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Zheng L, Zhou B, Yang Y, Zan B, Zhong B, Wu B, Feng Y, Liu Q, Hong L. Mn 2+-induced structural flexibility enhances the entire catalytic cycle and the cleavage of mismatches in prokaryotic argonaute proteins. Chem Sci 2024; 15:5612-5626. [PMID: 38638240 PMCID: PMC11023060 DOI: 10.1039/d3sc06221j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/01/2024] [Indexed: 04/20/2024] Open
Abstract
Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid-based biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicate that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.
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Affiliation(s)
- Lirong Zheng
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Department of Cell and Developmental Biology & Michigan Neuroscience Institute, University of Michigan Medical School 48105 Ann Arbor MI USA
| | - Bingxin Zhou
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
| | - Yu Yang
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bing Zan
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bozitao Zhong
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Banghao Wu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Feng
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Liu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University Shanghai 200240 China
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2
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Fu X, Sun J, Yu B, Ye Y, Sheng L, Ji J, Zheng J, Fan M, Shao J, Sun X. Investigating enzyme kinetics and fluorescence sensing strategy of CRISPR/Cas12a for foodborne pathogenic bacteria. Anal Chim Acta 2024; 1290:342203. [PMID: 38246741 DOI: 10.1016/j.aca.2024.342203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
Foodborne pathogenic bacteria are widespread in various foods, whose cross-contamination and re-contamination are critical influences on food safety. Rapid, accurate, and sensitive detection of foodborne pathogenic bacteria remains a topic of concern. CRISPR/Cas12a can recognize double-stranded DNA directly, showing great potential in nucleic acid detection. However, few studies have investigated the cleavage properties of CRISPR/Cas12a. In this study, the trans-cleavage properties of LbCas12a and AsCas12a were investigated to construct the detection methods for foodborne pathogenic bacteria. The highly sensitive fluorescent strategies for foodborne pathogens were constructed by analyzing the cleavage rates and properties of substrates at different substrate concentrations. Cas12a was activated in the presence of foodborne pathogenic target sequence was present, resulting in the cleavage of a single-stranded reporter ssDNA co-labelled by fluorescein quencher and fluorescein. The sensitivity and specificity of the Cas12a fluorescent strategy was investigated with Salmonella and Staphylococcus aureus as examples. The results showed that AsCas12a was slightly more capable of trans-cleavage than LbCas12a. The detection limits of AsCas12a for Salmonella and Staphylococcus aureus were 24.9 CFU mL-1 and 1.50 CFU mL-1, respectively. In all the seven bacteria, Staphylococcus aureus and Salmonella were accurately discriminated. The study provided a basis for constructing and improving the CRISPR/Cas12a fluorescence strategies. The AsCas12a-based detection strategy is expected to be a promising method for field detection.
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Affiliation(s)
- XuRan Fu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - JiaDi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Bingqian Yu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Yongli Ye
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Lina Sheng
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jian Ji
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jiayu Zheng
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Minghong Fan
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Jingdong Shao
- Comprehensive Technology Center of Zhangjiagang Customs, Zhangjiagang, Jiangsu, 215600, PR China
| | - XiuLan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
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3
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Zaplana T, Miele S, Tolonen AC. Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics. Front Bioeng Biotechnol 2024; 11:1324396. [PMID: 38239921 PMCID: PMC10794557 DOI: 10.3389/fbioe.2023.1324396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024] Open
Abstract
The Lachnospiraceae is a family of anaerobic bacteria in the class Clostridia with potential to advance the bio-economy and intestinal therapeutics. Some species of Lachnospiraceae metabolize abundant, low-cost feedstocks such as lignocellulose and carbon dioxide into value-added chemicals. Others are among the dominant species of the human colon and animal rumen, where they ferment dietary fiber to promote healthy gut and immune function. Here, we summarize recent studies of the physiology, cultivation, and genetics of Lachnospiraceae, highlighting their wide substrate utilization and metabolic products with industrial applications. We examine studies of these bacteria as Live Biotherapeutic Products (LBPs), focusing on in vivo disease models and clinical studies using them to treat infection, inflammation, metabolic syndrome, and cancer. We discuss key research areas including elucidation of intra-specific diversity and genetic modification of candidate strains that will facilitate the exploitation of Lachnospiraceae in industry and medicine.
