1
|
Bolduc V, Sizov K, Brull A, Esposito E, Chen GS, Uapinyoying P, Sarathy A, Johnson KR, Bönnemann CG. Allele-specific CRISPR-Cas9 editing inactivates a single nucleotide variant associated with collagen VI muscular dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102269. [PMID: 39171142 PMCID: PMC11338111 DOI: 10.1016/j.omtn.2024.102269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 07/12/2024] [Indexed: 08/23/2024]
Abstract
The application of allele-specific gene editing tools can expand the therapeutic options for dominant genetic conditions, either via gene correction or via allelic gene inactivation in situations where haploinsufficiency is tolerated. Here, we used allele-targeted CRISPR-Cas9 guide RNAs (gRNAs) to introduce inactivating frameshifting indels at an SNV in the COL6A1 gene (c.868G>A; G290R), a variant that acts as dominant negative and that is associated with a severe form of congenital muscular dystrophy. We expressed SpCas9 along with allele-targeted gRNAs, without providing a repair template, in primary fibroblasts derived from four patients and one control subject. Amplicon deep sequencing for two gRNAs tested showed that single-nucleotide deletions accounted for the majority of indels introduced. While activity of the two gRNAs was greater at the G290R allele, both gRNAs were also active at the wild-type allele. To enhance allele selectivity, we introduced deliberate additional mismatches to one gRNA. One of these optimized gRNAs showed minimal activity at the WT allele, while generating productive edits and improving collagen VI matrix in cultured patient fibroblasts. This study strengthens the potential of gene editing to treat dominant-negative disorders, but also underscores the challenges in achieving allele selectivity with gRNAs.
Collapse
Affiliation(s)
- Véronique Bolduc
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine Sizov
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Astrid Brull
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Esposito
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grace S. Chen
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prech Uapinyoying
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- Center for Genetic Medicine Research, Children’s National Research and Innovation Campus, Children’s National Hospital, Washington, DC 20012, USA
| | - Apurva Sarathy
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kory R. Johnson
- Bioinformatics Core, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carsten G. Bönnemann
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
2
|
Lau CH, Liang QL, Zhu H. Next-generation CRISPR technology for genome, epigenome and mitochondrial editing. Transgenic Res 2024:10.1007/s11248-024-00404-x. [PMID: 39158822 DOI: 10.1007/s11248-024-00404-x] [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: 06/04/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024]
Abstract
The application of rapidly growing CRISPR toolboxes and methods has great potential to transform biomedical research. Here, we provide a snapshot of up-to-date CRISPR toolboxes, then critically discuss the promises and hurdles associated with CRISPR-based nuclear genome editing, epigenome editing, and mitochondrial editing. The technical challenges and key solutions to realize epigenome editing in vivo, in vivo base editing and prime editing, mitochondrial editing in complex tissues and animals, and CRISPR-associated transposases and integrases in targeted genomic integration of very large DNA payloads are discussed. Lastly, we discuss the latest situation of the CRISPR/Cas9 clinical trials and provide perspectives on CRISPR-based gene therapy. Apart from technical shortcomings, ethical and societal considerations for CRISPR applications in human therapeutics and research are extensively highlighted.
Collapse
Affiliation(s)
- Cia-Hin Lau
- Department of Biology, College of Science, Shantou University, Shantou, 515063, Guangdong, China
| | - Qing-Le Liang
- Department of Clinical Laboratory Medicine, Chongqing University Jiangjin Hospital, Chongqing, China
| | - Haibao Zhu
- Department of Biology, College of Science, Shantou University, Shantou, 515063, Guangdong, China.
