guide further optimization efforts, leading to UNC9512. NanoBRET and 53BP1-dependent foci formation experiments confirmed cellular target engagement. These results show that UNC9512 is a best-in-class small molecule 53BP1 antagonist that can aid further studies investigating the role of 53BP1 in DNA repair, gene editing, and oncogenesis.
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Affiliation(s)
- Devan J Shell
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Caroline A Foley
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Qinhong Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Chelsea M Smith
- Lineberger Comprehensive Cancer Center, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shiva K R Guduru
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Ontario M5S 1A1, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Ontario M5S 1A1, Canada
| | - Jacqueline L Norris-Drouin
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew Axtman
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - P Brian Hardy
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gaorav Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Ontario M5S 1A1, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Ontario M5S 1A1, Canada
| | - Stephen V Frye
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I James
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H Pearce
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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18
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Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H. Engineering Tripartite Gene Editing Machinery for Highly Efficient Non-Viral Targeted Genome Integration. RESEARCH SQUARE 2023:rs.3.rs-3365585. [PMID: 37961210 PMCID: PMC10635301 DOI: 10.21203/rs.3.rs-3365585/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Non-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as a genome engineering catalyst (GATALYST) for efficient and safe targeted gene knock-in. Here we developed enGager, a system with enhanced GATALYST associated genome editor, comprising a set of novel genome editors in which the integration efficiency of a circular single-stranded (css) donor DNA is elevated by directly tethering of the cssDNA to a nuclear-localized Cas9 fused with ssDNA binding peptides. Improvements in site-directed genomic integration and expression of a knocked-in DNA encoding GFP were observed at multiple genomic loci in multiple cell lines. The enhancement of integration efficiency, compared to unfused Cas9 editors, ranges from 1.5- to more than 6-fold, with the enhancement most pronounced for transgenes of > 4Kb in length in primary cells. enGager-enhanced genome integration prefers ssDNA donors which, unlike traditional dsDNA donors, are not concatemerized or rearranged prior to and during integration Using an enGager fused to an optimized cssDNA binding peptide, exceptionally efficient, targeted integration of the chimeric antigen receptor (CAR) transgene was achieved in 33% of primary human T cells. Enhanced anti-tumor function of these CAR-T primary cells demonstrated the functional competence of the transgenes. The 'tripartite editors with ssDNA optimized genome engineering' (TESOGENASE™) systems help address the efficacy needs for therapeutic gene modification while avoiding the safety and payload size limitations of viral vectors currently used for CAR-T engineering.
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Affiliation(s)
- Hangu Nam
- Department of Bioengineering, Northeastern University, Boston, MA 02115, United States
| | - Keqiang Xie
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Ishita Majumdar
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Shaobo Yang
- Department of Bioengineering, Northeastern University, Boston, MA 02115, United States
| | - Jakob Starzyk
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Danna Lee
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Richard Shan
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Jiahe Li
- Department of Biomedical Engineering, College of Engineering and School of Medicine, University of Michigan, Ann Arbor, MI 48109, United States
| | - Hao Wu
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
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19
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Richardson RR, Steyert M, Khim SN, Crutcher GW, Brandenburg C, Robertson CD, Romanowski AJ, Inen J, Altas B, Poulopoulos A. Enhancing Precision and Efficiency of Cas9-Mediated Knockin Through Combinatorial Fusions of DNA Repair Proteins. CRISPR J 2023; 6:447-461. [PMID: 37713292 PMCID: PMC10611978 DOI: 10.1089/crispr.2023.0036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023] Open
Abstract
Cas9 targets genomic loci with high specificity. For knockin with double-strand break repair, however, Cas9 often leads to unintended on-target knockout rather than intended edits. This imprecision is a barrier for direct in vivo editing where clonal selection is not feasible. In this study, we demonstrate a high-throughput workflow to comparatively assess on-target efficiency and precision of editing outcomes. Using this workflow, we screened combinations of donor DNA and Cas9 variants, as well as fusions to DNA repair proteins. This yielded novel high-performance double-strand break repair editing agents and combinatorial optimizations, yielding increases in knockin efficiency and precision. Cas9-RC, a novel fusion Cas9 flanked by eRad18 and CtIP[HE], increased knockin performance in vitro and in vivo in the developing mouse brain. Continued comparative assessment of editing efficiency and precision with this framework will further the development of high-performance editing agents for in vivo knockin and future genome therapeutics.
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Affiliation(s)
- Ryan R. Richardson
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marilyn Steyert
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Saovleak N. Khim
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Garrett W. Crutcher
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cheryl Brandenburg
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Colin D. Robertson
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrea J. Romanowski
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey Inen
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bekir Altas
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alexandros Poulopoulos
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, Maryland, USA
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20
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Tabassum T, Pietrogrande G, Healy M, Wolvetang EJ. CRISPR-Cas9 Direct Fusions for Improved Genome Editing via Enhanced Homologous Recombination. Int J Mol Sci 2023; 24:14701. [PMID: 37834150 PMCID: PMC10572186 DOI: 10.3390/ijms241914701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
DNA repair in mammalian cells involves the coordinated action of a range of complex cellular repair machinery. Our understanding of these DNA repair processes has advanced to the extent that they can be leveraged to improve the efficacy and precision of Cas9-assisted genome editing tools. Here, we review how the fusion of CRISPR-Cas9 to functional domains of proteins that directly or indirectly impact the DNA repair process can enhance genome editing. Such studies have allowed the development of diverse technologies that promote efficient gene knock-in for safer genome engineering practices.