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Affiliation(s)
| | | | - Andrew C. Tolonen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry, Université Paris-Saclay, Evry, France
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4
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Vlassis A, Jensen TL, Mohr M, Jedrzejczyk DJ, Meng X, Kovacs G, Morera-Gómez M, Barghetti A, Muyo Abad S, Baumgartner RF, Natarajan KN, Nielsen LK, Warnecke T, Gill RT. CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells. iScience 2023; 26:108287. [PMID: 38034357 PMCID: PMC10682145 DOI: 10.1016/j.isci.2023.108287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/23/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023] Open
Abstract
Discovery of genomic safe harbor sites (SHSs) is fundamental for multiple transgene integrations, such as reporter genes, chimeric antigen receptors (CARs), and safety switches, which are required for safe cell products for regenerative cell therapies and immunotherapies. Here we identified and characterized potential SHS in human cells. Using the CRISPR-MAD7 system, we integrated transgenes at these sites in induced pluripotent stem cells (iPSCs), primary T and natural killer (NK) cells, and Jurkat cell line, and demonstrated efficient and stable expression at these loci. Subsequently, we validated the differentiation potential of engineered iPSC toward CD34+ hematopoietic stem and progenitor cells (HSPCs), lymphoid progenitor cells (LPCs), and NK cells and showed that transgene expression was perpetuated in these lineages. Finally, we demonstrated that engineered iPSC-derived NK cells retained expression of a non-virally integrated anti-CD19 CAR, suggesting that several of the investigated SHSs can be used to engineer cells for adoptive immunotherapies.
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Affiliation(s)
- Arsenios Vlassis
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Tanja L. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Marina Mohr
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Dominika J. Jedrzejczyk
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Xiangyou Meng
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Gergo Kovacs
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Andrea Barghetti
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Sergi Muyo Abad
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Roland F. Baumgartner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Kedar N. Natarajan
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Lars K. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tanya Warnecke
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Ryan T. Gill
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
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5
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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. Planta 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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6
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Mohr M, Damas N, Gudmand-Høyer J, Zeeberg K, Jedrzejczyk D, Vlassis A, Morera-Gómez M, Pereira-Schoning S, Puš U, Oliver-Almirall A, Lyholm Jensen T, Baumgartner R, Tate Weinert B, Gill RT, Warnecke T. The CRISPR-Cas12a Platform for Accurate Genome Editing, Gene Disruption, and Efficient Transgene Integration in Human Immune Cells. ACS Synth Biol 2023; 12:375-389. [PMID: 36750230 PMCID: PMC9942205 DOI: 10.1021/acssynbio.2c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
CRISPR-Cas12a nucleases have expanded the toolbox for targeted genome engineering in a broad range of organisms. Here, using a high-throughput engineering approach, we explored the potential of a novel CRISPR-MAD7 system for genome editing in human cells. We evaluated several thousand optimization conditions and demonstrated accurate genome reprogramming with modified MAD7. We identified crRNAs that allow for ≤95% non-homologous end joining (NHEJ) and 66% frameshift mutations in various genes and observed the high-cleavage fidelity of MAD7 resulting in undetectable off-target activity. We explored the dsDNA delivery efficiency of CRISPR-MAD7, and by using our optimized transfection protocol, we obtained ≤85% chimeric antigen receptor (CAR) insertions in primary T cells, thus exceeding the baseline integration efficiencies of therapeutically relevant transgenes using currently available virus-free technologies. Finally, we evaluated multiplex editing efficiency with CRISPR-MAD7 and demonstrated simultaneous ≤35% CAR transgene insertions and ≤80% gene disruption efficiencies. Both the platform and our transfection procedure are easily adaptable for further preclinical studies and could potentially be used for clinical manufacturing of CAR T cells.