| |
Collapse
|
3
|
Chen T, Chen G, Cao S, Tang X, Li W, Liu C, Gou H, Sun P, Mao Y, Pan Q, Zhang P, Zhu X. Dynamic Addressing Molecular Robot (DAMR): An Effective and Efficient Trial-and-Error Approach for the Analysis of Single Nucleotide Polymorphisms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402140. [PMID: 38884120 PMCID: PMC11336946 DOI: 10.1002/advs.202402140] [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: 03/14/2024] [Revised: 05/28/2024] [Indexed: 06/18/2024]
Abstract
Accurate and efficient molecular recognition plays a crucial role in the fields of molecular detection and diagnostics. Conventional trial-and-error-based molecular recognition approaches have always been challenged in distinguishing minimal differences between targets and non-targets, such as single nucleotide polymorphisms (SNPs) of oligonucleotides. To address these challenges, here, a novel concept of dynamic addressing analysis is proposed. In this concept, by dissecting the regions of the target and creating a corresponding recognizer, it is possible to eliminate the inaccuracy and inefficiency of recognition. To achieve this concept, a Dynamic Addressing Molecular Robot (DAMR), a DNA-based dynamic addressing device is developed which is capable of dynamically locating targets. DAMR is designed to first bind to the conserved region of the target while addressing the specific region dynamically until accurate recognition is achieved. DAMR has provided an approach for analyzing low-resolution targets and has been used for analyzing SNP of miR-196a2 in both cell and serum samples, which has opened new avenues for effective and efficient molecular recognition.
Collapse
Affiliation(s)
- Tianshu Chen
- Clinical Laboratory, Shanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai200127P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for PediatricsShanghai200127P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life SciencesShanghai UniversityShanghai200444P. R. China
| | - Siyu Cao
- Center for Molecular Recognition and Biosensing, School of Life SciencesShanghai UniversityShanghai200444P. R. China
| | - Xiaochen Tang
- Clinical Laboratory, Shanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai200127P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for PediatricsShanghai200127P. R. China
| | - Wenxing Li
- Department of Clinical Laboratory MedicineShanghai Tenth People's Hospital of Tongji UniversityShanghai200072P. R. China
| | - Chenbin Liu
- Department of Clinical Laboratory MedicineShanghai Tenth People's Hospital of Tongji UniversityShanghai200072P. R. China
| | - Hongquan Gou
- Department of Clinical Laboratory MedicineShanghai Tenth People's Hospital of Tongji UniversityShanghai200072P. R. China
| | - Pei Sun
- Center for Molecular Recognition and Biosensing, School of Life SciencesShanghai UniversityShanghai200444P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life SciencesShanghai UniversityShanghai200444P. R. China
| | - Qiuhui Pan
- Clinical Laboratory, Shanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai200127P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for PediatricsShanghai200127P. R. China
| | - Penghui Zhang
- Department of Laboratory MedicineShanghai Pudong New Area People's HospitalShanghai201299P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory MedicineShanghai Tenth People's Hospital of Tongji UniversityShanghai200072P. R. China
| |
Collapse
|
4
|
Kanbar K, El Darzi R, Jaalouk DE. Precision oncology revolution: CRISPR-Cas9 and PROTAC technologies unleashed. Front Genet 2024; 15:1434002. [PMID: 39144725 PMCID: PMC11321987 DOI: 10.3389/fgene.2024.1434002] [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: 05/16/2024] [Accepted: 07/02/2024] [Indexed: 08/16/2024] Open
Abstract
Cancer continues to present a substantial global health challenge, with its incidence and mortality rates persistently reflecting its significant impact. The emergence of precision oncology has provided a breakthrough in targeting oncogenic drivers previously deemed "undruggable" by conventional therapeutics and by limiting off-target cytotoxicity. Two groundbreaking technologies that have revolutionized the field of precision oncology are primarily CRISPR-Cas9 gene editing and more recently PROTAC (PROteolysis TArgeting Chimeras) targeted protein degradation technology. CRISPR-Cas9, in particular, has gained widespread recognition and acclaim due to its remarkable ability to modify DNA sequences precisely. Rather than editing the genetic code, PROTACs harness the ubiquitin proteasome degradation machinery to degrade proteins of interest selectively. Even though CRISPR-Cas9 and PROTAC technologies operate on different principles, they share a common goal of advancing precision oncology whereby both approaches have demonstrated remarkable potential in preclinical and promising data in clinical trials. CRISPR-Cas9 has demonstrated its clinical potential in this field due