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Fan X, Lei Y, Wang L, Wu X, Li D. Advancing CRISPR base editing technology through innovative strategies and ideas. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2699-5. [PMID: 39231901 DOI: 10.1007/s11427-024-2699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/06/2024] [Accepted: 08/13/2024] [Indexed: 09/06/2024]
Abstract
The innovation of CRISPR/Cas gene editing technology has developed rapidly in recent years. It is widely used in the fields of disease animal model construction, biological breeding, disease diagnosis and screening, gene therapy, cell localization, cell lineage tracking, synthetic biology, information storage, etc. However, developing idealized editors in various fields is still a goal for future development. This article focuses on the development and innovation of non-DSB editors BE and PE in the platform-based CRISPR system. It first explains the application of ideas for improvement such as "substitution", "combination", "adaptation", and "adjustment" in BE and PE development and then catalogues the ingenious inversions and leaps of thought reflected in the innovations made to CRISPR technology. It will then elaborate on the efforts currently being made to develop small editors to solve the problem of AAV overload and summarize the current application status of editors for in vivo gene modification using AAV as a delivery system. Finally, it summarizes the inspiration brought by CRISPR/Cas innovation and assesses future prospects for development of an idealized editor.
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Affiliation(s)
- Xiongwei Fan
- The Center for Heart Development, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yang Lei
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Xiushan Wu
- The Center for Heart Development, College of Life Science, Hunan Normal University, Changsha, 410081, China.
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou, 510100, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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2
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Wang J, Kan S, Liao X, Zhou J, Tembrock LR, Daniell H, Jin S, Wu Z. Plant organellar genomes: much done, much more to do. TRENDS IN PLANT SCIENCE 2024; 29:754-769. [PMID: 38220520 DOI: 10.1016/j.tplants.2023.12.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6000-6999, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Marine College, Shandong University, Weihai, 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiawei Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104-6030, USA.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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3
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Karpov DS. CRISPR-Cas Systems and Genome Editing: Beginning the Era of CRISPR/Cas Therapies for Humans. Int J Mol Sci 2024; 25:5292. [PMID: 38791336 PMCID: PMC11121477 DOI: 10.3390/ijms25105292] [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: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Harnessing of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated genes) systems for detection, chemical modification, and sequence editing of nucleic acids dramatically changed many fields of fundamental science, biotechnology, and biomedicine [...].
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Affiliation(s)
- Dmitry S Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia
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4
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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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5
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Jung WJ, Park SJ, Cha S, Kim K. Factors affecting the cleavage efficiency of the CRISPR-Cas9 system. Anim Cells Syst (Seoul) 2024; 28:75-83. [PMID: 38440123 PMCID: PMC10911232 DOI: 10.1080/19768354.2024.2322054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
The CRISPR-Cas system stands out as a promising genome editing tool due to its cost-effectiveness and time efficiency compared to other methods. This system has tremendous potential for treating various diseases, including genetic disorders and cancer, and promotes therapeutic research for a wide range of genetic diseases. Additionally, the CRISPR-Cas system simplifies the generation of animal models, offering a more accessible alternative to traditional methods. The CRISPR-Cas9 system can be used to cleave target DNA strands that need to be corrected, causing double-strand breaks (DSBs). DNA with DSBs can then be recovered by the DNA repair pathway that the CRISPR-Cas9 system uses to edit target gene sequences. High cleavage efficiency of the CRISPR-Cas9 system is thus imperative for effective gene editing. Herein, we explore several factors affecting the cleavage efficiency of the CRISPR-Cas9 system. These factors include the GC content of the protospacer-adjacent motif (PAM) proximal and distal regions, single-guide RNA (sgRNA) properties, and chromatin state. These considerations contribute to the efficiency of genome editing.
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Affiliation(s)
- Won Jun Jung
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo-Ji Park
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seongkwang Cha
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Neuroscience Research Institute, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
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6
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Zhang F, Liu ZY, Liu S, Zhang WG, Wang BB, Li CL, Xu JZ. Rapid screening of point mutations by mismatch amplification mutation assay PCR. Appl Microbiol Biotechnol 2024; 108:190. [PMID: 38305911 PMCID: PMC10837254 DOI: 10.1007/s00253-024-13036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/18/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Metabolic engineering frequently makes use of point mutation and saturation mutation library creation. At present, sequencing is the only reliable and direct technique to detect point mutation and screen saturation mutation library. In this study, mismatch amplification mutation assay (MAMA) PCR was used to detect point mutation and screen saturation mutation library. In order to fine-tune the expression of odhA encoding 2-oxoglutarate dehydrogenase E1 component, a saturating mutant library of the RBS of odhA was created in Corynebacterium glutamicum P12 based on the CRISPR-Cas2a genome editing system, which increased the L-proline production by 81.3%. MAMA PCR was used to filter out 42% of the non-mutant transformants in the mutant library, which effectively reduced the workload of the subsequent fermentation test and the number of sequenced samples. The rapid and sensitive MAMA-PCR method established in this study provides a general strategy for detecting point mutations and improving the efficiency of mutation library screening. KEY POINTS: • MAMA PCR was optimized and developed to detect point mutation. • MAMA PCR greatly improves the screening efficiency of point mutation. • Attenuation of odhA expression in P12 effectively improves proline production.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Zhen Yang Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Wei Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.
| | - Bing Bing Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Chang Lon Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Jian Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
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7
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Vu TV, Nguyen NT, Kim J, Hong JC, Kim J. Prime editing: Mechanism insight and recent applications in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:19-36. [PMID: 37794706 PMCID: PMC10754014 DOI: 10.1111/pbi.14188] [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: 07/21/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Prime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3' flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step-by-step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.