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Affiliation(s)
- Marina Mohr
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Nkerorema Damas
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Johanne Gudmand-Høyer
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Katrine Zeeberg
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Dominika Jedrzejczyk
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Arsenios Vlassis
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Sara Pereira-Schoning
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Urška Puš
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Anna Oliver-Almirall
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Tanja Lyholm Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Roland Baumgartner
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Brian Tate Weinert
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Ryan T. Gill
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark,Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States,
| | - Tanya Warnecke
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States,
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7
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Liu X, Qiu X, Han L, Yue Y, Xu S, Li F, Yao J, Sun L, Li Z. Three novel Cas12a orthologs with robust DNA cleavage activity suitable for nucleic acid detection. Gene 2023; 852:147055. [PMID: 36400115 DOI: 10.1016/j.gene.2022.147055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
Developing rapid and accurate pathogen detection methods is increasingly important, and CRISPR-Cas system can be optimized for this purpose. CRISPR-Cas12a is a single RNA-guided endonuclease system with the potential for nucleic acid detection. There is a broad diversity among Cas12a nucleases with robust detection capability. Herein, we characterised three Cas12a orthologs (ObCas12a, MbCas12a, and ScCas12a), including cis- and trans-cleavage activities, the identification of PAM, single-base resolution ability, and the application for nucleic acid detection. These Cas12a orthologs displayed robust cis- and trans-cleavage activities, and performed well in terms of specificity and sensitivity for nucleic acid detection. Furthermore, they have subtle differences in single-base resolution and recognised PAM sites in vitro. Therefore, these Cas12a nucleases are candidate proteins for CRISPR-based diagnostic methods. Addition of these enzymes to the nucleic acid detection toolbox will further expand the utility of this powerful technology.
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8
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Chen G, Wei T, Yang H, Li G, Li H. CRISPR-Based Therapeutic Gene Editing for Duchenne Muscular Dystrophy: Advances, Challenges and Perspectives. Cells 2022; 11:2964. [PMID: 36230926 PMCID: PMC9564082 DOI: 10.3390/cells11192964] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe neuromuscular disease arising from loss-of-function mutations in the dystrophin gene and characterized by progressive muscle degeneration, respiratory insufficiency, cardiac failure, and premature death by the age of thirty. Albeit DMD is one of the most common types of fatal genetic diseases, there is no curative treatment for this devastating disorder. In recent years, gene editing via the clustered regularly interspaced short palindromic repeats (CRISPR) system has paved a new path toward correcting pathological mutations at the genetic source, thus enabling the permanent restoration of dystrophin expression and function throughout the musculature. To date, the therapeutic benefits of CRISPR genome-editing systems have been successfully demonstrated in human cells, rodents, canines, and piglets with diverse DMD mutations. Nevertheless, there remain some nonignorable challenges to be solved before the clinical application of CRISPR-based gene therapy. Herein, we provide an overview of therapeutic CRISPR genome-editing systems, summarize recent advancements in their applications in DMD contexts, and discuss several potential obstacles lying ahead of clinical translation.
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Vasilev R, Gunitseva N, Shebanova R, Korzhenkov A, Vlaskina A, Evteeva M, Polushkina I, Nikitchina N, Toshchakov S, Kamenski P, Patrushev M, Mazunin I. Targeted Modification of Mammalian DNA by a Novel Type V Cas12a Endonuclease from Ruminococcus bromii. Int J Mol Sci 2022; 23:ijms23169289. [PMID: 36012553 PMCID: PMC9409102 DOI: 10.3390/ijms23169289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
Abstract
Type V Cas12a nucleases are DNA editors working in a wide temperature range and using expanded protospacer-adjacent motifs (PAMs). Though they are widely used, there is still a demand for discovering new ones. Here, we demonstrate a novel ortholog from Ruminococcus bromii sp. entitled RbCas12a, which is able to efficiently cleave target DNA templates, using the particularly high accessibility of PAM 5′-YYN and a relatively wide temperature range from 20 °C to 42 °C. In comparison to Acidaminococcus sp. (AsCas12a) nuclease, RbCas12a is capable of processing DNA more efficiently, and can be active upon being charged by spacer-only RNA at lower concentrations in vitro. We show that the human-optimized RbCas12a nuclease is also active in mammalian cells, and can be applied for efficient deletion incorporation into the human genome. Given the advantageous properties of RbCas12a, this enzyme shows potential for clinical and biotechnological applications within the field of genome editing.
