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Vercauteren S, Fiesack S, Maroc L, Verstraeten N, Dewachter L, Michiels J, Vonesch SC. The rise and future of CRISPR-based approaches for high-throughput genomics. FEMS Microbiol Rev 2024; 48:fuae020. [PMID: 39085047 PMCID: PMC11409895 DOI: 10.1093/femsre/fuae020] [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: 05/08/2024] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 08/02/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) has revolutionized the field of genome editing. To circumvent the permanent modifications made by traditional CRISPR techniques and facilitate the study of both essential and nonessential genes, CRISPR interference (CRISPRi) was developed. This gene-silencing technique employs a deactivated Cas effector protein and a guide RNA to block transcription initiation or elongation. Continuous improvements and a better understanding of the mechanism of CRISPRi have expanded its scope, facilitating genome-wide high-throughput screens to investigate the genetic basis of phenotypes. Additionally, emerging CRISPR-based alternatives have further expanded the possibilities for genetic screening. This review delves into the mechanism of CRISPRi, compares it with other high-throughput gene-perturbation techniques, and highlights its superior capacities for studying complex microbial traits. We also explore the evolution of CRISPRi, emphasizing enhancements that have increased its capabilities, including multiplexing, inducibility, titratability, predictable knockdown efficacy, and adaptability to nonmodel microorganisms. Beyond CRISPRi, we discuss CRISPR activation, RNA-targeting CRISPR systems, and single-nucleotide resolution perturbation techniques for their potential in genome-wide high-throughput screens in microorganisms. Collectively, this review gives a comprehensive overview of the general workflow of a genome-wide CRISPRi screen, with an extensive discussion of strengths and weaknesses, future directions, and potential alternatives.
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Affiliation(s)
- Silke Vercauteren
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Simon Fiesack
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Laetitia Maroc
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Natalie Verstraeten
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Liselot Dewachter
- de Duve Institute, Université catholique de Louvain, Hippokrateslaan 75, 1200 Brussels, Belgium
| | - Jan Michiels
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Sibylle C Vonesch
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
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2
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Rajanathadurai J, Perumal E, Sindya J. Advances in targeting cancer epigenetics using CRISPR-dCas9 technology: A comprehensive review and future prospects. Funct Integr Genomics 2024; 24:164. [PMID: 39292321 DOI: 10.1007/s10142-024-01455-3] [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: 07/09/2024] [Revised: 08/30/2024] [Accepted: 09/11/2024] [Indexed: 09/19/2024]
Abstract
Cancer, a complex and multifaceted group of diseases, continues to challenge the boundaries of medical science and healthcare. Its relentless impact on global health, both in terms of prevalence and mortality, underscores the urgent need for a comprehensive understanding of its underlying mechanisms and innovative therapeutic approaches. In recent years, significant progress has been achieved in identifying the genetic and epigenetic mechanisms that cause cancer development and treatment resistance. Researchers are currently investigating the possibility of epigenetic editing such as CRISPR-dCas9 (Clustered Regularly Interspaced Short Palindromic Repeats/deactivated CRISPR-associated protein 9) technologies, for targeting and modifying cancer related epigenetic alterations. A revolutionary form of precision cancer treatment called CRISPR-dCas9 is derived from the bacterial CRISPR-Cas (CRISPR-associated nuclease) system. CRISPR-dCas9 can be combined with epigenetic effectors (EE) to alter malignant epigenetic characteristics associated with cancer. The purpose of this review article is to provide a thorough analysis of recent advancements in utilizing CRISPR-dCas9 technology to target and modify epigenetic changes associated with cancer. This review aims to summarize the latest research developments, evaluate the effectiveness and limitations of CRISPR-dCas9 applications in cancer therapy, identify key challenges such as delivery methods and explore future directions for improving and expanding these technologies. Here, we address the various obstacles that may arise in clinical applications while showcasing the latest advancements and potential future uses of CRISPR-Cas9 in cancer therapy.
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Affiliation(s)
- Jeevitha Rajanathadurai
- Cancer Genomics Lab, Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, India
| | - Elumalai Perumal
- Cancer Genomics Lab, Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, India.
| | - Jospin Sindya
- Cancer Genomics Lab, Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, India
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3
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Ng BW, Kaukonen MK, McClements ME, Shamsnajafabadi H, MacLaren RE, Cehajic-Kapetanovic J. Genetic therapies and potential therapeutic applications of CRISPR activators in the eye. Prog Retin Eye Res 2024; 102:101289. [PMID: 39127142 DOI: 10.1016/j.preteyeres.2024.101289] [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: 06/06/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Conventional gene therapy involving supplementation only treats loss-of-function diseases and is limited by viral packaging sizes, precluding therapy of large genes. The discovery of CRISPR/Cas has led to a paradigm shift in the field of genetic therapy, with the promise of precise gene editing, thus broadening the range of diseases that can be treated. The initial uses of CRISPR/Cas have focused mainly on gene editing or silencing of abnormal variants via utilising Cas endonuclease to trigger the target cell endogenous non-homologous end joining. Subsequently, the technology has evolved to modify the Cas enzyme and even its guide RNA, leading to more efficient editing tools in the form of base and prime editing. Further advancements of this CRISPR/Cas technology itself have expanded its functional repertoire from targeted editing to programmable transactivation, shifting the therapeutic focus to precise endogenous gene activation or upregulation with the potential for epigenetic modifications. In vivo experiments using this platform have demonstrated the potential of CRISPR-activators (CRISPRa) to treat various loss-of-function diseases, as well as in regenerative medicine, highlighting their versatility to overcome limitations associated with conventional strategies. This review summarises the molecular mechanisms of CRISPRa platforms, the current applications of this technology in vivo, and discusses potential solutions to translational hurdles for this therapy, with a focus on ophthalmic diseases.
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Affiliation(s)
- Benjamin Wj Ng
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Maria K Kaukonen
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Michelle E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Hoda Shamsnajafabadi
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Jasmina Cehajic-Kapetanovic
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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4
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Ruan W, Xu S, An Y, Cui Y, Liu Y, Wang Y, Ismail M, Liu Y, Zheng M. Brain-Targeted Cas12a Ribonucleoprotein Nanocapsules Enable Synergetic Gene Co-Editing Leading to Potent Inhibition of Orthotopic Glioblastoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402178. [PMID: 38943253 PMCID: PMC11434219 DOI: 10.1002/advs.202402178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/26/2024] [Indexed: 07/01/2024]
Abstract
Gene-editing technology shows great potential in glioblastoma (GBM) therapy. Due to the complexity of GBM pathogenesis, a single gene-editing-based therapy is unlikely to be successful; therefore, a multi-gene knockout strategy is preferred for effective GBM inhibition. Here, a non-invasive, biodegradable brain-targeted CRISPR/Cas12a nanocapsule is used that simultaneously targeted dual oncogenes, EGFR and PLK1, for effective GBM therapy. This cargo nanoencapsulation technology enables the CRISPR/Cas12a system to achieve extended blood half-life, efficient blood-brain barrier (BBB) penetration, active tumor targeting, and selective release. In U87MG cells, the combinatorial gene editing system resulted in 61% and 33% knockout of EGFR and PLK1, respectively. Following systemic administration, the CRISPR/Cas12a system demonstrated promising brain tumor accumulation that led to extensive EGFR and PLK1 gene editing in both U87MG and patient-derived GSC xenograft mouse models with negligible off-target gene editing detected through NGS. Additionally, CRISPR/Cas12a nanocapsules that concurrently targeted the EGFR and PLK1 oncogenes showed superior tumor growth suppression and significantly improved the median survival time relative to nanocapsules containing single oncogene knockouts, signifying the potency of the multi-oncogene targeting strategy. The findings indicate that utilization of the CRISPR/Cas12a combinatorial gene editing technique presents a practical option for gene therapy in GBM.
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Affiliation(s)
- Weimin Ruan
- Henan-Macquarie University Joint Centre for Biomedical Innovation, Henan Key Laboratory of Brain Targeted Bio-nanomedicine, Henan International Joint Laboratory of Nanobiomedicine, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Sen Xu
- Henan-Macquarie University Joint Centre for Biomedical Innovation, Henan Key Laboratory of Brain Targeted Bio-nanomedicine, Henan International Joint Laboratory of Nanobiomedicine, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yang An
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Science, Henan University, Kaifeng, Henan, 475004, China
| | - Yingxue Cui
- Henan-Macquarie University Joint Centre for Biomedical Innovation, Henan Key Laboratory of Brain Targeted Bio-nanomedicine, Henan International Joint Laboratory of Nanobiomedicine, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yang Liu
- Henan-Macquarie University Joint Centre for Biomedical Innovation, Henan Key Laboratory of Brain Targeted Bio-nanomedicine, Henan International Joint Laboratory of Nanobiomedicine, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yibin Wang
- Henan-Macquarie University Joint Centre for Biomedical Innovation, Henan Key Laboratory of Brain Targeted Bio-nanomedicine, Henan International Joint Laboratory of Nanobiomedicine, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Muhammad Ismail
- Henan-Macquarie University Joint Centre for Biomedical Innovation, Henan Key Laboratory of Brain Targeted Bio-nanomedicine, Henan International Joint Laboratory of Nanobiomedicine, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yong Liu
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Wenzhou Medical University, 270 Xuanyuanxi Road, Wenzhou, Zhejiang, 325027, China
| | - Meng Zheng
- Henan-Macquarie University Joint Centre for Biomedical Innovation, Henan Key Laboratory of Brain Targeted Bio-nanomedicine, Henan International Joint Laboratory of Nanobiomedicine, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
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5
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Monchusi B, Dube P, Takundwa MM, Kenmogne VL, Thimiri Govinda Raj DB. Advances in CRISPR-Cas systems for blood cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 208:261-284. [PMID: 39266186 DOI: 10.1016/bs.pmbts.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
CRISPR-Cas systems have revolutionised precision medicine by enabling personalised treatments tailored to an individual's genetic profile. Various CRISPR technologies have been developed to target specific disease-causing genes in blood cancers, and some have advanced to clinical trials. Although some studies have explored the in vivo applications of CRISPR-Cas systems, several challenges continue to impede their widespread use. Furthermore, CRISPR-Cas technology has shown promise in improving the response of immunotherapies to blood cancers. The emergence of CAR-T cell therapy has shown considerable success in the targeting and correcting of disease-causing genes in blood cancers. Despite the promising potential of CRISPR-Cas in the treatment of blood cancers, issues related to safety, ethics, and regulatory approval remain significant hurdles. This comprehensive review highlights the transformative potential of CRISPR-Cas technology to revolutionise blood cancer therapy.