to its ability to modify genes directly and indirectly in a precise, efficient, reversible, adaptable, and tissue-specific manner, and its potential as a diagnostic tool. On the other hand, the ability to administer in low doses orally, broad targeting, tissue specificity, and controllability have reinforced the clinical potential of PROTAC. Thus, in the field of precision oncology, gene editing using CRISPR technology has revolutionized targeted interventions, while the emergence of PROTACs has further expanded the therapeutic landscape by enabling selective protein degradation. Rather than viewing them as mutually exclusive or competing methods in the field of precision oncology, their use is context-dependent (i.e., based on the molecular mechanisms of the disease) and they potentially could be used synergistically complementing the strengths of CRISPR and vice versa. Herein, we review the current status of CRISPR and PROTAC designs and their implications in the field of precision oncology in terms of clinical potential, clinical trial data, limitations, and compare their implications in precision clinical oncology.
Collapse
Affiliation(s)
- Karim Kanbar
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Roy El Darzi
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Diana E. Jaalouk
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| |
Collapse
|
5
|
Zhang Y, Wei J, Wang H, Wang Y. Characterization of NiCas12b for In Vivo Genome Editing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400469. [PMID: 39076074 DOI: 10.1002/advs.202400469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 07/08/2024] [Indexed: 07/31/2024]
Abstract
The RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12b system represents the third family of CRISPR-Cas systems that are harnessed for genome editing. However, only a few nucleases have demonstrated activity in human cells, and their in vivo therapeutic potential remains uncertain. In this study, a green fluorescent protein (GFP)-activation assay is conducted to screen a panel of 15 Cas12b orthologs, and four of them exhibited editing activity in mammalian cells. Particularly noteworthy is the NiCas12b derived from Nitrospira sp., which recognizes a "TTN" protospacer adjacent motif (PAM) and facilitates efficient genome editing in various cell lines. Importantly, NiCas12b also exhibits a high degree of specificity, rendering it suitable for therapeutic applications. As proof of concept, the adeno-associated virus (AAV) is employed to introduce NiCas12b to target the cholesterol regulatory gene proprotein convertase subtilisin/ kexin type 9 (Pcsk9) in the mouse liver. After 4 weeks of injections, an impressive is observed over 16.0% insertion/deletion (indel) efficiency, resulting in a significant reduction in serum cholesterol levels. NiCas12b provides a novel option for both basic research and clinical applications.
Collapse
Affiliation(s)
- Yunqian Zhang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jingjing Wei
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, 200438, China
| | - Hongyan Wang
- Obstetrics & Gynecology Hospital, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
- Children's Hospital, Fudan University, Shanghai, 201102, China
| | - Yongming Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| |
Collapse
|
6
|
Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [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: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
Collapse
Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| |
Collapse
|
7
|
Oh Y, Gwon LW, Lee HK, Hur JK, Park KH, Kim KP, Lee SH. Highly efficient and specific regulation of gene expression using enhanced CRISPR-Cas12f system. Gene Ther 2024; 31:358-365. [PMID: 38918512 DOI: 10.1038/s41434-024-00458-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
The recently developed CRISPR activator (CRISPRa) system uses a CRISPR-Cas effector-based transcriptional activator to effectively control the expression of target genes without causing DNA damage. However, existing CRISPRa systems based on Cas9/Cas12a necessitate improvement in terms of efficacy and accuracy due to limitations associated with the CRISPR-Cas module itself. To overcome these limitations and effectively and accurately regulate gene expression, we developed an efficient CRISPRa system based on the small CRISPR-Cas effector Candidatus Woesearchaeota Cas12f (CWCas12f). By engineering the CRISPR-Cas module, linking activation domains, and using various combinations of linkers and nuclear localization signal sequences, the optimized eCWCas12f-VPR system enabled effective and target-specific regulation of gene expression compared with that using the existing CRISPRa system. The eCWCas12f-VPR system developed in this study has substantial potential for controlling the transcription of endogenous genes in living organisms and serves as a foundation for future gene therapy and biological research.