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Affiliation(s)
- Tien V. Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Ngan Thi Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
- Nulla Bio Inc.JinjuKorea
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8
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Liu Y, Liu W, Wang B. Engineering CRISPR guide RNAs for programmable RNA sensors. Biochem Soc Trans 2023; 51:2061-2070. [PMID: 37955062 PMCID: PMC10754282 DOI: 10.1042/bst20221486] [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: 03/20/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023]
Abstract
As the most valuable feature of the CRISPR system, the programmability based on Watson-Crick base pairing has been widely exploited in engineering RNA sensors. The base pairing in these systems offers a connection between the RNA of interest and the CRISPR effector, providing a highly specific mechanism for RNA detection both in vivo and in vitro. In the last decade, despite the many successful RNA sensing approaches developed during the era of CRISPR explosion, a deeper understanding of the characteristics of CRISPR systems and the continuous expansion of the CRISPR family members indicates that the CRISPR-based RNA sensor remains a promising area from which a variety of new functions and applications can be engineered. Here, we present a systematic overview of the various strategies of engineering CRISPR gRNA for programmable RNA detection with an aim to clarify the role of gRNA's programmability among the present limitations and future development of CRISPR-enabled RNA sensors.
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Affiliation(s)
- Yang Liu
- MRC Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Wei Liu
- MRC Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou 311100, China
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9
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Perroud PF, Guyon-Debast A, Casacuberta JM, Paul W, Pichon JP, Comeau D, Nogué F. Improved prime editing allows for routine predictable gene editing in Physcomitrium patens. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6176-6187. [PMID: 37243510 PMCID: PMC10575697 DOI: 10.1093/jxb/erad189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
Efficient and precise gene editing is the gold standard of any reverse genetic study. The recently developed prime editing approach, a modified CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein] editing method, has reached the precision goal but its editing rate can be improved. We present an improved methodology that allows for routine prime editing in the model plant Physcomitrium patens, whilst exploring potential new prime editing improvements. Using a standardized protoplast transfection procedure, multiple prime editing guide RNA (pegRNA) structural and prime editor variants were evaluated targeting the APT reporter gene through direct plant selection. Together, enhancements of expression of the prime editor, modifications of the 3' extension of the pegRNA, and the addition of synonymous mutation in the reverse transcriptase template sequence of the pegRNA dramatically improve the editing rate without affecting the quality of the edits. Furthermore, we show that prime editing is amenable to edit a gene of interest through indirect selection, as demonstrated by the generation of a Ppdek10 mutant. Additionally, we determine that a plant retrotransposon reverse transcriptase enables prime editing. Finally, we show for the first time the possibility of performing prime editing with two independently coded peptides.
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Affiliation(s)
- Pierre-François Perroud
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Anouchka Guyon-Debast
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, 08193 Barcelona, Spain
| | - Wyatt Paul
- Limagrain Europe, Centre de Recherche de Chappes, 63720 Chappes, France
| | | | - David Comeau
- Limagrain Europe, Centre de Recherche de Chappes, 63720 Chappes, France
| | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
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10
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Duarte F, Vachey G, Caron NS, Sipion M, Rey M, Perrier AL, Hayden MR, Déglon N. Limitations of Dual-Single Guide RNA CRISPR Strategies for the Treatment of Central Nervous System Genetic Disorders. Hum Gene Ther 2023; 34:958-974. [PMID: 37658843 DOI: 10.1089/hum.2023.109] [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: 09/05/2023] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a toxic gain-of-function CAG expansion in the first exon of the huntingtin (HTT) gene. The monogenic nature of HD makes mutant HTT (mHTT) inactivation a promising therapeutic strategy. Single nucleotide polymorphisms frequently associated with CAG expansion have been explored to selectively inactivate mHTT allele using the CRISPR/Cas9 system. One of such allele-selective approaches consists of excising a region flanking the first exon of mHTT by inducing simultaneous double-strand breaks at upstream and downstream positions of the mHTT exon 1. The removal of the first exon of mHTT deletes the CAG expansion and important transcription regulatory sites, leading to mHTT inactivation. However, the frequency of deletion events is yet to be quantified either in vitro or in vivo. Here, we developed accurate quantitative digital polymerase chain reaction-based assays to assess HTT exon 1 deletion in vitro and in fully humanized HU97/18 mice. Our results demonstrate that dual-single guide RNA (sgRNA) strategies are efficient and that 67% of HTT editing events are leading to exon 1 deletion in HEK293T cells. In contrast, these sgRNA actively cleaved HTT in HU97/18 mice, but most editing events do not lead to exon 1 deletion (10% exon 1 deletion). We also showed that the in vivo editing pattern is not affected by CAG expansion but may potentially be due to the presence of multiple copies of wildtype (wt)/mHTT genes HU97/18 mice as well as the slow kinetics of AAV-mediated CRISPR/Cas9 delivery.