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Affiliation(s)
- Tahmina Tabassum
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
| | - Giovanni Pietrogrande
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
| | - Michael Healy
- Institute for Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia;
| | - Ernst J. Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
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21
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Yoshimatsu S, Okahara J, Yoshie J, Igarashi Y, Nakajima R, Sanosaka T, Qian E, Sato T, Kobayashi H, Morimoto S, Kishi N, Pillis DM, Malik P, Noce T, Okano H. Generation of a tyrosine hydroxylase-2A-Cre knockin non-human primate model by homology-directed-repair-biased CRISPR genome editing. CELL REPORTS METHODS 2023; 3:100590. [PMID: 37714158 PMCID: PMC10545943 DOI: 10.1016/j.crmeth.2023.100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/29/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
Non-human primates (NHPs) are the closest animal model to humans; thus, gene engineering technology in these species holds great promise for the elucidation of higher brain functions and human disease models. Knockin (KI) gene targeting is a versatile approach to modify gene(s) of interest; however, it generally suffers from the low efficiency of homology-directed repair (HDR) in mammalian cells, especially in non-expressed gene loci. In the current study, we generated a tyrosine hydroxylase (TH)-2A-Cre KI model of the common marmoset monkey (marmoset; Callithrix jacchus) using an HDR-biased CRISPR-Cas9 genome editing approach using Cas9-DN1S and RAD51. This model should enable labeling and modification of a specific neuronal lineage using the Cre-loxP system. Collectively, the current study paves the way for versatile gene engineering in NHPs, which may be a significant step toward further biomedical and preclinical applications.
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Affiliation(s)
- Sho Yoshimatsu
- Department of Physiology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan; Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan
| | - Junko Okahara
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan; Central Institute for Experimental Animals, Kawasaki City, Kanagawa 210-0821, Japan.
| | - Junko Yoshie
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan
| | - Yoko Igarashi
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan
| | - Ryusuke Nakajima
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Emi Qian
- Department of Physiology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tsukika Sato
- Department of Physiology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan; Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan
| | - Hiroya Kobayashi
- Department of Physiology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Satoru Morimoto
- Department of Physiology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Noriyuki Kishi
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan
| | - Devin M Pillis
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute (CBDI), Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute (CBDI), Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH 45229, USA; Division of Hematology, CBDI, CCHMC, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Toshiaki Noce
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan
| | - Hideyuki Okano
- Department of Physiology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan; Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako City, Saitama 351-0198, Japan.
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22
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Xu L, Lahiri P, Skowronski J, Bhatia N, Lattanzi A, Porteus MH. Molecular dynamics of genome editing with CRISPR-Cas9 and rAAV6 virus in human HSPCs to treat sickle cell disease. Mol Ther Methods Clin Dev 2023; 30:317-331. [PMID: 37637384 PMCID: PMC10447934 DOI: 10.1016/j.omtm.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Ex vivo gene correction with CRISPR-Cas9 and a recombinant adeno-associated virus serotype 6 (rAAV6) in autologous hematopoietic stem/progenitor cells (HSPCs) to treat sickle cell disease (SCD) has now entered early-phase clinical investigation. To facilitate the progress of CRISPR-Cas9/rAAV6 genome editing technology, we analyzed the molecular changes in key reagents and cellular responses during and after the genome editing procedure in human HSPCs. We demonstrated the high stability of rAAV6 to serve as the donor DNA template. We assessed the benefit of longer HSPC pre-stimulation in terms of increased numbers of edited cells. We observed that the p53 pathway was transiently activated, peaking at 6 h, and resolved over time. Notably, we revealed a strong correlation between p21 mRNA level and rAAV6 genome number in cells and beneficial effects of transient inhibition of p53 with siRNA on genome editing, cell proliferation, and cell survival. In terms of potential immunogenicity, we found that rAAV6 capsid protein was not detectable, while a trace amount of residual Cas9 protein was still detected at 48 h post-genome editing. We believe this information will provide important insights for future improvements of gene correction protocols in HSPCs.
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Affiliation(s)
- Liwen Xu
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Premanjali Lahiri
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Jason Skowronski
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Neehar Bhatia
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Annalisa Lattanzi
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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23
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Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H. TESOGENASE, An Engineered Nuclease Editor for Enhanced Targeted Genome Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.553855. [PMID: 37693500 PMCID: PMC10491117 DOI: 10.1101/2023.08.28.553855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Non-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as a g enome engineering c atalyst (GATALYST) for efficient and safe targeted gene knock-in. However, the engineering efficiency is bottlenecked by the nucleoplasm trafficking and genomic tethering of cssDNA donor, especially for extra-large transgene integration. Here we developed enGager, en hanced G ATALYST a ssociated g enome e ditor system by fusion of nucleus localization signal (NLS) peptide tagged Cas9 with various single stranded DNA binding protein modules through a GFP reporter Knock-in screening. The enGager system assembles an integrative genome integration machinery by forming tripartite complex for engineered nuclease editors, sgRNA and ssDNA donors, thereby facilitate the nucleus trafficking of DNA donors and increase their active local concentration at the targeted genomic site. When applied for genome integration with cssDNA donor templates to diverse genomic loci in various cell types, these enGagers outperform unfused editors. The enhancement of integration efficiency ranges from 1.5- to more than 6-fold, with the effect being more prominent for > 4Kb transgene knock-in in primary cells. We further demonstrated that enGager mediated enhancement for genome integration is ssDNA, but less dsDNA dependent. Using one of the mini-enGagers, we demonstrated large chimeric antigen receptor (CAR) transgene integration in primary T cells with exceptional efficiency and anti-tumor function. These tripartite e ditors with s sDNA o ptimized g enome en gineering system (TESOGENASE TM ) add a set of novel endonuclease editors into the gene-editing toolbox for potential cell and gene therapeutic development based on ssDNA mediated non-viral genome engineering. Highlight A reporter Knock-in screening establishes enGager system to identify TESOGENASE editor to improving ssDNA mediated genome integrationMini-TESOGENASEs developed by fusing Cas9 nuclease with novel ssDNA binding motifsmRNA mini-TESOGENASEs enhance targeted genome integration via various non-viral delivery approachesEfficient functional CAR-T cell engineering by mini-TESOGENASE.