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Affiliation(s)
- Ruslan Vasilev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
| | - Natalia Gunitseva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Regina Shebanova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Aleksei Korzhenkov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Anna Vlaskina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Marta Evteeva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Irina Polushkina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Natalia Nikitchina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- UMR7156–Molecular Genetics, Genomics, Microbiology, University of Strasbourg and Centre National de la Recherche Scientifique (CNRS), 67000 Strasbourg, France
| | - Stepan Toshchakov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maxim Patrushev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Ilya Mazunin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Medical Genomics LLC, 119192 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
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10
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Luk K, Liu P, Zeng J, Wang Y, Maitland SA, Idrizi F, Ponnienselvan K, Iyer S, Zhu LJ, Luban J, Bauer DE, Wolfe SA. Optimization of Nuclear Localization Signal Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells. GEN Biotechnol 2022; 1:271-284. [PMID: 38405215 PMCID: PMC10887433 DOI: 10.1089/genbio.2022.0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Type V CRISPR-Cas12a systems are an attractive Cas9-alternative nuclease platform for specific genome editing applications. However, previous studies demonstrate that there is a gap in overall activity between Cas12a and Cas9 in primary cells.1 Here we describe optimization to the NLS composition and architecture of Cas12a to facilitate highly efficient targeted mutagenesis in human transformed cell lines (HEK293T, Jurkat, and K562 cells) and primary cells (NK cells and CD34+ HSPCs), regardless of Cas12a ortholog. Our 3xNLS Cas12a architecture resulted in the most robust editing platform. The improved editing activity of Cas12a in both NK cells and CD34+ HSPCs resulted in pronounced phenotypic changes associated with target gene editing. Lastly, we demonstrated that optimization of the NLS composition and architecture of Cas12a did not increase editing at potential off-target sites in HEK293T or CD34+ HSPCs. Our new Cas12a NLS variant provides an improved nuclease platform for therapeutic genome editing.
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Affiliation(s)
- Kevin Luk
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute of Harvard and MIT, Harvard Medical School, Boston, MA, USA
| | - Yetao Wang
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Beijing, Beijing, CN
| | - Stacy A. Maitland
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Feston Idrizi
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Karthikeyan Ponnienselvan
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sukanya Iyer
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute of Harvard and MIT, Harvard Medical School, Boston, MA, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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11
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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12
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Huang H, Huang G, Tan Z, Hu Y, Shan L, Zhou J, Zhang X, Ma S, Lv W, Huang T, Liu Y, Wang D, Zhao X, Lin Y, Rong Z. Engineered Cas12a-Plus nuclease enables gene editing with enhanced activity and specificity. BMC Biol 2022; 20:91. [PMID: 35468792 PMCID: PMC9040236 DOI: 10.1186/s12915-022-01296-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background The CRISPR-Cas12a (formerly Cpf1) system is a versatile gene-editing tool with properties distinct from the broadly used Cas9 system. Features such as recognition of T-rich protospacer-adjacent motif (PAM) and generation of sticky breaks, as well as amenability for multiplex editing in a single crRNA and lower off-target nuclease activity, broaden the targeting scope of available tools and enable more accurate genome editing. However, the widespread use of the nuclease for gene editing, especially in clinical applications, is hindered by insufficient activity and specificity despite previous efforts to improve the system. Currently reported Cas12a variants achieve high