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Affiliation(s)
- Bernice Monchusi
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Phumuzile Dube
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Mutsa Monica Takundwa
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Vanelle Larissa Kenmogne
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa; Department of Surgery, University of the Witwatersrand, Johannesburg, South Africa
| | - Deepak Balaji Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa.
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He Y, Liu S, Chen L, Pu D, Zhong Z, Xu T, Ren Q, Dong C, Wang Y, Wang D, Zheng X, Guo F, Zhang T, Qi Y, Zhang Y. Versatile plant genome engineering using anti-CRISPR-Cas12a systems. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2704-7. [PMID: 39158766 DOI: 10.1007/s11427-024-2704-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/07/2024] [Indexed: 08/20/2024]
Abstract
CRISPR-Cas12a genome engineering systems have been widely used in plant research and crop breeding. To date, the performance and use of anti-CRISPR-Cas12a systems have not been fully established in plants. Here, we conduct in silico analysis to identify putative anti-CRISPR systems for Cas12a. These putative anti-CRISPR proteins, along with known anti-CRISPR proteins, are assessed for their ability to inhibit Cas12a cleavage activity in vivo and in planta. Among all anti-CRISPR proteins tested, AcrVA1 shows robust inhibition of Mb2Cas12a and LbCas12a in E. coli. Further tests show that AcrVA1 inhibits LbCas12a mediated genome editing in rice protoplasts and stable transgenic lines. Impressively, co-expression of AcrVA1 mitigates off-target effects by CRISPR-LbCas12a, as revealed by whole genome sequencing. In addition, transgenic plants expressing AcrVA1 exhibit different levels of inhibition to LbCas12a mediated genome editing, representing a novel way of fine-tuning genome editing efficiency. By controlling temporal and spatial expression of AcrVA1, we show that inducible and tissue specific genome editing can be achieved in plants. Furthermore, we demonstrate that AcrVA1 also inhibits LbCas12a-based CRISPR activation (CRISPRa) and based on this principle we build logic gates to turn on and off target genes in plant cells. Together, we have established an efficient anti-CRISPR-Cas12a system in plants and demonstrate its versatile applications in mitigating off-target effects, fine-tuning genome editing efficiency, achieving spatial-temporal control of genome editing, and generating synthetic logic gates for controlling target gene expression in plant cells.
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Affiliation(s)
- Yao He
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Long Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Dongkai Pu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Tang Xu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Yawei Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Danning Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xuelian Zheng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Fengbiao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430017, China.
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, 20850, USA.
| | - Yong Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
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Borrelli C, Roberts M, Eletto D, Hussherr MD, Fazilaty H, Valenta T, Lafzi A, Kretz JA, Guido Vinzoni E, Karakatsani A, Adivarahan S, Mannhart A, Kimura S, Meijs A, Baccouche Mhamedi F, Acar IE, Handler K, Ficht X, Platt RJ, Piscuoglio S, Moor AE. In vivo interaction screening reveals liver-derived constraints to metastasis. Nature 2024; 632:411-418. [PMID: 39048831 PMCID: PMC11306111 DOI: 10.1038/s41586-024-07715-3] [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: 05/07/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
It is estimated that only 0.02% of disseminated tumour cells are able to seed overt metastases1. While this suggests the presence of environmental constraints to metastatic seeding, the landscape of host factors controlling this process remains largely unclear. Here, combining transposon technology2 and fluorescence niche labelling3, we developed an in vivo CRISPR activation screen to systematically investigate the interactions between hepatocytes and metastatic cells. We identify plexin B2 as a critical host-derived regulator of liver colonization in colorectal and pancreatic cancer and melanoma syngeneic mouse models. We dissect a mechanism through which plexin B2 interacts with class IV semaphorins on tumour cells, leading to KLF4 upregulation and thereby promoting the acquisition of epithelial traits. Our results highlight the essential role of signals from the liver parenchyma for the seeding of disseminated tumour cells before the establishment of a growth-promoting niche. Our findings further suggest that epithelialization is required for the adaptation of CRC metastases to their new tissue environment. Blocking the plexin-B2-semaphorin axis abolishes metastatic colonization of the liver and therefore represents a therapeutic strategy for the prevention of hepatic metastases. Finally, our screening approach, which evaluates host-derived extrinsic signals rather than tumour-intrinsic factors for their ability to promote metastatic seeding, is broadly applicable and lays a framework for the screening of environmental constraints to metastasis in other organs and cancer types.
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Affiliation(s)
- Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Morgan Roberts
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Davide Eletto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tomas Valenta
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Atefeh Lafzi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elena Guido Vinzoni
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | - Ardian Mannhart
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Shoichiro Kimura
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ab Meijs
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Salvatore Piscuoglio
- IRCCS Humanitas Research Hospital, Milan, Italy
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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8
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Melore SM, Hamilton MC, Reddy TE. HyperCas12a enables highly-multiplexed epigenome editing screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602263. [PMID: 39026853 PMCID: PMC11257430 DOI: 10.1101/2024.07.08.602263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. High-throughput screens using dCas9 fused to epigenome editing domains have allowed researchers to assess the impact of activation or repression of both coding and non-coding genomic regions on a phenotype of interest, but assessment of genetic interactions between those elements has been limited to pairs. Here, we combine a hyper-efficient version of Lachnospiraceae bacterium dCas12a (dHyperLbCas12a) with RNA Polymerase II expression of long CRISPR RNA (crRNA) arrays to enable efficient highly-multiplexed epigenome editing. We demonstrate that this system is compatible with several activation and repression domains, including the P300 histone acetyltransferase domain and SIN3A interacting domain (SID). We also show that the dCas12a platform can perform simultaneous activation and repression using a single crRNA array via co-expression of multiple dCas12a orthologues. Lastly, demonstrate that the dCas12a system is highly effective for high-throughput screens. We use dHyperLbCas12a-KRAB and a ~19,000-member barcoded library of crRNA arrays containing six crRNAs each to dissect the independent and combinatorial contributions of CREs to the dose-dependent control of gene expression at a glucocorticoid-responsive locus. The tools and methods introduced here create new possibilities for highly multiplexed control of gene expression in a wide variety of biological systems.
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Affiliation(s)
- Schuyler M. Melore
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
| | - Marisa C. Hamilton
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
| | - Timothy E. Reddy
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
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9
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Hebert JD, Xu H, Tang YJ, Ruiz PA, Detrick CR, Wang J, Hughes NW, Donosa O, Andrejka L, Karmakar S, Aboiralor I, Tang R, Sage J, Cong L, Petrov DA, Winslow MM. Efficient and multiplexed somatic genome editing with Cas12a mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583774. [PMID: 38496463 PMCID: PMC10942438 DOI: 10.1101/2024.03.07.583774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells in vivo .
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10
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Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2024:10.1038/s41587-024-02224-0. [PMID: 38760567 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
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Affiliation(s)
- C C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - C M Wilson
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
| | | | - R Dai
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Q Chen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - N Teyssier
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - S Misiukiewicz
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - A Arab
- Arc Institute, Palo Alto, CA, USA
| | - T O'Loughlin
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - J C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - L A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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11
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Xun G, Zhu Z, Singh N, Lu J, Jain PK, Zhao H. Harnessing noncanonical crRNA for highly efficient genome editing. Nat Commun 2024; 15:3823. [PMID: 38714643 PMCID: PMC11076584 DOI: 10.1038/s41467-024-48012-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: 03/06/2024] [Accepted: 04/18/2024] [Indexed: 05/10/2024] Open
Abstract
The CRISPR-Cas12a system is more advantageous than the widely used CRISPR-Cas9 system in terms of specificity and multiplexibility. However, its on-target editing efficiency is typically much lower than that of the CRISPR-Cas9 system. Here we improved its on-target editing efficiency by simply incorporating 2-aminoadenine (base Z, which alters canonical Watson-Crick base pairing) into the crRNA to increase the binding affinity between crRNA and its complementary DNA target. The resulting CRISPR-Cas12a (named zCRISPR-Cas12a thereafter) shows an on-target editing efficiency comparable to that of the CRISPR-Cas9 system but with much lower off-target effects than the CRISPR-Cas9 system in mammalian cells. In addition, zCRISPR-Cas12a can be used for precise gene knock-in and highly efficient multiplex genome editing. Overall, the zCRISPR-Cas12a system is superior to the CRISPR-Cas9 system, and our simple crRNA engineering strategy may be extended to other CRISPR-Cas family members as well as their derivatives.