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Affiliation(s)
- Fábio Duarte
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Gabriel Vachey
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Nicholas S Caron
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital and Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Sipion
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Maria Rey
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Anselme L Perrier
- Université Paris-Saclay, CEA, CNRS, Laboratoire des Maladies Neurodégénératives: mécanismes, thérapies, imagerie, Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA, Molecular Imaging Research Center, Fontenay-aux-Roses, France
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital and Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole Déglon
- Laboratory of Cellular and Molecular Neurotherapies, Department of Clinical Neurosciences (DNC)
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Neuroscience Research Center (CRN); Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
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11
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Bush K, Corsi GI, Yan AC, Haynes K, Layzer JM, Zhou JH, Llanga T, Gorodkin J, Sullenger BA. Utilizing directed evolution to interrogate and optimize CRISPR/Cas guide RNA scaffolds. Cell Chem Biol 2023; 30:879-892.e5. [PMID: 37390831 PMCID: PMC10529641 DOI: 10.1016/j.chembiol.2023.06.007] [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: 08/18/2022] [Revised: 03/09/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
CRISPR-based editing has revolutionized genome engineering despite the observation that many DNA sequences remain challenging to target. Unproductive interactions formed between the single guide RNA's (sgRNA) Cas9-binding scaffold domain and DNA-binding antisense domain are often responsible for such limited editing resolution. To bypass this limitation, we develop a functional SELEX (systematic evolution of ligands by exponential enrichment) approach, termed BLADE (binding and ligand activated directed evolution), to identify numerous, diverse sgRNA variants that bind Streptococcus pyogenes Cas9 and support DNA cleavage. These variants demonstrate surprising malleability in sgRNA sequence. We also observe that particular variants partner more effectively with specific DNA-binding antisense domains, yielding combinations with enhanced editing efficiencies at various target sites. Using molecular evolution, CRISPR-based systems could be created to efficiently edit even challenging DNA sequences making the genome more tractable to engineering. This selection approach will be valuable for generating sgRNAs with a range of useful activities.
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Affiliation(s)
- Korie Bush
- Department of Surgery, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA; Moderna Genomics, Cambridge, MA 02139, USA
| | - Giulia I Corsi
- Center for non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; Tessera Therapeutics, Somerville, MA 02143, USA
| | - Amy C Yan
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Keith Haynes
- Department of Information Technology, Midlands Technical College, Columbia, SC 29202, USA
| | | | - Jonathan H Zhou
- Department of Surgery, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Telmo Llanga
- Department of Surgery, Duke University, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Jan Gorodkin
- Center for non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Bruce A Sullenger
- Department of Surgery, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA.
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12
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Higashitani Y, Horie K. Long-read sequence analysis of MMEJ-mediated CRISPR genome editing reveals complex on-target vector insertions that may escape standard PCR-based quality control. Sci Rep 2023; 13:11652. [PMID: 37468545 DOI: 10.1038/s41598-023-38397-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
CRISPR genome editing is a powerful tool for elucidating biological functions. To modify the genome as intended, it is essential to understand the various modes of recombination that can occur. In this study, we report complex vector insertions that were identified during the generation of conditional alleles by CRISPR editing using microhomology-mediated end joining (MMEJ). The targeting vector contained two loxP sequences and flanking 40-bp microhomologies. The genomic regions corresponding to the loxP sequences were cleaved with Cas9 in mouse embryonic stem cells. PCR screening for targeted recombination revealed a high frequency of bands of a larger size than expected. Nanopore sequencing of these bands revealed complex vector insertions mediated not only by MMEJ but also by non-homologous end joining and homologous recombination in at least 17% of the clones. A new band appeared upon improving the PCR conditions, suggesting the presence of unintentionally modified alleles that escape standard PCR screening. This prompted us to characterize the recombination of each allele of the genome-edited clones using heterozygous single nucleotide polymorphisms, leading to confirmation of the presence of homozygous alleles. Our study indicates that careful quality control of genome-edited clones is needed to exclude complex, unintended, on-target vector insertion.
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Affiliation(s)
- Yuki Higashitani
- Department of Physiology II, Nara Medical University, Kashihara, Nara, 634-8521, Japan
| | - Kyoji Horie
- Department of Physiology II, Nara Medical University, Kashihara, Nara, 634-8521, Japan.
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13
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Xu D, Zhang J, Zhao X, Hou Y, Jiang H, He W, Ma X, Pan W. CIDP: a multi-functional platform for designing CRISPR sgRNAs. HORTICULTURE RESEARCH 2023; 10:uhad092. [PMID: 37416728 PMCID: PMC10321375 DOI: 10.1093/hr/uhad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/01/2023] [Indexed: 07/08/2023]
Affiliation(s)
| | | | | | - Yuze Hou
- College of Data Science, Taiyuan University of Technology, Taiyuan, Shanxi 030600, China
| | - Heling Jiang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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14
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Seo SY, Min S, Lee S, Seo JH, Park J, Kim HK, Song M, Baek D, Cho SR, Kim HH. Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s. Nat Methods 2023:10.1038/s41592-023-01875-2. [PMID: 37188955 DOI: 10.1038/s41592-023-01875-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023]
Abstract
Recently, various small Cas9 orthologs and variants have been reported for use in in vivo delivery applications. Although small Cas9s are particularly suited for this purpose, selecting the most optimal small Cas9 for use at a specific target sequence continues to be challenging. Here, to this end, we have systematically compared the activities of 17 small Cas9s for thousands of target sequences. For each small Cas9, we have characterized the protospacer adjacent motif and determined optimal single guide RNA expression formats and scaffold sequence. High-throughput comparative analyses revealed distinct high- and low-activity groups of small Cas9s. We also developed DeepSmallCas9, a set of computational models predicting the activities of the small Cas9s at matched and mismatched target sequences. Together, this analysis and these computational models provide a useful guide for researchers to select the most suitable small Cas9 for specific applications.