activity with a compromise of specificity. Here, we used structure-guided protein engineering to improve both editing efficiency and targeting accuracy of Acidaminococcus sp. Cas12a (AsCas12a) and Lachnospiraceae bacterium Cas12a (LbCas12a). Results We created new AsCas12a variant termed “AsCas12a-Plus” with increased activity (1.5~2.0-fold improvement) and specificity (reducing off-targets from 29 to 23 and specificity index increased from 92% to 94% with 33 sgRNAs), and this property was retained in multiplex editing and transcriptional activation. When used to disrupt the oncogenic BRAFV600E mutant, AsCas12a-Plus showed less off-target activity while maintaining comparable editing efficiency and BRAFV600E cancer cell killing. By introducing the corresponding substitutions into LbCas12a, we also generated LbCas12a-Plus (activity improved ~1.1-fold and off-targets decreased from 20 to 12 while specificity index increased from 78% to 89% with 15 sgRNAs), suggesting this strategy may be generally applicable across Cas12a orthologs. We compared Cas12a-Plus, other variants described in this study, and the reported enCas12a-HF, enCas12a, and Cas12a-ultra, and found that Cas12a-Plus outperformed other variants with a good balance for enhanced activity and improved specificity. Conclusions Our discoveries provide alternative AsCas12a and LbCas12a variants with high specificity and activity, which expand the gene-editing toolbox and can be more suitable for clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01296-1.
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Affiliation(s)
- Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, 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
| | - 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
| | - Yongfei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lin Shan
- 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
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, 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
| | - 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
| | - Weiqi Lv
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Tao Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, 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
| | - 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
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoyang Zhao
- Department of Development, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 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 Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Zhili Rong
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, 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. .,Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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13
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Liu X, Qiu X, Xu S, Che Y, Han L, Kang Y, Yue Y, Chen S, Li F, Li Z. A CRISPR-Cas12a-Assisted Fluorescence Platform for Rapid and Accurate Detection of Nocardia cyriacigeorgica. Front Cell Infect Microbiol 2022; 12:835213. [PMID: 35310854 PMCID: PMC8924655 DOI: 10.3389/fcimb.2022.835213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/15/2022] [Indexed: 12/26/2022] Open
Abstract
Nocardia cyriacigeorgica has gradually become a common pathogen in clinical microbial infections. Identification of Nocardia at the species level is essential to assess the susceptibility and pathogenicity of antimicrobials. However, there is no suitable method for rapid and accurate laboratory detection of N. cyriacigeorgica. In this study, we combined PCR amplification with the CRISPR-Cas12a system to establish a novel detection platform, named CRISPR-PCR, and applied it to the detection of N. cyriacigeorgica in clinical samples. The Cas12a protein exhibited collateral cleavage activity following CRISPR RNA binding to specific targets, then indiscriminately cleaved nearby single-stranded DNA, and this was evaluated for diagnostic nucleic acid detection by measuring the fluorescence signal using a fluorescence reader. The assay takes only 2 h, including DNA extraction for 20 min, nucleic acid pre-amplification for 70 min, and fluorescence detection for 20 min. The limit of detection for N. cyriacigeorgica was 10-3 ng and the specificity was 100%. Thus, the N. cyriacigeorgica CRISPR-PCR assay is a rapid and specific method for detecting N. cyriacigeorgica, and the CRISPR-PCR fluorescence detection platform has great potential for detection of other pathogens.