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Affiliation(s)
- Guanhua Xun
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Zhixin Zhu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Nilmani Singh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Jingxia Lu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Huimin Zhao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA.
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12
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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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13
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Esmaeili Anvar N, Lin C, Ma X, Wilson LL, Steger R, Sangree AK, Colic M, Wang SH, Doench JG, Hart T. Efficient gene knockout and genetic interaction screening using the in4mer CRISPR/Cas12a multiplex knockout platform. Nat Commun 2024; 15:3577. [PMID: 38678031 PMCID: PMC11055879 DOI: 10.1038/s41467-024-47795-3] [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: 09/22/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Genetic interactions mediate the emergence of phenotype from genotype, but technologies for combinatorial genetic perturbation in mammalian cells are challenging to scale. Here, we identify background-independent paralog synthetic lethals from previous CRISPR genetic interaction screens, and find that the Cas12a platform provides superior sensitivity and assay replicability. We develop the in4mer Cas12a platform that uses arrays of four independent guide RNAs targeting the same or different genes. We construct a genome-scale library, Inzolia, that is ~30% smaller than a typical CRISPR/Cas9 library while also targeting ~4000 paralog pairs. Screens in cancer cells demonstrate discrimination of core and context-dependent essential genes similar to that of CRISPR/Cas9 libraries, as well as detection of synthetic lethal and masking/buffering genetic interactions between paralogs of various family sizes. Importantly, the in4mer platform offers a fivefold reduction in library size compared to other genetic interaction methods, substantially reducing the cost and effort required for these assays.
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Affiliation(s)
- Nazanin Esmaeili Anvar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX, USA
| | - Chenchu Lin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingdi Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX, USA
| | - Lori L Wilson
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Steger
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Annabel K Sangree
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Medina Colic
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sidney H Wang
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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14
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Jia HY, Zhang XY, Ye BC, Yin BC. An Orthogonal CRISPR/dCas12a System for RNA Imaging in Live Cells. Anal Chem 2024; 96:5913-5921. [PMID: 38563119 DOI: 10.1021/acs.analchem.3c05975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
CRISPR/Cas technology has made great progress in the field of live-cell imaging beyond genome editing. However, effective and easy-to-use CRISPR systems for labeling multiple RNAs of interest are still needed. Here, we engineered a CRISPR/dCas12a system that enables the specific recognition of the target RNA under the guidance of a PAM-presenting oligonucleotide (PAMmer) to mimic the PAM recognition mechanism for DNA substrates. We demonstrated the feasibility and specificity of this system for specifically visualizing endogenous mRNA. By leveraging dCas12a-mediated precursor CRISPR RNA (pre-crRNA) processing and the orthogonality of dCas12a from different bacteria, we further demonstrated the proposed system as a simple and versatile molecular toolkit for multiplexed imaging of different types of RNA transcripts in live cells with high specificity. This programmable dCas12a system not only broadens the RNA imaging toolbox but also facilitates diverse applications for RNA manipulation.
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Affiliation(s)
- Hai-Yan Jia
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Xin-Yue Zhang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang 832000, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang 832000, China
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15
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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16
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Zhang F, Wang JY, Li CL, Zhang WG. HyCas9-12aGEP: an efficient genome editing platform for Corynebacterium glutamicum. Front Bioeng Biotechnol 2024; 12:1327172. [PMID: 38532881 PMCID: PMC10963414 DOI: 10.3389/fbioe.2024.1327172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Corynebacterium glutamicum plays a crucial role as a significant industrial producer of metabolites. Despite the successful development of CRISPR-Cas9 and CRISPR-Cas12a-assisted genome editing technologies in C. glutamicum, their editing resolution and efficiency are hampered by the diverse on-target activities of guide RNAs (gRNAs). To address this problem, a hybrid CRISPR-Cas9-Cas12a genome editing platform (HyCas9-12aGEP) was developed in C. glutamicum in this study to co-express sgRNA (corresponding to SpCas9 guide RNA), crRNA (corresponding to FnCas12a guide RNA), or hfgRNA (formed by the fusion of sgRNA and crRNA). HyCas9-12aGEP improves the efficiency of mapping active gRNAs and outperforms both CRISPR-Cas9 and CRISPR-Cas12a in genome editing resolution and efficiency. In the experiment involving the deletion of the cg0697-0740 gene segment, an unexpected phenotype was observed, and HyCas9-12aGEP efficiently identified the responsible genotype from more than 40 genes. Here, HyCas9-12aGEP greatly improve our capability in terms of genome reprogramming in C. glutamicum.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | | | | | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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17
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Wang J, Torres IM, Shang M, Al-Armanazi J, Dilawar H, Hettiarachchi DU, Paladines-Parrales A, Chambers B, Pottle K, Soman M, Su B, Dunham RA. One-step knock-in of two antimicrobial peptide transgenes at multiple loci of catfish by CRISPR/Cas9-mediated multiplex genome engineering. Int J Biol Macromol 2024; 260:129384. [PMID: 38224812 DOI: 10.1016/j.ijbiomac.2024.129384] [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: 10/05/2023] [Revised: 11/23/2023] [Accepted: 01/01/2024] [Indexed: 01/17/2024]
Abstract
CRISPR/Cas9-mediated multiplex genome editing (MGE) conventionally uses multiple single-guide RNAs (sgRNAs) for gene-targeted mutagenesis via the non-homologous end joining (NHEJ) pathway. MGE has been proven to be highly efficient for functional gene disruption/knockout (KO) at multiple loci in mammalian cells or organisms. However, in the absence of a DNA donor, this approach is limited to small indels without transgene integration. Here, we establish the linear double-stranded DNA (dsDNA) and double-cut plasmid (dcPlasmid) combination-assisted MGE in channel catfish (Ictalurus punctatus), allowing combinational deletion mutagenesis and transgene knock-in (KI) at multiple sites through NHEJ/homology-directed repair (HDR) pathway in parallel. In this study, we used single-sgRNA-based genome editing (ssGE) and multi-sgRNA-based MGE (msMGE) to replace the luteinizing hormone (lh) and melanocortin-4 receptor (mc4r) genes with the cathelicidin (As-Cath) transgene and the myostatin (two target sites: mstn1, mstn2) gene with the cecropin (Cec) transgene, respectively. A total of 9000 embryos were microinjected from three families, and 1004 live fingerlings were generated and analyzed. There was no significant difference in hatchability (all P > 0.05) and fry survival (all P > 0.05) between ssGE and msMGE. Compared to ssGE, CRISPR/Cas9-mediated msMGE assisted by the mixture of dsDNA and dcPlasmid donors yielded a higher knock-in (KI) efficiency of As-Cath (19.93 %, [59/296] vs. 12.96 %, [45/347]; P = 0.018) and Cec (22.97 %, [68/296] vs. 10.80 %, [39/361]; P = 0.003) transgenes, respectively. The msMGE strategy can be used to generate transgenic fish carrying two transgenes at multiple loci. In addition, double and quadruple mutant individuals can be produced with high efficiency (36.3 % ∼ 71.1 %) in one-step microinjection. In conclusion, we demonstrated that the CRISPR/Cas9-mediated msMGE allows the one-step generation of simultaneous insertion of the As-Cath and Cec transgenes at four sites, and the simultaneous disruption of the lh, mc4r, mstn1 and mstn2 alleles. This msMGE system, aided by the mixture donors, promises to pioneer a new dimension in the drive and selection of multiple designated traits in other non-model organisms.
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Affiliation(s)
- Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America.
| | - Indira Medina Torres
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Jacob Al-Armanazi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Hamza Dilawar
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Darshika U Hettiarachchi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Abel Paladines-Parrales
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Barrett Chambers
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Kate Pottle
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Misha Soman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America.
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
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18
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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19
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Nguyen LT, Macaluso NC, Rakestraw NR, Carman DR, Pizzano BLM, Hautamaki RC, Rananaware SR, Roberts IE, Jain PK. Harnessing noncanonical crRNAs to improve functionality of Cas12a orthologs. Cell Rep 2024; 43:113777. [PMID: 38358883 PMCID: PMC11031708 DOI: 10.1016/j.celrep.2024.113777] [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: 07/09/2023] [Revised: 12/04/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
There is a broad diversity among Cas12a endonucleases that possess nucleic acid detection and gene-editing capabilities, but few are studied extensively. Here, we present an exhaustive investigation of 23 Cas12a orthologs, with a focus on their cis- and trans-cleavage activities in combination with noncanonical crRNAs. Through biochemical assays, we observe that some noncanonical crRNA:Cas12a effector complexes outperform their corresponding wild-type crRNA:Cas12a. Cas12a can recruit crRNA with modifications such as loop extensions and split scaffolds. Moreover, the tolerance of Cas12a to noncanonical crRNA is also observed in mammalian cells through the formation of indels. We apply the adaptability of Cas12a:crRNA complexes to detect SARS-CoV-2 in clinical nasopharyngeal swabs, saliva samples, and tracheal aspirates. Our findings further expand the toolbox for next-generation CRISPR-based diagnostics and gene editing.