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24
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Yigider E, Taspinar MS, Agar G. Advances in bread wheat production through CRISPR/Cas9 technology: a comprehensive review of quality and other aspects. PLANTA 2023; 258:55. [PMID: 37522927 DOI: 10.1007/s00425-023-04199-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
MAIN CONCLUSION This review provides a comprehensive overview of the CRISPR/Cas9 technique and the research areas of this gene editing tool in improving wheat quality. Wheat (Triticum aestivum L.), the basic nutrition for most of the human population, contributes 20% of the daily energy needed because of its, carbohydrate, essential amino acids, minerals, protein, and vitamin content. Wheat varieties that produce high yields and have enhanced nutritional quality will be required to fulfill future demands. Hexaploid wheat has A, B, and D genomes and includes three like but not identical copies of genes that influence important yield and quality. CRISPR/Cas9, which allows multiplex genome editing provides major opportunities in genome editing studies of plants, especially complicated genomes such as wheat. In this overview, we discuss the CRISPR/Cas9 technique, which is credited with bringing about a paradigm shift in genome editing studies. We also provide a summary of recent research utilizing CRISPR/Cas9 to investigate yield, quality, resistance to biotic/abiotic stress, and hybrid seed production. In addition, we provide a synopsis of the laboratory experience-based solution alternatives as well as the potential obstacles for wheat CRISPR studies. Although wheat's extensive genome and complicated polyploid structure previously slowed wheat genetic engineering and breeding progress, effective CRISPR/Cas9 systems are now successfully used to boost wheat development.
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Affiliation(s)
- Esma Yigider
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey
| | - Mahmut Sinan Taspinar
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey.
| | - Guleray Agar
- Faculty of Science, Department of Biology, Atatürk University, 25240, Erzurum, Turkey
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25
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Liu Y, Cottle WT, Ha T. Mapping cellular responses to DNA double-strand breaks using CRISPR technologies. Trends Genet 2023; 39:560-574. [PMID: 36967246 PMCID: PMC11062594 DOI: 10.1016/j.tig.2023.02.015] [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: 09/22/2021] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/15/2023]
Abstract
DNA double-strand breaks (DSBs) are one of the most genotoxic DNA lesions, driving a range of pathological defects from cancers to immunodeficiencies. To combat genomic instability caused by DSBs, evolution has outfitted cells with an intricate protein network dedicated to the rapid and accurate repair of these lesions. Pioneering studies have identified and characterized many crucial repair factors in this network, while the advent of genome manipulation tools like clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has reinvigorated interest in DSB repair mechanisms. This review surveys the latest methodological advances and biological insights gained by utilizing Cas9 as a precise 'damage inducer' for the study of DSB repair. We highlight rapidly inducible Cas9 systems that enable synchronized and efficient break induction. When combined with sequencing and genome-specific imaging approaches, inducible Cas9 systems greatly expand our capability to spatiotemporally characterize cellular responses to DSB at specific genomic coordinates, providing mechanistic insights that were previously unobtainable.
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Affiliation(s)
- Yang Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - W Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.
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26
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Tang Y, Zhang Z, Yang Z, Wu J. CRISPR/Cas9 and Agrobacterium tumefaciens virulence proteins synergistically increase efficiency of precise genome editing via homology directed repair in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3518-3530. [PMID: 36919203 PMCID: PMC10797490 DOI: 10.1093/jxb/erad096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
CRISPR/Cas9 genome editing and Agrobacterium tumefaciens-mediated genetic transformation are widely-used plant biotechnology tools derived from bacterial immunity-related systems, each involving DNA modification. The Cas9 endonuclease introduces DNA double-strand breaks (DSBs), and the A. tumefaciens T-DNA is released by the VirD2 endonuclease assisted by VirDl and attached by VirE2, transferred to the plant nucleus and integrated into the genome. Here, we explored the potential for synergy between the two systems and found that Cas9 and three virulence (Vir) proteins achieve precise genome editing via the homology directed repair (HDR) pathway in tobacco and rice plants. Compared with Cas9T (Cas9, VirD1, VirE2) and CvD (Cas9-VirD2) systems, the HDR frequencies of a foreign GFPm gene in the CvDT system (Cas9-VirD2, VirD1, VirE2) increased 52-fold and 22-fold, respectively. Further optimization of the CvDT process with a donor linker (CvDTL) achieved a remarkable increase in the efficiency of HDR-mediated genome editing. Additionally, the HDR efficiency of the three rice endogenous genes ACETOLACTATE SYNTHASE (ALS), PHYTOENE DESATURASE (PDS), and NITROGEN TRANSPORTER 1.1 B (NRT1.1B) increased 24-, 32- and 16-fold, respectively, in the CvDTL system, compared with corresponding Cas9TL (Cas9T process with a donor linker). Our results suggest that collaboration between CRISPR/Cas9 and Agrobacterium-mediated genetic transformation can make great progress towards highly efficient and precise genome editing via the HDR pathway.
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Affiliation(s)
- Ye Tang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhennan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Yang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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27
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Fichter KM, Setayesh T, Malik P. Strategies for precise gene edits in mammalian cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:536-552. [PMID: 37215153 PMCID: PMC10192336 DOI: 10.1016/j.omtn.2023.04.012] [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] [Indexed: 05/24/2023]
Abstract
CRISPR-Cas technologies have the potential to revolutionize genetic medicine. However, work is still needed to make this technology clinically efficient for gene correction. A barrier to making precise genetic edits in the human genome is controlling how CRISPR-Cas-induced DNA breaks are repaired by the cell. Since error-prone non-homologous end-joining is often the preferred cellular repair pathway, CRISPR-Cas-induced breaks often result in gene disruption. Homology-directed repair (HDR) makes precise genetic changes and is the clinically desired pathway, but this repair pathway requires a homology donor template and cycling cells. Newer editing strategies, such as base and prime editing, can affect precise repair for relatively small edits without requiring HDR and circumvent cell cycle dependence. However, these technologies have limitations in the extent of genetic editing and require the delivery of bulky cargo. Here, we discuss the pros and cons of precise gene correction using CRISPR-Cas-induced HDR, as well as base and prime editing for repairing small mutations. Finally, we consider emerging new technologies, such as recombination and transposases, which can circumvent both cell cycle and cellular DNA repair dependence for editing the genome.