Collapse
Affiliation(s)
- Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Lee Wha Gwon
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Hyomin K Lee
- Major in Medical Genetics, Department of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Junho K Hur
- Department of Genetics, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
- Department of Medicine, HY Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea
- Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Atlanta, GA, 30303, USA
| | - Kwang-Hyun Park
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Kee-Pyo Kim
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| |
Collapse
|
8
|
Wei J, Liu J, Wang Z, Yang Y, Tian Y, Wang S, Gao BQ, Gao S, Yang L, Tang J, Wang Y. Engineering of a high-fidelity Cas12a nuclease variant capable of allele-specific editing. PLoS Biol 2024; 22:e3002680. [PMID: 38865309 PMCID: PMC11168656 DOI: 10.1371/journal.pbio.3002680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
CRISPR-Cas12a, often regarded as a precise genome editor, still requires improvements in specificity. In this study, we used a GFP-activation assay to screen 14 new Cas12a nucleases for mammalian genome editing, successfully identifying 9 active ones. Notably, these Cas12a nucleases prefer pyrimidine-rich PAMs. Among these nucleases, we extensively characterized Mb4Cas12a obtained from Moraxella bovis CCUG 2133, which recognizes a YYN PAM (Y = C or T). Our biochemical analysis demonstrates that Mb4Cas12a can cleave double-strand DNA across a wide temperature range. To improve specificity, we constructed a SWISS-MODEL of Mb4Cas12a based on the FnCas12a crystal structure and identified 8 amino acids potentially forming hydrogen bonds at the target DNA-crRNA interface. By replacing these amino acids with alanine to disrupt the hydrogen bond, we tested the influence of each mutation on Mb4Cas12a specificity. Interestingly, the F370A mutation improved specificity with minimal influence on activity. Further study showed that Mb4Cas12a-F370A is capable of discriminating single-nucleotide polymorphisms. These new Cas12a orthologs and high-fidelity variants hold substantial promise for therapeutic applications.
Collapse
Affiliation(s)
- Jingjing Wei
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Jingtong Liu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Ziwen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuan Yang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Yuwen Tian
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Shengzhou Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Bao-Qing Gao
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Molecular Medicine, Children’s Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li Yang
- Center for Molecular Medicine, Children’s Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Junnan Tang
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongming Wang
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| |
Collapse
|
9
|
Rafiq MS, Shabbir MA, Raza A, Irshad S, Asghar A, Maan MK, Gondal MA, Hao H. CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance. BioDrugs 2024; 38:387-404. [PMID: 38605260 DOI: 10.1007/s40259-024-00656-3] [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] [Accepted: 03/08/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system's potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.
Collapse
Affiliation(s)
- Muhammad Shahzad Rafiq
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Ahmed Raza
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Shoaib Irshad
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Andleeb Asghar
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Kashif Maan
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Mushtaq Ahmed Gondal
- Institute of Continuing Education and Extension, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
10
|
Wu H, Sun Y, Wang Y, Luo L, Song Y. Advances in miniature CRISPR-Cas proteins and their applications in gene editing. Arch Microbiol 2024; 206:231. [PMID: 38652321 DOI: 10.1007/s00203-024-03962-0] [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: 03/07/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024]
Abstract
The CRISPR-Cas system consists of Cas proteins and single-stranded RNAs that recruit Cas proteins and specifically target the nucleic acid. Some Cas proteins can accurately cleave the target nucleic acid under the guidance of the single-stranded RNAs. Due to its exceptionally high specificity, the CRISPR-Cas system is now widely used in various fields such as gene editing, transcription regulation, and molecular diagnosis. However, the huge size of the most frequently utilized Cas proteins (Cas9, Cas12a, and Cas13, which contain 950-1,400 amino acids) can limit their applicability, especially in eukaryotic gene editing, where larger Cas proteins are difficult to deliver into the target cells. Recently discovered miniature CRISPR-Cas proteins, consisting of only 400 to 800 amino acids, offer the possibility of overcoming this limitation. This article systematically reviews the latest research progress of several miniature CRISPR-Cas proteins (Cas12f, Cas12j, Cas12k, and Cas12m) and their practical applications in the field of gene editing.