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Affiliation(s)
- Long T Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Nicolas C Macaluso
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Noah R Rakestraw
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Dylan R Carman
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Brianna L M Pizzano
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Raymond C Hautamaki
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, USA
| | | | - Isabel E Roberts
- Department of Chemical Engineering, John and Marcia Price College of Engineering, University of Utah, Salt Lake City, UT, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA; Health Cancer Center, University of Florida, Gainesville, FL, USA.
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20
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Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558350. [PMID: 37781594 PMCID: PMC10541102 DOI: 10.1101/2023.09.18.558350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
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21
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Yu L, Marchisio MA. Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2024; 52:1483-1497. [PMID: 38142459 PMCID: PMC10853767 DOI: 10.1093/nar/gkad1216] [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: 07/18/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
New, orthogonal transcription factors in eukaryotic cells have been realized by engineering nuclease-deficient CRISPR-associated proteins and/or their guide RNAs. In this work, we present a new kind of orthogonal transcriptional activators, in Saccharomyces cerevisiae, made by turning type V CRISPR RNA into a scaffold RNA (ScRNA) able to recruit a variable number of VP64 activation domains. The activator arises from the complex between the synthetic ScRNA and DNase-deficient type V Cas proteins: dCas12e and denAsCas12a. The transcription activation achieved via the newly engineered dCas:ScRNA system is up to 4.7-fold higher than that obtained with the direct fusion of VP64 to Cas proteins. The new transcription factors have been proven to be functional in circuits such as Boolean gates, converters, multiplex-gene and metabolic-pathway activation. Our results extend the CRISPR-Cas-based technology with a new effective tool that only demands RNA engineering and improves the current design of transcription factors based on type V Cas proteins.
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Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
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22
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Chen Y, Luo X, Kang R, Cui K, Ou J, Zhang X, Liang P. Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment. J Genet Genomics 2024; 51:159-183. [PMID: 37516348 DOI: 10.1016/j.jgg.2023.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Osteoarthritis (OA) is one of the most common degenerative joint diseases worldwide, causing pain, disability, and decreased quality of life. The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA. Currently, there is a lack of effective therapeutic strategies for OA treatment. With the development of CRISPR-based genome, epigenome, and RNA editing tools, OA treatment has been improved by targeting genetic risk factors, activating chondrogenic elements, and modulating inflammatory regulators. Supported by cell therapy and in vivo delivery vectors, genome, epigenome, and RNA editing tools may provide a promising approach for personalized OA therapy. This review summarizes CRISPR-based genome, epigenome, and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment. Moreover, in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.
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Affiliation(s)
- Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xiao Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Rui Kang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Kaixin Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Ou
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xiya Zhang
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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23
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Nuttle X, Burt ND, Currall B, Moysés-Oliveira M, Mohajeri K, Bhavsar R, Lucente D, Yadav R, Tai DJC, Gusella JF, Talkowski ME. Parallelized engineering of mutational models using piggyBac transposon delivery of CRISPR libraries. CELL REPORTS METHODS 2024; 4:100672. [PMID: 38091988 PMCID: PMC10831954 DOI: 10.1016/j.crmeth.2023.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/14/2023] [Accepted: 11/21/2023] [Indexed: 01/25/2024]
Abstract
New technologies and large-cohort studies have enabled novel variant discovery and association at unprecedented scale, yet functional characterization of these variants remains paramount to deciphering disease mechanisms. Approaches that facilitate parallelized genome editing of cells of interest or induced pluripotent stem cells (iPSCs) have become critical tools toward this goal. Here, we developed an approach that incorporates libraries of CRISPR-Cas9 guide RNAs (gRNAs) together with inducible Cas9 into a piggyBac (PB) transposon system to engineer dozens to hundreds of genomic variants in parallel against isogenic cellular backgrounds. This method empowers loss-of-function (LoF) studies through the introduction of insertions or deletions (indels) and copy-number variants (CNVs), though generating specific nucleotide changes is possible with prime editing. The ability to rapidly establish high-quality mutational models at scale will facilitate the development of isogenic cellular collections and catalyze comparative functional genomic studies investigating the roles of hundreds of genes and mutations in development and disease.
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Affiliation(s)
- Xander Nuttle
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Nicholas D Burt
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin Currall
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Mariana Moysés-Oliveira
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Kiana Mohajeri
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; PhD program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Derek J C Tai
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - James F Gusella
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Michael E Talkowski
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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24
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Lonez C, Breman E. Allogeneic CAR-T Therapy Technologies: Has the Promise Been Met? Cells 2024; 13:146. [PMID: 38247837 PMCID: PMC10814647 DOI: 10.3390/cells13020146] [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: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
This last decade, chimeric antigen receptor (CAR) T-cell therapy has become a real treatment option for patients with B-cell malignancies, while multiple efforts are being made to extend this therapy to other malignancies and broader patient populations. However, several limitations remain, including those associated with the time-consuming and highly personalized manufacturing of autologous CAR-Ts. Technologies to establish "off-the-shelf" allogeneic CAR-Ts with low alloreactivity are currently being developed, with a strong focus on gene-editing technologies. Although these technologies have many advantages, they have also strong limitations, including double-strand breaks in the DNA with multiple associated safety risks as well as the lack of modulation. As an alternative, non-gene-editing technologies provide an interesting approach to support the development of allogeneic CAR-Ts in the future, with possibilities of fine-tuning gene expression and easy development. Here, we will review the different ways allogeneic CAR-Ts can be manufactured and discuss which technologies are currently used. The biggest hurdles for successful therapy of allogeneic CAR-Ts will be summarized, and finally, an overview of the current clinical evidence for allogeneic CAR-Ts in comparison to its autologous counterpart will be given.
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25
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Liang R, He Z, Zhao KT, Zhu H, Hu J, Liu G, Gao Q, Liu M, Zhang R, Qiu JL, Gao C. Prime editing using CRISPR-Cas12a and circular RNAs in human cells. Nat Biotechnol 2024:10.1038/s41587-023-02095-x. [PMID: 38200119 DOI: 10.1038/s41587-023-02095-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
Genome editing with prime editors based on CRISPR-Cas9 is limited by the large size of the system and the requirement for a G/C-rich protospacer-adjacent motif (PAM) sequence. Here, we use the smaller Cas12a protein to develop four circular RNA-mediated prime editor (CPE) systems: nickase-dependent CPE (niCPE), nuclease-dependent CPE (nuCPE), split nickase-dependent CPE (sniCPE) and split nuclease-dependent CPE (snuCPE). CPE systems preferentially recognize T-rich genomic regions and possess a potential multiplexing capacity in comparison to corresponding Cas9-based systems. The efficiencies of the nuclease-based systems are up to 10.42%, whereas niCPE and sniCPE reach editing frequencies of up to 24.89% and 40.75% without positive selection in human cells, respectively. A derivative system, called one-sniCPE, combines all three RNA editing components under a single promoter. By arraying CRISPR RNAs for different targets in one circular RNA, we also demonstrate low-efficiency editing of up to four genes simultaneously with the nickase prime editors niCPE and sniCPE.
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Affiliation(s)
- Ronghong Liang
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zixin He
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Haocheng Zhu
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiacheng Hu
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Guanwen Liu
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | | | - Meiyan Liu
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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26
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Badon IW, Oh Y, Kim HJ, Lee SH. Recent application of CRISPR-Cas12 and OMEGA system for genome editing. Mol Ther 2024; 32:32-43. [PMID: 37952084 PMCID: PMC10787141 DOI: 10.1016/j.ymthe.2023.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
In 2012, it was discovered that precise gene editing could be induced in target DNA using the reprogrammable characteristics of the CRISPR system. Since then, several studies have investigated the potential of the CRISPR system to edit various biological organisms. For the typical CRISPR system obtained from bacteria and archaea, many application studies have been conducted and have spread to various fields. To date, orthologs with various characteristics other than CRISPR-Cas9 have been discovered and are being intensively studied in the field of gene editing. CRISPR-Cas12 and its varied orthologs are representative examples of genome editing tools and have superior properties in terms of in vivo target gene editing compared with Cas9. Recently, TnpB and Fanzor of the OMEGA (obligate mobile element guided activity) system were identified to be the ancestor of CRISPR-Cas12 on the basis of phylogenetic analysis. Notably, the compact sizes of Cas12 and OMEGA endonucleases allow adeno-associated virus (AAV) delivery; hence, they are set to challenge Cas9 for in vivo gene therapy. This review is focused on these RNA-guided reprogrammable endonucleases: their structure, biochemistry, off-target effects, and applications in therapeutic gene editing.
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Affiliation(s)
- Isabel Wen Badon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ho-Joong Kim
- Department of Chemistry, Chosun University, Gwangju 61452, Republic of Korea.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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27
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Bryson JW, Rosser SJ. Multiplexed Transactivation of Mammalian Cells Using dFnCas12a-VPR. Methods Mol Biol 2024; 2774:193-204. [PMID: 38441766 DOI: 10.1007/978-1-0716-3718-0_13] [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] [Indexed: 03/07/2024]
Abstract
CRISPR activation provides an invaluable tool for experimental biologists to convert correlations into causation by directly observing phenotypic changes upon targeted changes in gene expression. With few exceptions, most diseases are caused by complex polygenic interactions, with multiple genes contributing to define the output of a gene network. As such researchers are increasingly interested in tools that can offer not only control but also the capacity to simultaneously upregulate multiple genes. The adaptation of CRISPR/Cas12a has provided a system especially suited to the tightly coordinated overexpression of multiple targeted genes. Here we describe an approach to test for active targeting crRNAs for dFnCas12a-VPR, before proceeding to generate and validate longer crRNA arrays for multiplexed targeting of genes of interest.