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Affiliation(s)
- Katye M. Fichter
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tahereh Setayesh
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Hematology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
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28
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Yu C, Hou L, Huang Y, Cui X, Xu S, Wang L, Yan S. The multi-BRCT domain protein DDRM2 promotes the recruitment of RAD51 to DNA damage sites to facilitate homologous recombination. THE NEW PHYTOLOGIST 2023; 238:1073-1084. [PMID: 36727295 DOI: 10.1111/nph.18787] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
DNA double-strand breaks (DSBs) are the most toxic form of DNA damage in cells. Homologous recombination (HR) is an error-free repair mechanism for DSBs as well as a basis for gene targeting using genome-editing techniques. Despite the importance of HR, the HR mechanism in plants is poorly understood. Through genetic screens for DNA damage response mutants (DDRMs), we find that the Arabidopsis ddrm2 mutant is hypersensitive to DSB-inducing reagents. DDRM2 encodes a protein with four BRCA1 C-terminal (BRCT) domains and is highly conserved in plants including bryophytes, the earliest land plant lineage. The plant-specific transcription factor SOG1 binds to the promoter of DDRM2 and activates its expression. In consistence, the expression of DDRM2 is induced by DSBs in a SOG1-dependent manner. In support, genetic analysis suggests that DDRM2 functions downstream of SOG1. Similar to the sog1 mutant, the ddrm2 mutant shows dramatically reduced HR efficiency. Mechanistically, DDRM2 interacts with the core HR protein RAD51 and is required for the recruitment of RAD51 to DSB sites. Our study reveals that SOG1-DDRM2-RAD51 is a novel module for HR, providing a potential target for improving the efficiency of gene targeting.
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Affiliation(s)
- Chen Yu
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Longhui Hou
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiaoyu Cui
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shijun Xu
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
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Anuchina AA, Zaynitdinova MI, Demchenko AG, Evtushenko NA, Lavrov AV, Smirnikhina SA. Bridging Gaps in HDR Improvement: The Role of MAD2L2, SCAI, and SCR7. Int J Mol Sci 2023; 24:ijms24076704. [PMID: 37047677 PMCID: PMC10095018 DOI: 10.3390/ijms24076704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/07/2023] Open
Abstract
This study aimed to enhance homology-directed repair (HDR) efficiency in CRISPR/Cas-mediated genome editing by targeting three key factors regulating the balance between HDR and non-homologous end joining (NHEJ): MAD2L2, SCAI, and Ligase IV. In order to achieve this, a cellular model using mutated eGFP was designed to monitor HDR events. Results showed that MAD2L2 knockdown and SCR7 treatment significantly improved HDR efficiency during Cas9-mediated HDR repair of the mutated eGFP gene in the HEK293T cell line. Fusion protein Cas9-SCAI did not improve HDR. This study is the first to demonstrate that MAD2L2 knockdown during CRISPR-mediated gene editing in HEK293T cells can increase precise correction by up to 10.2 times. The study also confirmed a moderate but consistent effect of SCR7, an inhibitor of Ligase IV, which increased HDR by 1.7 times. These findings provide valuable insights into improving HDR-based genome editing efficiency.
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Affiliation(s)
- Arina A. Anuchina
- Research Centre for Medical Genetics, Moskvorechie 1, 115522 Moscow, Russia
| | | | - Anna G. Demchenko
- Research Centre for Medical Genetics, Moskvorechie 1, 115522 Moscow, Russia
| | - Nadezhda A. Evtushenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
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30
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Zhou J, Luan X, Liu Y, Wang L, Wang J, Yang S, Liu S, Zhang J, Liu H, Yao D. Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1478. [PMID: 37050104 PMCID: PMC10097296 DOI: 10.3390/plants12071478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.
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Affiliation(s)
- Junming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Songnan Yang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
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31
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Chauhan VP, Sharp PA, Langer R. Altered DNA repair pathway engagement by engineered CRISPR-Cas9 nucleases. Proc Natl Acad Sci U S A 2023; 120:e2300605120. [PMID: 36881621 PMCID: PMC10242711 DOI: 10.1073/pnas.2300605120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/10/2023] [Indexed: 03/08/2023] Open
Abstract
CRISPR-Cas9 introduces targeted DNA breaks that engage competing DNA repair pathways, producing a spectrum of imprecise insertion/deletion mutations (indels) and precise templated mutations (precise edits). The relative frequencies of these pathways are thought to primarily depend on genomic sequence and cell state contexts, limiting control over mutational outcomes. Here, we report that engineered Cas9 nucleases that create different DNA break structures engage competing repair pathways at dramatically altered frequencies. We accordingly designed a Cas9 variant (vCas9) that produces breaks which suppress otherwise dominant nonhomologous end-joining (NHEJ) repair. Instead, breaks created by vCas9 are predominantly repaired by pathways utilizing homologous sequences, specifically microhomology-mediated end-joining (MMEJ) and homology-directed repair (HDR). Consequently, vCas9 enables efficient precise editing through HDR or MMEJ while suppressing indels caused by NHEJ in dividing and nondividing cells. These findings establish a paradigm of targeted nucleases custom-designed for specific mutational applications.
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Affiliation(s)
- Vikash P. Chauhan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Phillip A. Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Robert Langer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
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32
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Castiello MC, Ferrari S, Villa A. Correcting inborn errors of immunity: From viral mediated gene addition to gene editing. Semin Immunol 2023; 66:101731. [PMID: 36863140 PMCID: PMC10109147 DOI: 10.1016/j.smim.2023.101731] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/25/2023] [Accepted: 02/14/2023] [Indexed: 03/04/2023]
Abstract
Allogeneic hematopoietic stem cell transplantation is an effective treatment to cure inborn errors of immunity. Remarkable progress has been achieved thanks to the development and optimization of effective combination of advanced conditioning regimens and use of immunoablative/suppressive agents preventing rejection as well as graft versus host disease. Despite these tremendous advances, autologous hematopoietic stem/progenitor cell therapy based on ex vivo gene addition exploiting integrating γ-retro- or lenti-viral vectors, has demonstrated to be an innovative and safe therapeutic strategy providing proof of correction without the complications of the allogeneic approach. The recent advent of targeted gene editing able to precisely correct genomic variants in an intended locus of the genome, by introducing deletions, insertions, nucleotide substitutions or introducing a corrective cassette, is emerging in the clinical setting, further extending the therapeutic armamentarium and offering a cure to inherited immune defects not approachable by conventional gene addition. In this review, we will analyze the current state-of-the art of conventional gene therapy and innovative protocols of genome editing in various primary immunodeficiencies, describing preclinical models and clinical data obtained from different trials, highlighting potential advantages and limits of gene correction.