Collapse
Affiliation(s)
- Huimin Wu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yixiang Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yimai Wang
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Liqiang Luo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China.
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China.
| |
Collapse
|
11
|
Bolduc V, Sizov K, Brull A, Esposito E, Chen GS, Uapinyoying P, Sarathy A, Johnson K, Bönnemann CG. Allele-specific CRISPR/Cas9 editing inactivates a single nucleotide variant associated with collagen VI muscular dystrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586265. [PMID: 38585815 PMCID: PMC10996683 DOI: 10.1101/2024.03.22.586265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The application of allele-specific gene editing tools can expand the therapeutic options for dominant genetic conditions, either via gene correction or via allelic gene inactivation in situations where haploinsufficiency is tolerated. Here, we used allele-targeted CRISPR/Cas9 guide RNAs (gRNAs) to introduce inactivating frameshifting indels at a single nucleotide variant in the COL6A1 gene (c.868G>A; G290R), a variant that acts as dominant negative and that is associated with a severe form of congenital muscular dystrophy. We expressed spCas9 along with allele-targeted gRNAs, without providing a repair template, in primary fibroblasts derived from four patients and one control subject. Amplicon deep-sequencing for two gRNAs tested showed that single nucleotide deletions accounted for the majority of indels introduced. While activity of the two gRNAs was greater at the G290R allele, both gRNAs were also active at the wild-type allele. To enhance allele-selectivity, we introduced deliberate additional mismatches to one gRNA. One of these optimized gRNAs showed minimal activity at the WT allele, while generating productive edits and improving collagen VI matrix in cultured patient fibroblasts. This study strengthens the potential of gene editing to treat dominant-negative disorders, but also underscores the challenges in achieving allele selectivity with gRNAs.
Collapse
Affiliation(s)
- Véronique Bolduc
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Katherine Sizov
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Astrid Brull
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eric Esposito
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Grace S Chen
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Prech Uapinyoying
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Genetic Medicine Research, Children's National Research and Innovation Campus, Children's National Hospital, Washington, DC, 20012, USA
| | - Apurva Sarathy
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kory Johnson
- Bioinformatics Core, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
12
|
De Marchi D, Shaposhnikov R, Gobaa S, Pastorelli D, Batt G, Magni P, Pasotti L. Design and Model-Driven Analysis of Synthetic Circuits with the Staphylococcus aureus Dead-Cas9 (sadCas9) as a Programmable Transcriptional Regulator in Bacteria. ACS Synth Biol 2024; 13:763-780. [PMID: 38374729 DOI: 10.1021/acssynbio.3c00541] [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: 02/21/2024]
Abstract
Synthetic circuit design is crucial for engineering microbes that process environmental cues and provide biologically relevant outputs. To reliably scale-up circuit complexity, the availability of parts toolkits is central. Streptococcus pyogenes (sp)-derived CRISPR interference/dead-Cas9 (CRISPRi/spdCas9) is widely adopted for implementing programmable regulations in synthetic circuits, and alternative CRISPRi systems will further expand our toolkits of orthogonal components. Here, we showcase the potential of CRISPRi using the engineered dCas9 from Staphylococcus aureus (sadCas9), not previously used in bacterial circuits, that is attractive for its low size and high specificity. We designed a collection of ∼20 increasingly complex circuits and variants in Escherichia coli, including circuits with static function like one-/two-input logic gates (NOT, NAND), circuits with dynamic behavior like incoherent feedforward loops (iFFLs), and applied sadCas9 to fix a T7 polymerase-based cascade. Data demonstrated specific and efficient target repression (100-fold) and qualitatively successful functioning for all circuits. Other advantageous features included low sadCas9-borne cell load and orthogonality with spdCas9. However, different circuit variants showed quantitatively unexpected and previously unreported steady-state responses: the dynamic range, switch point, and slope of NOT/NAND gates changed for different output promoters, and a multiphasic behavior was observed in iFFLs, differing from the expected bell-shaped or sigmoidal curves. Model analysis explained the observed curves by complex interplays among components, due to reporter gene-borne cell load and regulator competition. Overall, CRISPRi/sadCas9 successfully expanded the available toolkit for bacterial engineering. Analysis of our circuit collection depicted the impact of generally neglected effects modulating the shape of component dose-response curves, to avoid drawing wrong conclusions on circuit functioning.