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Affiliation(s)
- James W Bryson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susan J Rosser
- Department of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK.
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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28
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Yu L, Marchisio MA. dCas12a:Pre-crRNA: A New Tool to Induce mRNA Degradation in Saccharomyces cerevisiae Synthetic Gene Circuits. Methods Mol Biol 2024; 2760:95-114. [PMID: 38468084 DOI: 10.1007/978-1-0716-3658-9_6] [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] [Indexed: 03/13/2024]
Abstract
We describe a new way to trigger mRNA degradation in Saccharomyces cerevisiae synthetic gene circuits. Our method demands to modify either the 5'- or the 3'-UTR that flanks a target gene with elements from the pre-crRNA of type V Cas12a proteins and expresses a DNase-deficient Cas12a (dCas12a). dCas12a recognizes and cleaves the pre-crRNA motifs on mRNA sequences. Our tool does not require complex engineering operations and permits an efficient control of protein expression via mRNA degradation.
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Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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29
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Koonin EV, Gootenberg JS, Abudayyeh OO. Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox. Biochemistry 2023; 62:3465-3487. [PMID: 37192099 PMCID: PMC10734277 DOI: 10.1021/acs.biochem.3c00159] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Indexed: 05/18/2023]
Abstract
CRISPR systems mediate adaptive immunity in bacteria and archaea through diverse effector mechanisms and have been repurposed for versatile applications in therapeutics and diagnostics thanks to their facile reprogramming with RNA guides. RNA-guided CRISPR-Cas targeting and interference are mediated by effectors that are either components of multisubunit complexes in class 1 systems or multidomain single-effector proteins in class 2. The compact class 2 CRISPR systems have been broadly adopted for multiple applications, especially genome editing, leading to a transformation of the molecular biology and biotechnology toolkit. The diversity of class 2 effector enzymes, initially limited to the Cas9 nuclease, was substantially expanded via computational genome and metagenome mining to include numerous variants of Cas12 and Cas13, providing substrates for the development of versatile, orthogonal molecular tools. Characterization of these diverse CRISPR effectors uncovered many new features, including distinct protospacer adjacent motifs (PAMs) that expand the targeting space, improved editing specificity, RNA rather than DNA targeting, smaller crRNAs, staggered and blunt end cuts, miniature enzymes, promiscuous RNA and DNA cleavage, etc. These unique properties enabled multiple applications, such as harnessing the promiscuous RNase activity of the type VI effector, Cas13, for supersensitive nucleic acid detection. class 1 CRISPR systems have been adopted for genome editing, as well, despite the challenge of expressing and delivering the multiprotein class 1 effectors. The rich diversity of CRISPR enzymes led to rapid maturation of the genome editing toolbox, with capabilities such as gene knockout, base editing, prime editing, gene insertion, DNA imaging, epigenetic modulation, transcriptional modulation, and RNA editing. Combined with rational design and engineering of the effector proteins and associated RNAs, the natural diversity of CRISPR and related bacterial RNA-guided systems provides a vast resource for expanding the repertoire of tools for molecular biology and biotechnology.
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Affiliation(s)
- Eugene V. Koonin
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Jonathan S. Gootenberg
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Omar O. Abudayyeh
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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30
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Guo X, Geng L, Jiang C, Yao W, Jin J, Liu Z, Mu Y. Multiplexed genome engineering for porcine fetal fibroblasts with gRNA-tRNA arrays based on CRISPR/Cas9. Anim Biotechnol 2023; 34:4703-4712. [PMID: 36946758 DOI: 10.1080/10495398.2023.2187402] [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] [Indexed: 03/23/2023]
Abstract
Multiplex gene modifications are highly required for various fields of porcine research. In many species, the CRISPR/Cas9 system has been widely applied for genomic editing and provides a potential tool for introducing multiplex genome mutations simultaneously. Here, we present a CRISPR-Cas9 gRNA-tRNA array (GTR-CRISPR) for multiplexed engineering of porcine fetal fibroblasts (PFFs). We successfully produced multiple sgRNAs using only one Pol III promoter by taking advantage of the endogenous tRNA processing mechanism in porcine cells. Using an all-in-one construct carrying GTR and Cas9, we disrupted the IGFBP3, MSTN, MC4R, and SOCS2 genes in multiple codon regions in one PFF cell simultaneously. This technique allows the simultaneous disruption of four genes with 5.5% efficiency. As a result, this approach may effectively target multiple genes at the same time, making it a powerful tool for establishing multiple genes mutant cells in pigs.
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Affiliation(s)
- Xiaochen Guo
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Lishuang Geng
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Chaoqian Jiang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Wang Yao
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Junxue Jin
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
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31
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Bigini F, Lee SH, Sun YJ, Sun Y, Mahajan VB. Unleashing the potential of CRISPR multiplexing: Harnessing Cas12 and Cas13 for precise gene modulation in eye diseases. Vision Res 2023; 213:108317. [PMID: 37722240 PMCID: PMC10685911 DOI: 10.1016/j.visres.2023.108317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
Gene therapy is a flourishing field with the potential to revolutionize the treatment of genetic diseases. The emergence of CRISPR-Cas9 has significantly advanced targeted and efficient genome editing. Although CRISPR-Cas9 has demonstrated promising potential applications in various genetic disorders, it faces limitations in simultaneously targeting multiple genes. Novel CRISPR systems, such as Cas12 and Cas13, have been developed to overcome these challenges, enabling multiplexing and providing unique advantages. Cas13, in particular, targets mRNA instead of genomic DNA, permitting precise gene expression control and mitigating off-target effects. This review investigates the potential of Cas12 and Cas13 in ocular gene therapy applications, such as suppression of inflammation and cell death. In addition, the capabilities of Cas12 and Cas13 are explored in addressing potential targets related with disease mechanisms such as aberrant isoforms, mitochondrial genes, cis-regulatory sequences, modifier genes, and long non-coding RNAs. Anatomical accessibility and relative immune privilege of the eye provide an ideal organ system for evaluating these novel techniques' efficacy and safety. By targeting multiple genes concurrently, CRISPR-Cas12 and Cas13 systems hold promise for treating a range of ocular disorders, including glaucoma, retinal dystrophies, and age-related macular degeneration. Nonetheless, additional refinement is required to ascertain the safety and efficacy of these approaches in ocular disease treatments. Thus, the development of Cas12 and Cas13 systems marks a significant advancement in gene therapy, offering the potential to devise effective treatments for ocular disorders.
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Affiliation(s)
- Fabio Bigini
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA 94304, USA; Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Soo Hyeon Lee
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA 94304, USA
| | - Young Joo Sun
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA 94304, USA
| | - Yang Sun
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA; Stanford Maternal & Child Health Research Institute, Palo Alto, CA 94304, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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Mahata B, Cabrera A, Brenner DA, Guerra-Resendez RS, Li J, Goell J, Wang K, Guo Y, Escobar M, Parthasarathy AK, Szadowski H, Bedford G, Reed DR, Kim S, Hilton IB. Compact engineered human mechanosensitive transactivation modules enable potent and versatile synthetic transcriptional control. Nat Methods 2023; 20:1716-1728. [PMID: 37813990 PMCID: PMC10630135 DOI: 10.1038/s41592-023-02036-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023]
Abstract
Engineered transactivation domains (TADs) combined with programmable DNA binding platforms have revolutionized synthetic transcriptional control. Despite recent progress in programmable CRISPR-Cas-based transactivation (CRISPRa) technologies, the TADs used in these systems often contain poorly tolerated elements and/or are prohibitively large for many applications. Here, we defined and optimized minimal TADs built from human mechanosensitive transcription factors. We used these components to construct potent and compact multipartite transactivation modules (MSN, NMS and eN3x9) and to build the CRISPR-dCas9 recruited enhanced activation module (CRISPR-DREAM) platform. We found that CRISPR-DREAM was specific and robust across mammalian cell types, and efficiently stimulated transcription from diverse regulatory loci. We also showed that MSN and NMS were portable across Type I, II and V CRISPR systems, transcription activator-like effectors and zinc finger proteins. Further, as proofs of concept, we used dCas9-NMS to efficiently reprogram human fibroblasts into induced pluripotent stem cells and demonstrated that mechanosensitive transcription factor TADs are efficacious and well tolerated in therapeutically important primary human cell types. Finally, we leveraged the compact and potent features of these engineered TADs to build dual and all-in-one CRISPRa AAV systems. Altogether, these compact human TADs, fusion modules and delivery architectures should be valuable for synthetic transcriptional control in biomedical applications.
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Affiliation(s)
- Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Alan Cabrera
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Jing Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jacob Goell
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kaiyuan Wang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Yannie Guo
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mario Escobar
- Department of BioSciences, Rice University, Houston, TX, USA
| | | | - Hailey Szadowski
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Guy Bedford
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Daniel R Reed
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Sunghwan Kim
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA.
- Department of BioSciences, Rice University, Houston, TX, USA.