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Affiliation(s)
- Maria Carmina Castiello
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (IRGB-CNR), Milan, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Anna Villa
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (IRGB-CNR), Milan, Italy.
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Bhoopalan SV, Yen JS, Levine RM, Sharma A. Editing human hematopoietic stem cells: advances and challenges. Cytotherapy 2023; 25:261-269. [PMID: 36123234 DOI: 10.1016/j.jcyt.2022.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 02/07/2023]
Abstract
Genome editing of hematopoietic stem and progenitor cells is being developed for the treatment of several inherited disorders of the hematopoietic system. The adaptation of CRISPR-Cas9-based technologies to make precise changes to the genome, and developments in altering the specificity and efficiency, and improving the delivery of nucleases to target cells have led to several breakthroughs. Many clinical trials are ongoing, and several pre-clinical models have been reported that would allow these genetic therapies to one day offer a potential cure to patients with diseases where limited options currently exist. However, there remain several challenges with respect to establishing safety, expanding accessibility and improving the manufacturing processes of these therapeutic products. This review focuses on some of the recent advances in the field of genome editing of hematopoietic stem and progenitor cells and illustrates the ongoing challenges.
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Affiliation(s)
- Senthil Velan Bhoopalan
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jonathan S Yen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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34
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Strategies for generation of mice via CRISPR/HDR-mediated knock-in. Mol Biol Rep 2023; 50:3189-3204. [PMID: 36701041 DOI: 10.1007/s11033-023-08278-8] [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: 05/24/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023]
Abstract
CRISPR/Cas9 framework is generally used to generate genetically modified mouse models. The clustered regularly interspaced short palindromic repeat gene editing technique, can efficiently generate knock-outs using the non-homologous end-joining repair pathway. Small knock-ins also work precisely using a repair template with help of homology-directed-repair (HDR) mechanism. However, when the fragment size is larger than 4-5 kb, the knock-in tends to be error prone and the efficiency decreases. Certain types of modifications, in particular insertions of very large DNA fragments (10-100 kb) or entire gene replacements, are still difficult. The HDR process needs further streamlining and improvement. Here in this review, we describe methods to enhance the efficiency of the knock-in through checking each step from the guide design to the microinjection and choice of the oocyte donors. This helps in understanding the parameters that can be modified to get improved knock-in efficiency via CRISPR targeting.
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35
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Progresses, Challenges, and Prospects of CRISPR/Cas9 Gene-Editing in Glioma Studies. Cancers (Basel) 2023; 15:cancers15020396. [PMID: 36672345 PMCID: PMC9856991 DOI: 10.3390/cancers15020396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
Glioma refers to a tumor that is derived from brain glial stem cells or progenitor cells and is the most common primary intracranial tumor. Due to its complex cellular components, as well as the aggressiveness and specificity of the pathogenic site of glioma, most patients with malignant glioma have poor prognoses following surgeries, radiotherapies, and chemotherapies. In recent years, an increasing amount of research has focused on the use of CRISPR/Cas9 gene-editing technology in the treatment of glioma. As an emerging gene-editing technology, CRISPR/Cas9 utilizes the expression of certain functional proteins to repair tissues or treat gene-deficient diseases and could be applied to immunotherapies through the expression of antigens, antibodies, or receptors. In addition, some research also utilized CRISPR/Cas9 to establish tumor models so as to study tumor pathogenesis and screen tumor prognostic targets. This paper mainly discusses the roles of CRISPR/Cas9 in the treatment of glioma patients, the exploration of the pathogenesis of neuroglioma, and the screening targets for clinical prognosis. This paper also raises the future research prospects of CRISPR/Cas9 in glioma, as well as the opportunities and challenges that it will face in clinical treatment in the future.
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36
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Singh S, Chaudhary R, Deshmukh R, Tiwari S. Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals. PLANT MOLECULAR BIOLOGY 2023; 111:1-20. [PMID: 36315306 DOI: 10.1007/s11103-022-01321-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
We summarise recent advancements to achieve higher homologous recombination based gene targeting efficiency in different animals and plants. The genome editing has revolutionized the agriculture and human therapeutic sectors by its ability to create precise, stable and predictable mutations in the genome. It depends upon targeted double-strand breaks induction by the engineered endonucleases, which then gets repaired by highly conserved endogenous DNA repair mechanisms. The repairing could be done either through non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways. The HDR-based editing can be applied for precise gene targeting such as insertion of a new gene, gene replacement and altering of the regulatory sequence of a gene to control the existing protein expression. However, HDR-mediated editing is considered challenging because of lower efficiency in higher eukaryotes, thus, preventing its widespread application. This article reviews the recent progress of HDR-mediated editing and discusses novel strategies such as cell cycle synchronization, modulation of DNA damage repair factors, engineering of Cas protein favoring HDR and CRISPR-Cas reagents delivery methods to improve efficiency for generating knock-in events in both plants and animals. Further, multiplexing of described methods may be promising towards achieving higher donor template-assisted homologous recombination efficiency at the target locus.
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Affiliation(s)
- Surender Singh
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Roni Chaudhary
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | | | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India.