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Affiliation(s)
- Sang-Yeon Seo
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Sungtae Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Hwa Seo
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hui Kwon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Myungjae Song
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dawoon Baek
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Rehabilitation Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Sung-Rae Cho
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate Program of Biomedical Engineering, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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15
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Chenouard V, Leray I, Tesson L, Remy S, Allan A, Archer D, Caulder A, Fortun A, Bernardeau K, Cherifi Y, Teboul L, David L, Anegon I. Excess of guide RNA reduces knockin efficiency and drastically increases on-target large deletions. iScience 2023; 26:106399. [PMID: 37034986 PMCID: PMC10074149 DOI: 10.1016/j.isci.2023.106399] [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: 10/12/2022] [Revised: 01/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
CRISPR-Cas9 cleavage efficacy and accuracy are the main challenges gene editing faces, and they are particularly affected by the optimal formation of the ribonucleoprotein (RNP) complex. We used nano differential scanning fluorimetry, a label and immobilization-free assay, to demonstrate that an equimolar ratio of Cas9 and guide RNA (gRNA) is optimal for RNP complex formation. We almost achieved 50% of green fluorescent protein (GFP) to blue fluorescent protein (BFP) conversion using a biallelic homozygous GFP human induced pluripotent stem cell line, when 0.4 μM of Cas9, equimolar Cas9/gRNA ratio and 2 μM of single-stranded oligonucleotide, were used and showed that increasing Cas9/gRNA ratio did not further improve KI efficiency. Additionally, excess gRNA decreased point mutation KI efficiency in rat embryos and drastically increased the occurrence of on-target large deletions. These findings highlight the importance of CRISPR/Cas9 stoichiometric optimization to ensure efficient and accurate KI generation, which will be applicable to other in vitro as well as in vivo models.
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Affiliation(s)
- Vanessa Chenouard
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
- genOway, Lyon 69007, France
| | - Isabelle Leray
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
| | - Laurent Tesson
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
| | - Severine Remy
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
| | - Alasdair Allan
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Daniel Archer
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Adam Caulder
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Agnès Fortun
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, Plateforme P2R, SFR Bonamy, F-44000 Nantes, France
- Cibles et Médicaments des Infections et du Cancer, IICiMed, Nantes Université, UR 1155, F-44000 Nantes, France
| | - Karine Bernardeau
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, Plateforme P2R, SFR Bonamy, F-44000 Nantes, France
| | | | - Lydia Teboul
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Laurent David
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
| | - Ignacio Anegon
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
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16
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Cromer MK, Majeti KR, Rettig GR, Murugan K, Kurgan GL, Bode NM, Hampton JP, Vakulskas CA, Behlke MA, Porteus MH. Comparative analysis of CRISPR off-target discovery tools following ex vivo editing of CD34 + hematopoietic stem and progenitor cells. Mol Ther 2023; 31:1074-1087. [PMID: 36793210 PMCID: PMC10124080 DOI: 10.1016/j.ymthe.2023.02.011] [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: 09/13/2022] [Revised: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
While a number of methods exist to investigate CRISPR off-target (OT) editing, few have been compared head-to-head in primary cells after clinically relevant editing processes. Therefore, we compared in silico tools (COSMID, CCTop, and Cas-OFFinder) and empirical methods (CHANGE-Seq, CIRCLE-Seq, DISCOVER-Seq, GUIDE-Seq, and SITE-Seq) after ex vivo hematopoietic stem and progenitor cell (HSPC) editing. We performed editing using 11 different gRNAs complexed with Cas9 protein (high-fidelity [HiFi] or wild-type versions), then performed targeted next-generation sequencing of nominated OT sites identified by in silico and empirical methods. We identified an average of less than one OT site per guide RNA (gRNA) and all OT sites generated using HiFi Cas9 and a 20-nt gRNA were identified by all OT detection methods with the exception of SITE-seq. This resulted in high sensitivity for the majority of OT nomination tools and COSMID, DISCOVER-Seq, and GUIDE-Seq attained the highest positive predictive value (PPV). We found that empirical methods did not identify OT sites that were not also identified by bioinformatic methods. This study supports that refined bioinformatic algorithms could be developed that maintain both high sensitivity and PPV, thereby enabling more efficient identification of potential OT sites without compromising a thorough examination for any given gRNA.