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33
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Griffith AL, Zheng F, McGee AV, Miller NW, Szegletes ZM, Reint G, Gademann F, Nwolah I, Hegde M, Liu YV, Goodale A, Doench JG. Optimization of Cas12a for multiplexed genome-scale transcriptional activation. CELL GENOMICS 2023; 3:100387. [PMID: 37719144 PMCID: PMC10504673 DOI: 10.1016/j.xgen.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 09/19/2023]
Abstract
Cas12a CRISPR technology, unlike Cas9, allows for facile multiplexing of guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here, we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition, and we compare these results with those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.
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Affiliation(s)
- Audrey L. Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Fengyi Zheng
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Abby V. McGee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Nathan W. Miller
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Zsofia M. Szegletes
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Ganna Reint
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Fabian Gademann
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Ifunanya Nwolah
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Yanjing V. Liu
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
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34
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Wang M, Chen M, Wu X, Huang X, Yu B. CRISPR applications in cancer diagnosis and treatment. Cell Mol Biol Lett 2023; 28:73. [PMID: 37674114 PMCID: PMC10481571 DOI: 10.1186/s11658-023-00483-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/17/2023] [Indexed: 09/08/2023] Open
Abstract
Cancer remains a significant global health challenge, necessitating the exploration of novel and more precise therapeutic options beyond conventional treatments. In this regard, clustered regularly interspaced short palindromic repeats (CRISPR) systems have emerged as highly promising tools for clinical gene editing applications. The CRISPR family encompasses diverse CRISPR-associated (Cas) proteins that possess the ability to recognize specific target sequences. The initial CRISPR system consisted of the Cas9 protein and a single-guide RNA, which guide Cas9 to the desired target sequence, facilitating precise double-stranded cleavage. In addition to the traditional cis-cleavage activity, the more recently discovered Cas12 and Cas13 proteins exhibit trans-cleavage activity, which expands their potential applications in cancer diagnosis. In this review, we provide an overview of the functional characteristics of Cas9, Cas12, and Cas13. Furthermore, we highlight the latest advancements and applications of these CRISPR systems in cancer gene therapy and molecular diagnosis. We also emphasize the importance of understanding the strengths and limitations of each CRISPR system to maximize their clinical utility. By providing a comprehensive overview of the current state of CRISPR technology in cancer research, we aim to inspire further exploration and innovation in this rapidly evolving field.
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Affiliation(s)
- Mingxia Wang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Menghui Chen
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Xia Wu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Xinbo Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| | - Bo Yu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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35
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Anvar NE, Lin C, Ma X, Wilson LL, Steger R, Sangree AK, Colic M, Wang SH, Doench JG, Hart T. Efficient gene knockout and genetic interactions: the IN4MER CRISPR/Cas12a multiplex knockout platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522655. [PMID: 36712129 PMCID: PMC9881895 DOI: 10.1101/2023.01.03.522655] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genetic interactions mediate the emergence of phenotype from genotype, but initial technologies for combinatorial genetic perturbation in mammalian cells suffer from inefficiency and are challenging to scale. Recent focus on paralog synthetic lethality in cancer cells offers an opportunity to evaluate different approaches and improve on the state of the art. Here we report a meta-analysis of CRISPR genetic interactions screens, identifying a candidate set of background-independent paralog synthetic lethals, and find that the Cas12a platform provides superior sensitivity and assay replicability. We demonstrate that Cas12a can independently target up to four genes from a single guide array, and we build on this knowledge by constructing a genome-scale library that expresses arrays of four guides per clone, a platform we call 'in4mer'. Our genome-scale human library, with only 49k clones, is substantially smaller than a typical CRISPR/Cas9 monogenic library while also targeting more than four thousand paralog pairs, triples, and quads. Proof of concept screens in four cell lines demonstrate discrimination of core and context-dependent essential genes similar to that of state-of-the-art CRISPR/Cas9 libraries, as well as detection of synthetic lethal and masking/buffering genetic interactions between paralogs of various family sizes, a capability not offered by any extant library. Importantly, the in4mer platform offers a fivefold reduction in the number of clones required to assay genetic interactions, dramatically improving the cost and effort required for these studies.
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Affiliation(s)
- Nazanin Esmaeili Anvar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX, USA
| | - Chenchu Lin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingdi Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, Houston, TX, USA
| | - Lori L. Wilson
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Steger
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Annabel K. Sangree
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Medina Colic
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sidney H. Wang
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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36
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Zhan X, Tu Z, Song W, Nie B, Li S, Zhang J, Zhang F. Cas13a-based multiplex RNA targeting for potato virus Y. PLANTA 2023; 258:70. [PMID: 37620620 DOI: 10.1007/s00425-023-04216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
MAIN CONCLUSION The Cas13a-based multiplex RNA targeting system can be engineered to confer resistance to RNA viruses, whereas the number and expression levels of gRNAs have no significant effect on viral interference. The CRISPR-Cas systems provide adaptive immunity to bacterial and archaeal species against invading phages and foreign plasmids. The class 2 type VI CRISPR/Cas effector Cas13a has been harnessed to confer the protection against RNA viruses in diverse eukaryotic species. However, whether the number and expression levels of guide RNAs (gRNAs) have effects on the efficiency of RNA virus inhibition is unknown. Here, we repurpose CRISPR/Cas13a in combination with an endogenous tRNA-processing system (polycistronic tRNA-gRNA) to target four genes of potato virus Y (PVY) with varying expression levels. We expressed Cas13a and four different gRNAs in potato lines, and the transgenic plants expressing multiple gRNAs displayed similar suppression of PVY accumulation and reduced disease symptoms as those expressing a single gRNA. Moreover, PTG/Cas13a-transformed plants with different expression levels of multiple gRNAs displayed similar resistance to PVY strains. Collectively, this study suggests that the Cas13a-based multiplex RNA targeting system can be utilized to engineer resistance to RNA viruses in plants, whereas the number and expression levels of gRNAs have no significant effect on CRISPR/Cas13a-mediated viral interference in plants.
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Affiliation(s)
- Xiaohui Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei Hongshan Laboratory, Hubei University, Wuhan, 430062, China
| | - Zhen Tu
- Key Laboratory of Potato Biology and Biotechnology, Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenlei Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei Hongshan Laboratory, Hubei University, Wuhan, 430062, China
| | - Bihua Nie
- Key Laboratory of Potato Biology and Biotechnology, Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei Hongshan Laboratory, Hubei University, Wuhan, 430062, China
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei Hongshan Laboratory, Hubei University, Wuhan, 430062, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fengjuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei Hongshan Laboratory, Hubei University, Wuhan, 430062, China.
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37
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Lue NZ, Liau BB. Base editor screens for in situ mutational scanning at scale. Mol Cell 2023; 83:2167-2187. [PMID: 37390819 PMCID: PMC10330937 DOI: 10.1016/j.molcel.2023.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
A fundamental challenge in biology is understanding the molecular details of protein function. How mutations alter protein activity, regulation, and response to drugs is of critical importance to human health. Recent years have seen the emergence of pooled base editor screens for in situ mutational scanning: the interrogation of protein sequence-function relationships by directly perturbing endogenous proteins in live cells. These studies have revealed the effects of disease-associated mutations, discovered novel drug resistance mechanisms, and generated biochemical insights into protein function. Here, we discuss how this "base editor scanning" approach has been applied to diverse biological questions, compare it with alternative techniques, and describe the emerging challenges that must be addressed to maximize its utility. Given its broad applicability toward profiling mutations across the proteome, base editor scanning promises to revolutionize the investigation of proteins in their native contexts.
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Affiliation(s)
- Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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38
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Bendixen L, Jensen TI, Bak RO. CRISPR-Cas-mediated transcriptional modulation: The therapeutic promises of CRISPRa and CRISPRi. Mol Ther 2023; 31:1920-1937. [PMID: 36964659 PMCID: PMC10362391 DOI: 10.1016/j.ymthe.2023.03.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
The CRISPR-Cas system is commonly known for its ability to cleave DNA in a programmable manner, which has democratized gene editing and facilitated recent breakthroughs in gene therapy. However, newer iterations of the technology using nuclease-disabled Cas enzymes have spurred a variety of different types of genetic engineering platforms such as transcriptional modulation using the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) systems. This review introduces the creation of these programmable transcriptional modulators, various methods of delivery utilized for these systems, and recent technological developments. CRISPRa and CRISPRi have also been implemented in genetic screens for interrogating gene function and discovering genes involved in various biological pathways. We describe recent compelling examples of how these tools have become powerful means to unravel genetic networks and uncovering important information about devastating diseases. Finally, we provide an overview of preclinical studies in which transcriptional modulation has been used therapeutically, and we discuss potential future directions of these novel modalities.
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Affiliation(s)
- Louise Bendixen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Trine I Jensen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark.