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37
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Ivanenko AV, Evtushenko NA, Gurskaya NG. Genome Editing in Therapy of Genodermatoses. Mol Biol 2022. [DOI: 10.1134/s0026893322060085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Bekaert B, Boel A, Cosemans G, De Witte L, Menten B, Heindryckx B. CRISPR/Cas gene editing in the human germline. Semin Cell Dev Biol 2022; 131:93-107. [PMID: 35305903 DOI: 10.1016/j.semcdb.2022.03.012] [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: 11/15/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022]
Abstract
The ease and efficacy of CRISPR/Cas9 germline gene editing in animal models paved the way to human germline gene editing (HGGE), by which permanent changes can be introduced into the embryo. Distinct genes can be knocked out to examine their function during embryonic development. Alternatively, specific sequences can be introduced which can be applied to correct disease-causing mutations. To date, it has been shown that the success of HGGE is dependent on various experimental parameters and that various hurdles (i.e. loss-of-heterozygosity and mosaicism) need to be overcome before clinical applications should be considered. Due to the shortage of human germline material and the ethical constraints concerning HGGE, alternative models such as stem cells have been evaluated as well, in terms of their predictive value on the genetic outcome for HGGE approaches. This review will give an overview of the state of the art of HGGE in oocytes and embryos, and its accompanying challenges.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - A Boel
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - L De Witte
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Ghent University, Department of Biomolecular Medicine, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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Xu K, Zhang YF, Guo DY, Qin L, Ashraf M, Ahmad N. Recent advances in yeast genome evolution with stress tolerance for green biological manufacturing. Biotechnol Bioeng 2022; 119:2689-2697. [PMID: 35841179 DOI: 10.1002/bit.28183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/20/2022] [Accepted: 07/13/2022] [Indexed: 01/04/2023]
Abstract
Green biological manufacturing is a revolutionary industrial model utilizing yeast as a significant microbial cell factory to produce biofuels and other biochemicals. However, biotransformation efficiency is often limited owing to several stress factors resulting from environmental changes or metabolic imbalance, leading to the slow growth of cells, compromised yield, and enhanced energy consumption. These factors make biological manufacturing competitively less economical. In this regard, minimizing the stress impact on microbial cell factories and strong robust performance have been an interesting area of interest in the last few decades. In this review, we focused on revealing the stress factors and their associated mechanisms for yeast in biological manufacturing. To improve yeast tolerance, rational and irrational strategies were introduced, and the molecular basis of genome evolution in yeast was also summarized. Furthermore, strategies of genome-directed evolution such as homology directed repair and nonhomologous end-joining, and the synthetic chromosome recombination and modification by LoxP-mediated evolution and their association with stress tolerance was highlighted. We hope that genome evolution provides new insights for solving the limitations of the natural phenotypes of microorganisms in industrial fermentation for the production of valuable compounds.
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Affiliation(s)
- Ke Xu
- Department of Life Science, Tangshan Key Laboratory of Agricultural Pathogenic Fungi and Toxins, Tangshan Normal University, Tangshan.,Department of Chemical Engineering, Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, PR China
| | - Yun-Feng Zhang
- Department of Life Science, Tangshan Key Laboratory of Agricultural Pathogenic Fungi and Toxins, Tangshan Normal University, Tangshan
| | - Dong-Yu Guo
- Department of Life Science, Tangshan Key Laboratory of Agricultural Pathogenic Fungi and Toxins, Tangshan Normal University, Tangshan
| | - Lei Qin
- Department of Chemical Engineering, Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, PR China
| | - Munaza Ashraf
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - Nadeem Ahmad
- Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
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Campos JS, Henrickson SE. Defining and targeting patterns of T cell dysfunction in inborn errors of immunity. Front Immunol 2022; 13:932715. [PMID: 36189259 PMCID: PMC9516113 DOI: 10.3389/fimmu.2022.932715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022] Open
Abstract
Inborn errors of immunity (IEIs) are a group of more than 450 monogenic disorders that impair immune development and function. A subset of IEIs blend increased susceptibility to infection, autoimmunity, and malignancy and are known collectively as primary immune regulatory disorders (PIRDs). While many aspects of immune function are altered in PIRDs, one key impact is on T-cell function. By their nature, PIRDs provide unique insights into human T-cell signaling; alterations in individual signaling molecules tune downstream signaling pathways and effector function. Quantifying T-cell dysfunction in PIRDs and the underlying causative mechanisms is critical to identifying existing therapies and potential novel therapeutic targets to treat our rare patients and gain deeper insight into the basic mechanisms of T-cell function. Though there are many types of T-cell dysfunction, here we will focus on T-cell exhaustion, a key pathophysiological state. Exhaustion has been described in both human and mouse models of disease, where the chronic presence of antigen and inflammation (e.g., chronic infection or malignancy) induces a state of altered immune profile, transcriptional and epigenetic states, as well as impaired T-cell function. Since a subset of PIRDs amplify T-cell receptor (TCR) signaling and/or inflammatory cytokine signaling cascades, it is possible that they could induce T-cell exhaustion by genetically mimicking chronic infection. Here, we review the fundamentals of T-cell exhaustion and its possible role in IEIs in which genetic mutations mimic prolonged or amplified T-cell receptor and/or cytokine signaling. Given the potential insight from the many forms of PIRDs in understanding T-cell function and the challenges in obtaining primary cells from these rare disorders, we also discuss advances in CRISPR-Cas9 genome-editing technologies and potential applications to edit healthy donor T cells that could facilitate further study of mechanisms of immune dysfunctions in PIRDs. Editing T cells to match PIRD patient genetic variants will allow investigations into the mechanisms underpinning states of dysregulated T-cell function, including T-cell exhaustion.
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Affiliation(s)
- Jose S. Campos
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Sarah E. Henrickson
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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Finney M, Romanowski J, Adelman ZN. Strategies to improve homology-based repair outcomes following CRISPR-based gene editing in mosquitoes: lessons in how to keep any repair disruptions local. Virol J 2022; 19:128. [PMID: 35908059 PMCID: PMC9338592 DOI: 10.1186/s12985-022-01859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
Programmable gene editing systems such as CRISPR-Cas have made mosquito genome engineering more practical and accessible, catalyzing the development of cutting-edge genetic methods of disease vector control. This progress, however, has been limited by the low efficiency of homology-directed repair (HDR)-based sequence integration at DNA double-strand breaks (DSBs) and a lack of understanding about DSB repair in mosquitoes. Innovative efforts to optimize HDR sequence integration by inhibiting non-homologous end joining or promoting HDR have been performed in mammalian systems, however many of these approaches have not been applied to mosquitoes. Here, we review some of the most relevant steps of DNA DSB repair choice and highlight promising approaches that influence this choice to enhance HDR in the context of mosquito gene editing.