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Affiliation(s)
- M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Kiran R Majeti
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Karthik Murugan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Gavin L Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Jessica P Hampton
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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17
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Park J, Kang SJ, Go S, Lee J, An J, Chung HS, Jeong C, Ahn DR. Split-tracrRNA as an efficient tracrRNA system with an improved potential of scalability. Biomater Sci 2023; 11:3241-3251. [PMID: 36938935 DOI: 10.1039/d2bm01901a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Due to the relatively long sequence, tracrRNAs are chemically less synthesizable than crRNAs, leading to limited scalability of RNA guides for CRISPR-Cas9 systems. To develop shortened versions of RNA guides with improved cost-effectiveness, we have developed a split-tracrRNA system by nicking the 67-mer tracrRNA (tracrRNA(67)). Cellular gene editing assays and in vitro DNA cleavage assays revealed that the position of the nick is critical for maintaining the activity of tracrRNA(67). TracrRNA(41 + 23), produced by nicking in stem loop 2, showed gene editing efficiency and specificity comparable to those of tracrRNA(67). Removal of the loop of stem loop 2 was further possible without compromising the efficiency and specificity when the stem duplex was stabilized via a high GC content. Binding assays and single-molecule experiments suggested that efficient split-tracrRNAs could be engineered as long as their binding affinity to Cas9 and their reaction kinetics are similar to those of tracrRNA(67).
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Affiliation(s)
- Jihyun Park
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
| | - Seong Jae Kang
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
| | - Seulgi Go
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea. .,Department of Pharmacology, College of Medicine, Korea University, Seoul 02841, Korea
| | - Jeongmin Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea. .,Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Jinsu An
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea. .,Division of Biomedical Science and Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea
| | - Hak Suk Chung
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea. .,Division of Biomedical Science and Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea
| | - Cherlhyun Jeong
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea. .,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, South Korea
| | - Dae-Ro Ahn
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea. .,Division of Biomedical Science and Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea
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18
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Illa-Berenguer E, LaFayette PR, Parrott WA. Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice. Front Genome Ed 2023; 5:1074641. [PMID: 37032710 PMCID: PMC10080323 DOI: 10.3389/fgeed.2023.1074641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
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Affiliation(s)
- Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- *Correspondence: Eudald Illa-Berenguer,
| | - Peter R. LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Wayne A. Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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19
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Christie KA, Guo JA, Silverstein RA, Doll RM, Mabuchi M, Stutzman HE, Lin J, Ma L, Walton RT, Pinello L, Robb GB, Kleinstiver BP. Precise DNA cleavage using CRISPR-SpRYgests. Nat Biotechnol 2023; 41:409-416. [PMID: 36203014 PMCID: PMC10023266 DOI: 10.1038/s41587-022-01492-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Methods for in vitro DNA cleavage and molecular cloning remain unable to precisely cleave DNA directly adjacent to bases of interest. Restriction enzymes (REs) must bind specific motifs, whereas wild-type CRISPR-Cas9 or CRISPR-Cas12 nucleases require protospacer adjacent motifs (PAMs). Here we explore the utility of our previously reported near-PAMless SpCas9 variant, named SpRY, to serve as a universal DNA cleavage tool for various cloning applications. By performing SpRY DNA digests (SpRYgests) using more than 130 guide RNAs (gRNAs) sampling a wide diversity of PAMs, we discovered that SpRY is PAMless in vitro and can cleave DNA at practically any sequence, including sites refractory to cleavage with wild-type SpCas9. We illustrate the versatility and effectiveness of SpRYgests to improve the precision of several cloning workflows, including those not possible with REs or canonical CRISPR nucleases. We also optimize a rapid and simple one-pot gRNA synthesis protocol to streamline SpRYgest implementation. Together, SpRYgests can improve various DNA engineering applications that benefit from precise DNA breaks.
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Affiliation(s)
- Kathleen A Christie
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jimmy A Guo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Rachel A Silverstein
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Roman M Doll
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Biosciences/Cancer Biology Program, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hannah E Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Jiecong Lin
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital Charlestown, Boston, MA, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Russell T Walton
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luca Pinello
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital Charlestown, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
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20
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Gao K, Li J, Song H, Han H, Wang Y, Yin B, Farmer DL, Murthy N, Wang A. In utero delivery of mRNA to the heart, diaphragm and muscle with lipid nanoparticles. Bioact Mater 2023; 25:387-398. [PMID: 36844366 PMCID: PMC9950423 DOI: 10.1016/j.bioactmat.2023.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/26/2023] [Accepted: 02/11/2023] [Indexed: 02/19/2023] Open
Abstract
Nanoparticle-based drug delivery systems have the potential to revolutionize medicine, but their low vascular permeability and rapid clearance by phagocytic cells have limited their medical impact. Nanoparticles delivered at the in utero stage can overcome these key limitations due to the high rate of angiogenesis and cell division in fetal tissue and the under-developed immune system. However, very little is known about nanoparticle drug delivery at the fetal stage of development. In this report, using Ai9 CRE reporter mice, we demonstrate that lipid nanoparticle (LNP) mRNA complexes can deliver mRNA in utero, and can access and transfect major organs, such as the heart, the liver, kidneys, lungs and the gastrointestinal tract with remarkable efficiency and low toxicity. In addition, at 4 weeks after birth, we demonstrate that 50.99 ± 5.05%, 36.62 ± 3.42% and 23.7 ± 3.21% of myofiber in the diaphragm, heart and skeletal muscle, respectively, were transfected. Finally, we show here that Cas9 mRNA and sgRNA complexed to LNPs were able to edit the fetal organs in utero. These experiments demonstrate the possibility of non-viral delivery of mRNA to organs outside of the liver in utero, which provides a promising strategy for treating a wide variety of devastating diseases before birth.