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39
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Zhang X, Wang X, Lv J, Huang H, Wang J, Zhuo M, Tan Z, Huang G, Liu J, Liu Y, Li M, Lin Q, Li L, Ma S, Huang T, Lin Y, Zhao X, Rong Z. Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing. Genome Biol 2023; 24:145. [PMID: 37353840 PMCID: PMC10288759 DOI: 10.1186/s13059-023-02992-z] [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: 05/04/2022] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly free gRNAs without Cas nuclease binding, limits their editing efficiency and durability. RESULTS Here, we engineer circular free gRNAs (cgRNAs) to increase their stability, and thus availability for Cas12a and Cas13d processing and loading, to boost editing. cgRNAs increases the efficiency of Cas12a-based transcription activators and genomic DNA cleavage by approximately 2.1- to 40.2-fold for single gene editing and 1.7- to 2.1-fold for multiplexed gene editing than their linear counterparts, without compromising specificity, across multiple sites and cell lines. Similarly, the RNA interference efficiency of Cas13d is increased by around 1.8-fold. In in vivo mouse liver, cgRNAs are more potent in activating gene expression and cleaving genomic DNA. CONCLUSIONS CgRNAs enable more efficient programmable DNA and RNA editing for Cas12a and Cas13d with broad applicability for fundamental research and gene therapy.
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Affiliation(s)
- Xin Zhang
- Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, 523058, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Xinlong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Jiahong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Ma Zhuo
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Zhihong Tan
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Jiawei Liu
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Yuchen Liu
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Mengrao Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Qixiao Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, China
| | - Tao Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Xiaoyang Zhao
- Department of Development, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Zhili Rong
- Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, 523058, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
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40
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Ma S, Liao K, Li M, Wang X, Lv J, Zhang X, Huang H, Li L, Huang T, Guo X, Lin Y, Rong Z. Phase-separated DropCRISPRa platform for efficient gene activation in mammalian cells and mice. Nucleic Acids Res 2023; 51:5271-5284. [PMID: 37094074 PMCID: PMC10250237 DOI: 10.1093/nar/gkad301] [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: 06/27/2022] [Revised: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) plays a critical role in regulating gene transcription via the formation of transcriptional condensates. However, LLPS has not been reported to be engineered as a tool to activate endogenous gene expression in mammalian cells or in vivo. Here, we developed a droplet-forming CRISPR (clustered regularly interspaced short palindromic repeats) gene activation system (DropCRISPRa) to activate transcription with high efficiency via combining the CRISPR-SunTag system with FETIDR-AD fusion proteins, which contain an N-terminal intrinsically disordered region (IDR) of a FET protein (FUS or TAF15) and a transcription activation domain (AD, VP64/P65/VPR). In this system, the FETIDR-AD fusion protein formed phase separation condensates at the target sites, which could recruit endogenous BRD4 and RNA polymerase II with an S2 phosphorylated C-terminal domain (CTD) to enhance transcription elongation. IDR-FUS9Y>S and IDR-FUSG156E, two mutants with deficient and aberrant phase separation respectively, confirmed that appropriate phase separation was required for efficient gene activation. Further, the DropCRISPRa system was compatible with a broad set of CRISPR-associated (Cas) proteins and ADs, including dLbCas12a, dAsCas12a, dSpCas9 and the miniature dUnCas12f1, and VP64, P65 and VPR. Finally, the DropCRISPRa system could activate target genes in mice. Therefore, this study provides a robust tool to activate gene expression for foundational research and potential therapeutics.
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Affiliation(s)
- Shufeng Ma
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Kaitong Liao
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Mengrao Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xinlong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Affiliated Dongguan Hospital, Southern Medical University, (Dongguan People's Hospital), Dongguan 523058, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Tao Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xiaohua Guo
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
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41
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Yu Y, Gao Y, He L, Fang B, Ge W, Yang P, Ju Y, Xie X, Lei L. Biomaterial-based gene therapy. MedComm (Beijing) 2023; 4:e259. [PMID: 37284583 PMCID: PMC10239531 DOI: 10.1002/mco2.259] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 06/08/2023] Open
Abstract
Gene therapy, a medical approach that involves the correction or replacement of defective and abnormal genes, plays an essential role in the treatment of complex and refractory diseases, such as hereditary diseases, cancer, and rheumatic immune diseases. Nucleic acids alone do not easily enter the target cells due to their easy degradation in vivo and the structure of the target cell membranes. The introduction of genes into biological cells is often dependent on gene delivery vectors, such as adenoviral vectors, which are commonly used in gene therapy. However, traditional viral vectors have strong immunogenicity while also presenting a potential infection risk. Recently, biomaterials have attracted attention for use as efficient gene delivery vehicles, because they can avoid the drawbacks associated with viral vectors. Biomaterials can improve the biological stability of nucleic acids and the efficiency of intracellular gene delivery. This review is focused on biomaterial-based delivery systems in gene therapy and disease treatment. Herein, we review the recent developments and modalities of gene therapy. Additionally, we discuss nucleic acid delivery strategies, with a focus on biomaterial-based gene delivery systems. Furthermore, the current applications of biomaterial-based gene therapy are summarized.
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Affiliation(s)
- Yi Yu
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Yijun Gao
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Liming He
- Department of StomatologyChangsha Stomatological HospitalChangshaChina
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Wenhui Ge
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Pu Yang
- Department of Plastic and Aesthetic (Burn) SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Yikun Ju
- Department of Plastic and Aesthetic (Burn) SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Xiaoyan Xie
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Lanjie Lei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
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42
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Li J, Liang Q, Zhou H, Zhou M, Huang H. Profiling the impact of the promoters on CRISPR-Cas12a system in human cells. Cell Mol Biol Lett 2023; 28:41. [PMID: 37198545 PMCID: PMC10190037 DOI: 10.1186/s11658-023-00454-9] [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: 01/28/2023] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
The plasmid vector platform is the most commonly used vector for the expression of the versatile CRISPR-Cas technique and the promoter is a crucial element for the expression vector, thus profiling the impact of the promoters on CRISPR editors provides the basic information for the gene-editing toolkits and can be a guideline for its design. Herein, we made a parallel comparison among four commonly used promoters (CAG, ~ 1700 bp; EF1a core, ~ 210 bp; CMV, ~ 500 bp; and PGK, ~ 500 bp) in CRISPR-Cas12a system in mammalian cells to explore the impact of promoters on this powerful tool. We found that without badly damaging targeting specificity, the CAG promoter-driving Cas12a editor exhibited the most active (efficiency takes as 100%, specificity index = ~ 75%) in genomic cleavage, multiplex editing, transcriptional activation, and base editing, followed by promoter CMV (efficiency = 70 ~ 90% (vs CAG), specificity index = ~ 78%), and then EF1a core and PGK (both efficiency = 40-60%, vs CAG) but with higher specificity (specificity index = ~ 84% and ~ 82%, respectively). Therefore, CAG is recommended in the CRISPR-Cas12a system for the applications that need a robust editing activity but without size limitation, CMV mostly can be an alternative for CAG when requiring a smaller space, EF1a is similar to PGK with relatively high specificity, but has a smaller size, thus is more suitable for in vivo therapeutic applications. The data outlined the properties of the widely used promoters in the CRISPR-Cas12a system, which can be a guide for its applications and can be a useful resource for the gene-editing field.
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Affiliation(s)
- Jinhe Li
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630 China
| | - Qinchun Liang
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630 China
- Guangzhou Key Laboratory of Neuropathic Pain Mechanism at Spinal Cord Level, Guangzhou, 510630 China
| | - HuaPing Zhou
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095 China
| | - Ming Zhou
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095 China
| | - Hongxin Huang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095 China
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43
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Jiang C, Geng L, Wang J, Liang Y, Guo X, Liu C, Zhao Y, Jin J, Liu Z, Mu Y. Multiplexed Gene Engineering Based on dCas9 and gRNA-tRNA Array Encoded on Single Transcript. Int J Mol Sci 2023; 24:ijms24108535. [PMID: 37239880 DOI: 10.3390/ijms24108535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Simultaneously, multiplexed genome engineering and targeting multiple genomic loci are valuable to elucidating gene interactions and characterizing genetic networks that affect phenotypes. Here, we developed a general CRISPR-based platform to perform four functions and target multiple genome loci encoded in a single transcript. To establish multiple functions for multiple loci targets, we fused four RNA hairpins, MS2, PP7, com and boxB, to stem-loops of gRNA (guide RNA) scaffolds, separately. The RNA-hairpin-binding domains MCP, PCP, Com and λN22 were fused with different functional effectors. These paired combinations of cognate-RNA hairpins and RNA-binding proteins generated the simultaneous, independent regulation of multiple target genes. To ensure that all proteins and RNAs are expressed in one transcript, multiple gRNAs were constructed in a tandemly arrayed tRNA (transfer RNA)-gRNA architecture, and the triplex sequence was cloned between the protein-coding sequences and the tRNA-gRNA array. By leveraging this system, we illustrate the transcriptional activation, transcriptional repression, DNA methylation and DNA demethylation of endogenous targets using up to 16 individual CRISPR gRNAs delivered on a single transcript. This system provides a powerful platform to investigate synthetic biology questions and engineer complex-phenotype medical applications.