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Affiliation(s)
- Micaela Finney
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Joseph Romanowski
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Zach N Adelman
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA.
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. BIOIMPACTS 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Hillen AEJ, Hruzova M, Rothgangl T, Breur M, Bugiani M, van der Knaap MS, Schwank G, Heine VM. In vivo targeting of a variant causing vanishing white matter using CRISPR/Cas9. Mol Ther Methods Clin Dev 2022; 25:17-25. [PMID: 35317047 PMCID: PMC8917273 DOI: 10.1016/j.omtm.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/19/2022] [Indexed: 11/17/2022]
Abstract
Vanishing white matter (VWM) is a leukodystrophy caused by recessive variants in subunits of eIF2B. At present, no curative treatment is available and patients often die at young age. Due to its monogenic nature, VWM is a promising candidate for the development of CRISPR/Cas9-mediated gene therapy. Here we tested a dual-AAV approach in VWM mice encoding CRISPR/Cas9 and a DNA donor template to correct a pathogenic variant in Eif2b5. We performed sequencing analysis to assess gene correction rates and examined effects on the VWM phenotype, including motor behavior. Sequence analysis demonstrated that over 90% of CRISPR/Cas9-induced edits at the targeted locus are insertion or deletion (indel) mutations, rather than precise corrections from the DNA donor template by homology-directed repair. Around half of the CRISPR/Cas9-treated animals died prematurely. VWM mice showed no improvement in motor skills, weight, or neurological scores at 7 months of age, and CRISPR/Cas9-treated controls displayed an induced VWM phenotype. In conclusion, CRISPR/Cas9-induced DNA double-strand breaks (DSBs) at the Eif2b5 locus did not lead to sufficient correction of the VWM variant. Moreover, indel formation in Eif2b5 induced an exacerbated VWM phenotype. Therefore, DSB-independent strategies like base- or prime editing might better suited for VWM correction.
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Affiliation(s)
- Anne E J Hillen
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Marjolein Breur
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marianna Bugiani
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
| | - Gerald Schwank
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vivi M Heine
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands.,Department of Child and Adolescence Psychiatry, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
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Abstract
The rapid development of CRISPR-Cas genome editing tools has greatly changed the way to conduct research and holds tremendous promise for clinical applications. During genome editing, CRISPR-Cas enzymes induce DNA breaks at the target sites and subsequently the DNA repair pathways are recruited to generate diverse editing outcomes. Besides off-target cleavage, unwanted editing outcomes including chromosomal structural variations and exogenous DNA integrations have recently raised concerns for clinical safety. To eliminate these unwanted editing byproducts, we need to explore the underlying mechanisms for the formation of diverse editing outcomes from the perspective of DNA repair. Here, we describe the involved DNA repair pathways in sealing Cas enzyme-induced DNA double-stranded breaks and discuss the origins and effects of unwanted editing byproducts on genome stability. Furthermore, we propose the potential risk of inhibiting DNA repair pathways to enhance gene editing. The recent combined studies of DNA repair and CRISPR-Cas editing provide a framework for further optimizing genome editing to enhance editing safety.
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45
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Lei T, Du S, Peng Z, Chen L. Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review). Int J Mol Med 2022; 50:90. [PMID: 35583003 PMCID: PMC9162042 DOI: 10.3892/ijmm.2022.5145] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for the preservation of genomic integrity and the maintenance of cellular homeostasis. Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism for any type of DNA DSB during the majority of the cell cycle. NHEJ defects regulate tumor sensitivity to ionizing radiation and anti-neoplastic agents, resulting in immunodeficiencies and developmental abnormalities in malignant cells. p53-binding protein 1 (53BP1) is a key mediator involved in DSB repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. 53BP1 promotes DSB repair via NHEJ and antagonizes DNA end overhang resection. At present, novel lines of evidence have revealed the molecular mechanisms underlying the recruitment of 53BP1 and DNA break-responsive effectors to DSB sites, and the promotion of NHEJ-mediated DSB repair via 53BP1, while preventing homologous recombination. In the present review article, recent advances made in the elucidation of the structural and functional characteristics of 53BP1, the mechanisms of 53BP1 recruitment and interaction with the reshaping of the chromatin architecture around DSB sites, the post-transcriptional modifications of 53BP1, and the up- and downstream pathways of 53BP1 are discussed. The present review article also focuses on the application perspectives, current challenges and future directions of 53BP1 research.
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Affiliation(s)
- Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, P.R. China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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46
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Chen Y, Wen R, Yang Z, Chen Z. Genome editing using CRISPR/Cas9 to treat hereditary hematological disorders. Gene Ther 2022; 29:207-216. [PMID: 33750926 DOI: 10.1038/s41434-021-00247-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023]
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system is a versatile and convenient genome-editing tool with prospects in gene therapy. This technique is based on customized site-specific nucleases with programmable guiding RNAs that cleave and introduce double-strand breaks (DSBs) at the target locus and achieve precise genome modification by triggering DNA repair mechanisms. Human hematopoietic stem/progenitor cells (HSPCs) are conventional cell targets for gene therapy in hematological diseases and have been widely used in most studies. Induced pluripotent stem cells (iPSCs) can be generated from a variety of somatic cells and hold great promise for personalized cell-based therapies. CRISPR/Cas9-mediated genome editing in autologous HSPCs and iPSCs is an ideal therapeutic solution for treating hereditary hematological disorders. Here, we review and summarize the latest studies about CRISPR/Cas9-mediated genome editing in patient-derived HSPCs and iPSCs to treat hereditary hematological disorders. Current challenges and prospects are also discussed.