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Affiliation(s)
- Kewa Gao
- Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA, 95817, United States,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA, 95817, United States
| | - Jie Li
- Department of Bioengineering, University of California, Berkeley, CA, 94704, United States
| | - Hengyue Song
- Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA, 95817, United States,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA, 95817, United States,Department of Burns and Plastic Surgery, The Third Xiangya Hospital of Central South University, Hunan, 410013, China
| | - Hesong Han
- Department of Bioengineering, University of California, Berkeley, CA, 94704, United States
| | - Yongheng Wang
- Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA, 95817, United States,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA, 95817, United States,Department of Biomedical Engineering, University of California, Davis, CA, 95616, United States
| | - Boyan Yin
- Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA, 95817, United States,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA, 95817, United States
| | - Diana L. Farmer
- Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA, 95817, United States,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA, 95817, United States
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, CA, 94704, United States,Corresponding author. Department of Bioengineering, University of California, Berkeley, CA, 94704, United States.
| | - Aijun Wang
- Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA, 95817, United States,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA, 95817, United States,Department of Biomedical Engineering, University of California, Davis, CA, 95616, United States,Corresponding author. Center for Surgical Bioengineering, Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA, 95817, United States.
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21
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Buffa V, Alvarez Vargas JR, Galy A, Spinozzi S, Rocca CJ. Hematopoietic stem and progenitors cells gene editing: Beyond blood disorders. Front Genome Ed 2023; 4:997142. [PMID: 36698790 PMCID: PMC9868335 DOI: 10.3389/fgeed.2022.997142] [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: 07/18/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
Lessons learned from decades-long practice in the transplantation of hematopoietic stem and progenitor cells (HSPCs) to treat severe inherited disorders or cancer, have set the stage for the current ex vivo gene therapies using autologous gene-modified hematopoietic stem and progenitor cells that have treated so far, hundreds of patients with monogenic disorders. With increased knowledge of hematopoietic stem and progenitor cell biology, improved modalities for patient conditioning and with the emergence of new gene editing technologies, a new era of hematopoietic stem and progenitor cell-based gene therapies is poised to emerge. Gene editing has the potential to restore physiological expression of a mutated gene, or to insert a functional gene in a precise locus with reduced off-target activity and toxicity. Advances in patient conditioning has reduced treatment toxicities and may improve the engraftment of gene-modified cells and specific progeny. Thanks to these improvements, new potential treatments of various blood- or immune disorders as well as other inherited diseases will continue to emerge. In the present review, the most recent advances in hematopoietic stem and progenitor cell gene editing will be reported, with a focus on how this approach could be a promising solution to treat non-blood-related inherited disorders and the mechanisms behind the therapeutic actions discussed.
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Affiliation(s)
- Valentina Buffa
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - José Roberto Alvarez Vargas
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Anne Galy
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Simone Spinozzi
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Céline J. Rocca
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France,*Correspondence: Céline J. Rocca,
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22
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Huang Z, Liu G. Current advancement in the application of prime editing. Front Bioeng Biotechnol 2023; 11:1039315. [PMID: 36873365 PMCID: PMC9978821 DOI: 10.3389/fbioe.2023.1039315] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
Prime editing (PE) is a precise genome manipulation technology based on the "search and replace" approach of the CRISPR-Cas9 system, while it does not require the exogenous donor DNA and the DNA double-strand breaks (DSBs). Comparing the base editing technology, the editing scope of prime editing has been widely expanded. Prime editing has been successfully applied in a variety of plant cells, animal cells and the model microorganism Escherichia coli so far, and it has shown a good application potential in breeding and genomic functional study of animals and plants, disease treatment, and modification of the microbial strains. In this paper, the basic strategies of prime editing are briefly described, and its research progress is summarized and prospected from the application of multiple species. In addition, a variety of optimization strategies for improving its efficiency and specificity of prime editing are outlined.
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Affiliation(s)
- Zhangrao Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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23
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Trieu A, Belaffif MB, Hirannaiah P, Manjunatha S, Wood R, Bathula Y, Billingsley RL, Arpan A, Sacks EJ, Clemente TE, Moose SP, Reichert NA, Swaminathan K. Transformation and gene editing in the bioenergy grass Miscanthus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:148. [PMID: 36578060 PMCID: PMC9798709 DOI: 10.1186/s13068-022-02241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/08/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites. RESULTS We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors. CONCLUSIONS We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.
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Affiliation(s)
- Anthony Trieu
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Mohammad B. Belaffif
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Pradeepa Hirannaiah
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Shilpa Manjunatha
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Rebekah Wood
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Yokshitha Bathula
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Rebecca L. Billingsley
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Anjali Arpan
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Erik J. Sacks
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, E.R. Madigan Laboratory, University of Illinois Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Thomas E. Clemente
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Stephen P. Moose
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, E.R. Madigan Laboratory, University of Illinois Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Nancy A. Reichert
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Kankshita Swaminathan
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
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24
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Kuzmin AA, Tomilin AN. Building Blocks of Artificial CRISPR-Based Systems beyond Nucleases. Int J Mol Sci 2022; 24:ijms24010397. [PMID: 36613839 PMCID: PMC9820447 DOI: 10.3390/ijms24010397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Tools developed in the fields of genome engineering, precise gene regulation, and synthetic gene networks have an increasing number of applications. When shared with the scientific community, these tools can be used to further unlock the potential of precision medicine and tissue engineering. A large number of different genetic elements, as well as modifications, have been used to create many different systems and to validate some technical concepts. New studies have tended to optimize or improve existing elements or approaches to create complex synthetic systems, especially those based on the relatively new CRISPR technology. In order to maximize the output of newly developed approaches and to move from proof-of-principle experiments to applications in regenerative medicine, it is important to navigate efficiently through the vast number of genetic elements to choose those most suitable for specific needs. In this review, we have collected information regarding the main genetic elements and their modifications, which can be useful in different synthetic systems with an emphasis of those based on CRISPR technology. We have indicated the most suitable elements and approaches to choose or combine in planning experiments, while providing their deeper understanding, and have also stated some pitfalls that should be avoided.