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Affiliation(s)
- Xueping Liu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaotong Qiu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuai Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Che
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lichao Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yutong Kang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Yue
- Key Laboratory of the Ministry of Education for the Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, China
| | - Shenglin Chen
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Fang Li
- Department of Medicine, Tibet University, Lhasa, China
| | - Zhenjun Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- *Correspondence: Zhenjun Li,
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14
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Chaplin AV, Shcherbakova VA, Pikina AP, Sokolova SR, Korzhanova M, Belova VA, Korostin DO, Rebrikov DV, Kardonsky DA, Urban AS, Zakharzhevskaya NB, Suzina NE, Podoprigora IV, Das MS, Kholopova DO, Efimov BA. Diplocloster agilis gen. nov., sp. nov. and Diplocloster modestus sp. nov., two novel anaerobic fermentative members of Lachnospiraceae isolated from human faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005222] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Three novel strains of Gram-stain-negative, obligately anaerobic, spore-forming straight or slightly curved rods with pointed ends occurring singly or in pairs were isolated from the faeces of healthy human children. The strains were characterized by mesophilic fermentative metabolism and production of acetate, ethanol and H2 as the end metabolic products. Strains ASD3451 and ASD5720T were motile, fermented lactose and raffinose, and weakly fermented maltose. Strain ASD4241T was non-motile and did not ferment the carbohydrates listed above but fermented starch. Strains ASD3451 and ASD5720T shared average nucleotide identity higher than 98.5 % with each other, while ASD4241T had only 88.5-89 % identity to them. Based on phylogenetic and chemotaxonomic analyses, we propose Diplocloster agilis gen. nov., sp. nov. (ASD5720T=JCM 34353T=VKM B-3497T) and Diplocloster modestus sp. nov. (ASD4241T=JCM 34351T=VKM B-3498T) within the family
Lachnospiraceae
.
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Affiliation(s)
- Andrei V. Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoria A. Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Alla P. Pikina
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofia R. Sokolova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Margarita Korzhanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry A. Kardonsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Anatoly S. Urban
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia B. Zakharzhevskaya
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Irina V. Podoprigora
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Milana S. Das
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Daria O. Kholopova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris A. Efimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
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15
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Zhou J, Chen P, Wang H, Liu H, Li Y, Zhang Y, Wu Y, Paek C, Sun Z, Lei J, Yin L. Cas12a variants designed for lower genome-wide off-target effect through stringent PAM recognition. Mol Ther 2022; 30:244-255. [PMID: 34687846 PMCID: PMC8753454 DOI: 10.1016/j.ymthe.2021.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/08/2021] [Accepted: 10/10/2021] [Indexed: 01/07/2023] Open
Abstract
Cas12a is an RNA-guided endonuclease that has been widely used for convenient multiplex gene editing with low off-target effects. To minimize off-targeting in gene editing, we engineered a variant of LbCas12a (termed Lb-K538R) with more stringent PAM recognition, lower off-targeting capability, and similar editing efficiency in vivo compared with LbCas12a. We also demonstrated that Lb2Cas12a from Lachnospiraceae bacterium MA2020 has extensive gene-editing activities in mammalian cells. Similar to Lb-K538R, the designed Lb2Cas12a variant (termed Lb2-K518R) not only had a more stringent PAM sequence change from YYN to TYN (Y is T or C, N is A, T, C, or G), but also displayed lower off-target effects, thereby enabling more potential target site selections with low off-targeting than the common TTTV (V is A, G, or C) PAM. To determine whether this type of mutation at the homologous position had similar effects in other Cas12a, As-K548R was evaluated. Based on the results of the genome-wide off-target test, As-K548R displayed lower off-target effects. Collectively, our findings indicate that the Cas proteins could be designed to be stringent in PAM recognition to reduce their off-target effects, which suggests a promising and practical approach for minimizing off-targets effects in genome editing.