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Affiliation(s)
- Yan Chen
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
| | - Ruiting Wen
- Department of Hematology, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
| | - Zhigang Yang
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
- Department of Hematology, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China
| | - Zhanghui Chen
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, PR China.
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47
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Jia W, Zhang X, Wang H, Teng Q, Xue J, Zhang G. Construction and immune efficacy of a recombinant turkey herpesvirus vaccine strain expressing fusion protein of genotype VII Newcastle disease virus. Vet Microbiol 2022; 268:109429. [DOI: 10.1016/j.vetmic.2022.109429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 12/24/2022]
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Wang M, Xu J, Meng J, Huang X. Synthetic Circular gRNA Mediated Biological Function of CRISPR-(d)Cas9 System. Front Cell Dev Biol 2022; 10:863431. [PMID: 35445012 PMCID: PMC9013764 DOI: 10.3389/fcell.2022.863431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/16/2022] [Indexed: 02/05/2023] Open
Abstract
Ever since the gene editing function was discovered in the CRISPR-Cas9 system, numerous applications and utilities were investigated in order to apply this technique to medical use. However, the clinical practice was limited by unsatisfactory efficiency and unacceptable off-target editing. Modifications from different aspects of the Cas9 protein and gRNAs were published that aimed to improve its function in one way or another. Under the inspiration of Jacob L. Litke and Samie R. Jaffrey, we propose a novel gRNA design that could achieve rapid circular gRNA assembly inside the cells. This circular design consists of the gRNA of interested flanked by Twister ribozymes. The function of this circular gRNA was proved in vitro in both CRISPR-dCas9 and CRISPR-Cas9 systems. It presented a remarkable reduction in the off-target rate in accompany with reduced efficiency. With future improvement in its efficiency, this tool broadens our understanding and possibility of the CRISPR application.
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Affiliation(s)
- Mingxia Wang
- Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jinming Xu
- Shantou University Medical College, Shantou, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China
| | - Xinbo Huang
- Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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Ou-Yang H, Yang SH, Chen W, Yang SH, Cidem A, Sung LY, Chen CM. Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals. Int J Mol Sci 2022; 23:3973. [PMID: 35409332 PMCID: PMC9000021 DOI: 10.3390/ijms23073973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inverted repeat (IR) DNA sequences compose cruciform structures. Some genetic disorders are the result of genome inversion or translocation by cruciform DNA structures. The present study examined whether exogenous DNA integration into the chromosomes of transgenic animals was related to cruciform DNA structures. Large imperfect cruciform structures were frequently predicted around predestinated transgene integration sites in host genomes of microinjection-based transgenic (Tg) animals (αLA-LPH Tg goat, Akr1A1eGFP/eGFP Tg mouse, and NFκB-Luc Tg mouse) or CRISPR/Cas9 gene-editing (GE) animals (αLA-AP1 GE mouse). Transgene cassettes were imperfectly matched with their predestinated sequences. According to the analyzed data, we proposed a putative model in which the flexible cruciform DNA structures acted as a legible template for DNA integration into linear DNAs or double-strand break (DSB) alleles. To demonstrate this model, artificial inverted repeat knock-in (KI) reporter plasmids were created to analyze the KI rate using the CRISPR/Cas9 system in NIH3T3 cells. Notably, the KI rate of the 5′ homologous arm inverted repeat donor plasmid (5′IR) with the ROSA gRNA group (31.5%) was significantly higher than the knock-in reporter donor plasmid (KIR) with the ROSA gRNA group (21.3%, p < 0.05). However, the KI rate of the 3′ inverted terminal repeat/inverted repeat donor plasmid (3′ITRIR) group was not different from the KIR group (23.0% vs. 22.0%). These results demonstrated that the legibility of the sequence with the cruciform DNA existing in the transgene promoted homologous recombination (HR) with a higher KI rate. Our findings suggest that flexible cruciform DNAs folded by IR sequences improve the legibility and accelerate DNA 3′-overhang integration into the host genome via homologous recombination machinery.
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Affiliation(s)
- Huan Ou-Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Shiao-Hsuan Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Reproductive Medicine Center, Department of Gynecology, Changhua Christian Hospital, Changhua 515, Taiwan
| | - Wei Chen
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shang-Hsun Yang
- Department of Physiology, National Cheng Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Abdulkadir Cidem
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Li-Ying Sung
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Mu Chen
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong-Hsing Translational Medicine Research Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
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50
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Ravendran S, Hernández SS, König S, Bak RO. CRISPR/Cas-Based Gene Editing Strategies for DOCK8 Immunodeficiency Syndrome. Front Genome Ed 2022; 4:793010. [PMID: 35373187 PMCID: PMC8969908 DOI: 10.3389/fgeed.2022.793010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Defects in the DOCK8 gene causes combined immunodeficiency termed DOCK8 immunodeficiency syndrome (DIDS). DIDS previously belonged to the disease category of autosomal recessive hyper IgE syndrome (AR-HIES) but is now classified as a combined immunodeficiency (CID). This genetic disorder induces early onset of susceptibility to severe recurrent viral and bacterial infections, atopic diseases and malignancy resulting in high morbidity and mortality. This pathological state arises from impairment of actin polymerization and cytoskeletal rearrangement, which induces improper immune cell migration-, survival-, and effector functions. Owing to the severity of the disease, early allogenic hematopoietic stem cell transplantation is recommended even though it is associated with risk of unintended adverse effects, the need for compatible donors, and high expenses. So far, no alternative therapies have been developed, but the monogenic recessive nature of the disease suggests that gene therapy may be applied. The advent of the CRISPR/Cas gene editing system heralds a new era of possibilities in precision gene therapy, and positive results from clinical trials have already suggested that the tool may provide definitive cures for several genetic disorders. Here, we discuss the potential application of different CRISPR/Cas-mediated genetic therapies to correct the DOCK8 gene. Our findings encourage the pursuit of CRISPR/Cas-based gene editing approaches, which may constitute more precise, affordable, and low-risk definitive treatment options for DOCK8 deficiency.
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Affiliation(s)
| | | | | | - Rasmus O. Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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