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25
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Okafor I, Ha T. Single Molecule FRET Analysis of CRISPR Cas9 Single Guide RNA Folding Dynamics. J Phys Chem B 2022; 127:45-51. [PMID: 36563314 PMCID: PMC9841515 DOI: 10.1021/acs.jpcb.2c05428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CRISPR Cas9 is an RNA guided endonuclease that is part of a bacterial adaptive immune system. Single guide RNA (sgRNA) can be designed to target genomic DNA, making Cas9 a programmable DNA binding/cutting enzyme and allowing applications such as epigenome editing, controlling transcription, and targeted DNA insertion. Some of the main hurdles against an even wider adoption are off-target effects and variability in Cas9 editing outcomes. Most studies that aim to understand the mechanisms that underlie these two areas have focused on Cas9 DNA binding, DNA unwinding, and target cleavage. The assembly of Cas9 RNA ribonucleoprotein complex (RNP) precedes all these steps and includes sgRNA folding and Cas9 binding to sgRNA. We know from the crystal structure of the Cas9 RNP what the final sgRNA conformation is. However, the assembly dynamics has not been studied in detail and a better understanding of RNP assembly could lead to better-designed sgRNAs and better editing outcomes. To study this process, we developed a single molecule FRET assay to monitor the conformation of the sgRNA and the binding of Cas9 to sgRNA. We labeled the sgRNA with a donor fluorophore and an acceptor fluorophore such that when the sgRNA folds, there are changes in FRET efficiency. We measured sgRNA folding dynamics under different ion conditions, under various methods of folding (refolding vs vectorial), and with or without Cas9. sgRNA that closely mimics the sgRNA construct used for high resolution structural analysis of the Cas9-gRNA complex showed two main FRET states without Cas9, and Cas9 addition shifted the distribution toward the higher FRET state attributed to the properly assembled complex. Even in the absence of Cas9, folding the sgRNA vectorially using a superhelicase-dependent release of the sgRNA in the direction of transcription resulted in almost exclusively high FRET state. An addition of Cas9 during vectorial folding greatly reduced a slow-folding fraction. Our studies shed light on the heterogeneous folding dynamics of sgRNA and the impact of co-transcriptional folding and Cas9 binding in sgRNA folding. Further studies of sequence dependence may inform rational design of sgRNAs for optimal function.
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Affiliation(s)
- Ikenna
C. Okafor
- Department
of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Taekjip Ha
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States,Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States,Department
of Biomedical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States,Howard
Hughes Medical Institute, Baltimore, Maryland 21205, United States,
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26
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Shaytan AK, Novikov RV, Vinnikov RS, Gribkova AK, Glukhov GS. From DNA-protein interactions to the genetic circuit design using CRISPR-dCas systems. Front Mol Biosci 2022; 9:1070526. [PMID: 36589238 PMCID: PMC9795063 DOI: 10.3389/fmolb.2022.1070526] [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: 10/15/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023] Open
Abstract
In the last decade, the CRISPR-Cas technology has gained widespread popularity in different fields from genome editing and detecting specific DNA/RNA sequences to gene expression control. At the heart of this technology is the ability of CRISPR-Cas complexes to be programmed for targeting particular DNA loci, even when using catalytically inactive dCas-proteins. The repertoire of naturally derived and engineered dCas-proteins including fusion proteins presents a promising toolbox that can be used to construct functional synthetic genetic circuits. Rational genetic circuit design, apart from having practical relevance, is an important step towards a deeper quantitative understanding of the basic principles governing gene expression regulation and functioning of living organisms. In this minireview, we provide a succinct overview of the application of CRISPR-dCas-based systems in the emerging field of synthetic genetic circuit design. We discuss the diversity of dCas-based tools, their properties, and their application in different types of genetic circuits and outline challenges and further research directions in the field.