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Affiliation(s)
- Chaoqian Jiang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Lishuang Geng
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jinpeng Wang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yingjuan Liang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Xiaochen Guo
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Chang Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yunjing Zhao
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Junxue Jin
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
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Kang H, Fitch JC, Varghese RP, Thorne CA, Cusanovich DA. SGRN: A Cas12a-driven Synthetic Gene Regulatory Network System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539911. [PMID: 37214915 PMCID: PMC10197538 DOI: 10.1101/2023.05.08.539911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Gene regulatory networks, which control gene expression patterns in development and in response to stimuli, use regulatory logic modules to coordinate inputs and outputs. One example of a regulatory logic module is the gene regulatory cascade (GRC), where a series of transcription factor genes turn on in order. Synthetic biologists have derived artificial systems that encode regulatory rules, including GRCs. Furthermore, the development of single-cell approaches has enabled the discovery of gene regulatory modules in a variety of experimental settings. However, the tools available for validating these observations remain limited. Based on a synthetic GRC using DNA cutting-defective Cas9 (dCas9), we designed and implemented an alternative synthetic GRC utilizing DNA cutting-defective Cas12a (dCas12a). Comparing the ability of these two systems to express a fluorescent reporter, the dCas9 system was initially more active, while the dCas12a system was more streamlined. Investigating the influence of individual components of the systems identified nuclear localization as a major driver of differences in activity. Improving nuclear localization for the dCas12a system resulted in 1.5-fold more reporter-positive cells and a 15-fold increase in reporter intensity relative to the dCas9 system. We call this optimized system the "Synthetic Gene Regulatory Network" (SGRN, pronounced "sojourn").
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Affiliation(s)
- HyunJin Kang
- Asthma and Airway Disease Research Center (ADRC), University of Arizona, Tucson, AZ
| | - John C Fitch
- Flow Cytometry Shared Resource, University of Arizona, Tucson, AZ
| | - Reeba P Varghese
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ
| | - Curtis A Thorne
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ
| | - Darren A Cusanovich
- Asthma and Airway Disease Research Center (ADRC), University of Arizona, Tucson, AZ
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ
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45
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Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
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Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
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46
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Cetin R, Wegner M, Luwisch L, Saud S, Achmedov T, Süsser S, Vera-Guapi A, Müller K, Matthess Y, Quandt E, Schaubeck S, Beisel CL, Kaulich M. Optimized metrics for orthogonal combinatorial CRISPR screens. Sci Rep 2023; 13:7405. [PMID: 37149686 PMCID: PMC10164157 DOI: 10.1038/s41598-023-34597-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/04/2023] [Indexed: 05/08/2023] Open
Abstract
CRISPR-based gene perturbation enables unbiased investigations of single and combinatorial genotype-to-phenotype associations. In light of efforts to map combinatorial gene dependencies at scale, choosing an efficient and robust CRISPR-associated (Cas) nuclease is of utmost importance. Even though SpCas9 and AsCas12a are widely used for single, combinatorial, and orthogonal screenings, side-by-side comparisons remain sparse. Here, we systematically compared combinatorial SpCas9, AsCas12a, and CHyMErA in hTERT-immortalized retinal pigment epithelial cells and extracted performance-critical parameters for combinatorial and orthogonal CRISPR screens. Our analyses identified SpCas9 to be superior to enhanced and optimized AsCas12a, with CHyMErA being largely inactive in the tested conditions. Since AsCas12a contains RNA processing activity, we used arrayed dual-gRNAs to improve AsCas12a and CHyMErA applications. While this negatively influenced the effect size range of combinatorial AsCas12a applications, it enhanced the performance of CHyMErA. This improved performance, however, was limited to AsCas12a dual-gRNAs, as SpCas9 gRNAs remained largely inactive. To avoid the use of hybrid gRNAs for orthogonal applications, we engineered the multiplex SpCas9-enAsCas12a approach (multiSPAS) that avoids RNA processing for efficient orthogonal gene editing.
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Affiliation(s)
- Ronay Cetin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Leah Luwisch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sarada Saud
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Tatjana Achmedov
- Helmholtz-Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), 97080, Würzburg, Germany
| | - Sebastian Süsser
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Antonella Vera-Guapi
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Konstantin Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Yves Matthess
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Eva Quandt
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195, Barcelona, Spain
| | - Simone Schaubeck
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Chase L Beisel
- Helmholtz-Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- Frankfurt Cancer Institute, 60596, Frankfurt am Main, Germany.
- Cardio-Pulmonary Institute, 60590, Frankfurt am Main, Germany.
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47
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Kalkan AK, Palaz F, Sofija S, Elmousa N, Ledezma Y, Cachat E, Rios-Solis L. Improving recombinant protein production in CHO cells using the CRISPR-Cas system. Biotechnol Adv 2023; 64:108115. [PMID: 36758652 DOI: 10.1016/j.biotechadv.2023.108115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
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Affiliation(s)
- Ali Kerem Kalkan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Environmental Engineering Department, Gebze Technical University, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Semeniuk Sofija
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nada Elmousa
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Yuri Ledezma
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; Biology Department, Faculty of Pure and Natural Sciences, Universidad Mayor de San Andrés, Bolivia
| | - Elise Cachat
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK; UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Leonardo Rios-Solis
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
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48
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Kawasaki S, Ono H, Hirosawa M, Kuwabara T, Sumi S, Lee S, Woltjen K, Saito H. Programmable mammalian translational modulators by CRISPR-associated proteins. Nat Commun 2023; 14:2243. [PMID: 37076490 PMCID: PMC10115826 DOI: 10.1038/s41467-023-37540-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Translational modulation based on RNA-binding proteins can be used to construct artificial gene circuits, but RNA-binding proteins capable of regulating translation efficiently and orthogonally remain scarce. Here we report CARTRIDGE (Cas-Responsive Translational Regulation Integratable into Diverse Gene control) to repurpose Cas proteins as translational modulators in mammalian cells. We demonstrate that a set of Cas proteins efficiently and orthogonally repress or activate the translation of designed mRNAs that contain a Cas-binding RNA motif in the 5'-UTR. By linking multiple Cas-mediated translational modulators, we designed and built artificial circuits like logic gates, cascades, and half-subtractor circuits. Moreover, we show that various CRISPR-related technologies like anti-CRISPR and split-Cas9 platforms could be similarly repurposed to control translation. Coupling Cas-mediated translational and transcriptional regulation enhanced the complexity of synthetic circuits built by only introducing a few additional elements. Collectively, CARTRIDGE has enormous potential as a versatile molecular toolkit for mammalian synthetic biology.
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Affiliation(s)
- Shunsuke Kawasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Moe Hirosawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takeru Kuwabara
- Faculty of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shunsuke Sumi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Suji Lee
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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49
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Terron HM, Maranan DS, Burgard LA, LaFerla FM, Lane S, Leissring MA. A Dual-Function "TRE-Lox" System for Genetic Deletion or Reversible, Titratable, and Near-Complete Downregulation of Cathepsin D. Int J Mol Sci 2023; 24:ijms24076745. [PMID: 37047718 PMCID: PMC10095275 DOI: 10.3390/ijms24076745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
Commonly employed methods for reversibly disrupting gene expression, such as those based on RNAi or CRISPRi, are rarely capable of achieving >80-90% downregulation, making them unsuitable for targeting genes that require more complete disruption to elicit a phenotype. Genetic deletion, on the other hand, while enabling complete disruption of target genes, often produces undesirable irreversible consequences such as cytotoxicity or cell death. Here we describe the design, development, and detailed characterization of a dual-function "TRE-Lox" system for effecting either (a) doxycycline (Dox)-mediated downregulation or (b) genetic deletion of a target gene-the lysosomal aspartyl protease cathepsin D (CatD)-based on targeted insertion of a tetracycline-response element (TRE) and two LoxP sites into the 5' end of the endogenous CatD gene (CTSD). Using an optimized reverse-tetracycline transrepressor (rtTR) variant fused with the Krüppel-associated box (KRAB) domain, we show that CatD expression can be disrupted by as much as 98% in mouse embryonic fibroblasts (MEFs). This system is highly sensitive to Dox (IC50 = 1.46 ng/mL) and results in rapid (t1/2 = 0.57 d) and titratable downregulation of CatD. Notably, even near-total disruption of CatD expression was completely reversed by withdrawal of Dox. As expected, transient expression of Cre recombinase results in complete deletion of the CTSD gene. The dual functionality of this novel system will facilitate future studies of the involvement of CatD in various diseases, particularly those attributable to partial loss of CatD function. In addition, the TRE-Lox approach should be applicable to the regulation of other target genes requiring more complete disruption than can be achieved by traditional methods.
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Affiliation(s)
- Heather M Terron
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Derek S Maranan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Luke A Burgard
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Frank M LaFerla
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Shelley Lane
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Malcolm A Leissring
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
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50
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Dong MB, Tang K, Zhou X, Shen J, Chen K, Kim HR, Zhou J, Cao H, Vandenbulcke E, Zhang Y, Chow RD, Du A, Suzuki K, Fang SY, Majety M, Dai X, Chen S. Cas12a/Cpf1 knock-in mice enable efficient multiplexed immune cell engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532657. [PMID: 36993642 PMCID: PMC10055166 DOI: 10.1101/2023.03.14.532657] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cas9 transgenic animals have drastically accelerated the discovery of novel immune modulators. But due to its inability to process its own CRISPR RNAs (crRNAs), simultaneous multiplexed gene perturbations using Cas9 remains limited, especially by pseudoviral vectors. Cas12a/Cpf1, however, can process concatenated crRNA arrays for this purpose. Here, we created conditional and constitutive LbCas12a knock-in transgenic mice. With these mice, we demonstrated efficient multiplexed gene editing and surface protein knockdown within individual primary immune cells. We showed genome editing across multiple types of primary immune cells including CD4 and CD8 T cells, B cells, and bone-marrow derived dendritic cells. These transgenic animals, along with the accompanying viral vectors, together provide a versatile toolkit for a broad range of ex vivo and in vivo gene editing applications, including fundamental immunological discovery and immune gene engineering.
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