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Affiliation(s)
- Jin Zhou
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peng Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hongjian Wang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huan Liu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yongzheng Li
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Youpeng Zhang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yankang Wu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chonil Paek
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zaiqiao Sun
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Lei
- Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China,Corresponding author: Lei Yin, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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16
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Zhu D, Wang J, Yang D, Xi J, Li J. High-Throughput Profiling of Cas12a Orthologues and Engineered Variants for Enhanced Genome Editing Activity. Int J Mol Sci 2021; 22:ijms222413301. [PMID: 34948095 PMCID: PMC8706968 DOI: 10.3390/ijms222413301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas12a (formerly Cpf1), an RNA-guided endonuclease of the Class II Type V-A CRISPR system, provides a promising tool for genome engineering. Over 10 Cas12a orthologues have been identified and employed for gene editing in human cells. However, the functional diversity among emerging Cas12a orthologues remains poorly explored. Here, we report a high-throughput comparative profiling of editing activities across 16 Cas12a orthologues in human cells by constructing genome-integrated, self-cleaving, paired crRNA–target libraries containing >40,000 guide RNAs. Three Cas12a candidates exhibited promising potential owing to their compact structures and editing efficiency comparable with those of AsCas12a and LbCas12a, which are well characterized. We generated three arginine substitution variants (3Rv) via structure-guided protein engineering: BsCas12a-3Rv (K155R/N512R/K518R), PrCas12a-3Rv (E162R/N519R/K525R), and Mb3Cas12a-3Rv (D180R/N581R/K587R). All three Cas12a variants showed enhanced editing activities and expanded targeting ranges (NTTV, NTCV, and TRTV) compared with the wild-type Cas12a effectors. The base preference analysis among the three Cas12a variants revealed that PrCas12a-3Rv shows the highest activity at target sites with canonical PAM TTTV and non-canonical PAM TTCV, while Mb3Cas12a-3Rv exhibits recognition features distinct from the others by accommodating for more nucleotide A at position −3 for PAM TATV and at position −4 for PAM ATCV. Thus, the expanded Cas12a toolbox and an improved understanding of Cas12a activities should facilitate their use in genome engineering.
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Affiliation(s)
| | | | | | - Jianzhong Xi
- Correspondence: (J.X.); (J.L.); Tel.: +86-10-6276-0698 (J.X.); +86-10-6275-6627 (J.L.)
| | - Juan Li
- Correspondence: (J.X.); (J.L.); Tel.: +86-10-6276-0698 (J.X.); +86-10-6275-6627 (J.L.)
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17
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Abstract
Theoretically, a DNA sequence-specific recognition protein that can distinguish a DNA sequence equal to or more than 16 bp could be unique to mammalian genomes. Long-sequence-specific nucleases, such as naturally occurring Homing Endonucleases and artificially engineered ZFN, TALEN, and Cas9-sgRNA, have been developed and widely applied in genome editing. In contrast to other counterparts, which recognize DNA target sites by the protein moieties themselves, Cas9 uses a single-guide RNA (sgRNA) as a template for DNA target recognition. Due to the simplicity in designing and synthesizing a sgRNA for a target site, Cas9-sgRNA has become the most current tool for genome editing. Moreover, the RNA-guided DNA recognition activity of Cas9-sgRNA is independent of both of the nuclease activities of it on the complementary strand by the HNH domain and the non-complementary strand by the RuvC domain, and HNH nuclease activity null mutant (H840A) and RuvC nuclease activity null mutant (D10A) were identified. In accompaniment with the sgRNA, Cas9, Cas9(D10A), Cas9(H840A), and Cas9(D10A, H840A) can be used to achieve double strand breakage, complementary strand breakage, non-complementary strand breakage, and no breakage on-target site, respectively. Based on such unique characteristics, many engineered enzyme activities, such as DNA methylation, histone methylation, histone acetylation, cytidine deamination, adenine deamination, and primer-directed mutation, could be introduced within or around the target site. In order to prevent off-targeting by the lasting expression of Cas9 derivatives, a lot of transient expression methods, including the direct delivery of Cas9-sgRNA riboprotein, were developed. The issue of biosafety is indispensable in in vivo applications; Cas9-sgRNA packaged into virus-like particles or extracellular vesicles have been designed and some in vivo therapeutic trials have been reported.
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Affiliation(s)
- Chin-Kai Chuang
- Animal Technology Research Center, Division of Animal Technology, Agricultural Technology Research Institute, No. 52, Kedong 2nd Rd., Zhunan Township, Miaoli County 35053, Taiwan;
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