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Affiliation(s)
- A. K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Computer Science, HSE University, Moscow, Russia,*Correspondence: A. K. Shaytan,
| | - R. V. Novikov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - R. S. Vinnikov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - A. K. Gribkova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - G. S. Glukhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen, China
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27
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Hoy A, Zheng YY, Sheng J, Royzen M. Bio-Orthogonal Chemistry Conjugation Strategy Facilitates Investigation of N-methyladenosine and Thiouridine Guide RNA Modifications on CRISPR Activity. CRISPR J 2022; 5:787-798. [PMID: 36378256 PMCID: PMC9805849 DOI: 10.1089/crispr.2022.0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The CRISPR-Cas9 system is an important genome editing tool that holds enormous potential toward the treatment of human genetic diseases. Clinical success of CRISPR technology is dependent on the incorporation of modifications into the single-guide RNA (sgRNA). However, chemical synthesis of modified sgRNAs, which are over 100 nucleotides in length, is difficult and low-yielding. We developed a conjugation strategy that utilized bio-orthogonal chemistry to efficiently assemble functional sgRNAs containing nucleobase modifications. The described approach entails the chemical synthesis of two shorter RNA oligonucleotides: a 31-mer containing tetrazine (Tz) group and a 70-mer modified with a trans-cyclooctene (TCO) moiety. The two oligonucleotides were conjugated to form functional sgRNAs. The two-component conjugation methodology was utilized to synthesize a library of sgRNAs containing nucleobase modifications such as N1-methyladenosine (m1A), N6-methyladenosine (m6A), 2-thiouridine (s2U), and 4-thiouridine (s4U). The impact of these RNA modifications on overall CRISPR activity were investigated in vitro and in Cas9-expressing HEK293T cells.
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Affiliation(s)
- Alyssa Hoy
- Department of Chemistry, University at Albany, SUNY, Albany, New York, USA
| | - Ya Ying Zheng
- Department of Chemistry, University at Albany, SUNY, Albany, New York, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, SUNY, Albany, New York, USA.,Address correspondence to: Jia Sheng, Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA,
| | - Maksim Royzen
- Department of Chemistry, University at Albany, SUNY, Albany, New York, USA.,Address correspondence to: Maksim Royzen, Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA,
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28
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Miyata M, Yoshida J, Takagishi I, Horie K. Comparison of CRISPR-Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells. DNA Res 2022; 30:6854440. [PMID: 36448318 PMCID: PMC9847339 DOI: 10.1093/dnares/dsac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The genome contains large functional units ranging in size from hundreds of kilobases to megabases, such as gene clusters and topologically associating domains. To analyse these large functional units, the technique of deleting the entire functional unit is effective. However, deletion of such large regions is less efficient than conventional genome editing, especially in cultured cells, and a method that can ensure success is anticipated. Here, we compared methods to delete the 2.5-Mb Krüppel-associated box zinc finger protein (KRAB-ZFP) gene cluster in mouse embryonic stem cells using CRISPR-Cas9. Three methods were used: first, deletion by non-homologous end joining (NHEJ); second, homology-directed repair (HDR) using a single-stranded oligodeoxynucleotide (ssODN); and third, HDR employing targeting vectors with a selectable marker and 1-kb homology arms. NHEJ-mediated deletion was achieved in 9% of the transfected cells. Inversion was also detected at similar efficiency. The deletion frequency of NHEJ and HDR was found to be comparable when the ssODN was transfected. Deletion frequency was highest when targeting vectors were introduced, with deletions occurring in 31-63% of the drug-resistant clones. Biallelic deletion was observed when targeting vectors were used. This study will serve as a benchmark for the introduction of large deletions into the genome.
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Affiliation(s)
- Masayuki Miyata
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Junko Yoshida
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Itsuki Takagishi
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Kyoji Horie
- To whom correspondence should be addressed. Tel: +81 744 23 4696. Fax: +81 744 23 4696.
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29
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Kang K, Song Y, Kim I, Kim TJ. Therapeutic Applications of the CRISPR-Cas System. Bioengineering (Basel) 2022; 9:bioengineering9090477. [PMID: 36135023 PMCID: PMC9495783 DOI: 10.3390/bioengineering9090477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The clustered regularly interspaced palindromic repeat (CRISPR)-Cas system has revolutionized genetic engineering due to its simplicity, stability, and precision since its discovery. This technology is utilized in a variety of fields, from basic research in medicine and biology to medical diagnosis and treatment, and its potential is unbounded as new methods are developed. The review focused on medical applications and discussed the most recent treatment trends and limitations, with an emphasis on CRISPR-based therapeutics for infectious disease, oncology, and genetic disease, as well as CRISPR-based diagnostics, screening, immunotherapy, and cell therapy. Given its promising results, the successful implementation of the CRISPR-Cas system in clinical practice will require further investigation into its therapeutic applications.
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Affiliation(s)
- Kyungmin Kang
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Youngjae Song
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Inho Kim
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
| | - Tae-Jung Kim
- Department of Hospital Pathology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea
- Correspondence: ; Tel.: +82-2-3779-2157
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30
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Dong C, Gou Y, Lian J. SgRNA engineering for improved genome editing and expanded functional assays. Curr Opin Biotechnol 2022; 75:102697. [PMID: 35217295 DOI: 10.1016/j.copbio.2022.102697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
Abstract
The CRISPR/Cas system has been established as the most powerful and practical genome engineering tool for both fundamental researches and biotechnological applications. Great efforts have been devoted to engineering the CRISPR system with better performance and novel functions. As an essential component, single guide RNAs (sgRNAs) have been extensively designed and engineered with desirable functions. This review highlights representative studies that optimize the sgRNA nucleotide sequences for improved genome editing performance (e.g. activity and specificity) as well as add extra aptamers and end extensions for expanded CRISPR-based functional assays (e.g. transcriptional regulation, genome imaging, and prime editor). The perspectives for further sgRNA engineering to establish more powerful and versatile CRISPR/Cas systems are also discussed.
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Affiliation(s)
- Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China.
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