Collapse
Affiliation(s)
- Davide De Marchi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Roman Shaposhnikov
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Samy Gobaa
- Institut Pasteur, Université Paris Cité, Biomaterials and Microfluidics Core Facility, 28 Rue du Docteur Roux, 75015 Paris, France
| | - Daniele Pastorelli
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
- Institut Pasteur, Inria, Université Paris Cité, 28 rue du Docteur Roux, 75015 Paris, France
| |
Collapse
|
13
|
Chen S, Wu C, Qian C, Pang Y, Guo K, Wang T, Bai L, Qian F, Ye Z, Liu Z, Qiao Z, Wang Y, Wang R. Ultraspecific One-Pot CRISPR-Based "Green-Yellow-Red" Multiplex Detection Strategy Integrated with Portable Cartridge for Point-of-Care Diagnosis. Anal Chem 2024. [PMID: 38324761 DOI: 10.1021/acs.analchem.3c05493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Versatile, informative, sensitive, and specific nucleic acid detection plays a crucial role in point-of-care pathogen testing, genotyping, and disease monitoring. In this study, we present a novel one-pot Cas12b-based method coupled with the "Green-Yellow-Red" strategy for multiplex detection. By integrating RT-LAMP amplification and Cas12b cleavage in a single tube, the entire detection process can be completed within 1 h. Our proposed method exhibits high specificity, enabling the discrimination of single-base mutations with detection sensitivity approaching single molecule levels. Additionally, the fluorescent results can be directly observed by the naked eye or automatically analyzed using our custom-designed software Result Analyzer. To realize point-of-care detection, we developed a portable cartridge capable of both heating and fluorescence excitation. In a clinical evaluation involving 20 potentially SARS-CoV-2-infected samples, our method achieved a 100% positive detection rate when compared to standard RT-PCR. Furthermore, the identification of SARS-CoV-2 variants using our method yielded results that were consistent with the sequencing results. Notably, our proposed method demonstrates excellent transferability, allowing for the simultaneous detection of various pathogens and the identification of mutations as low as 0.5% amidst a high background interference. These findings highlight the tremendous potential of our developed method for molecular diagnostics.
Collapse
Affiliation(s)
- Shuaiwei Chen
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of life science, Fudan University, Shanghai 200438, China
| | - Cui Wu
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Chunyan Qian
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of life science, Fudan University, Shanghai 200438, China
- Clinical Laboratory, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 311100, China
| | - Yanan Pang
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Kaiming Guo
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of life science, Fudan University, Shanghai 200438, China
| | - Ting Wang
- Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Department of Hematology, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Linlin Bai
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of life science, Fudan University, Shanghai 200438, China
| | - Feng Qian
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of life science, Fudan University, Shanghai 200438, China
| | - Zunzhong Ye
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zhenping Liu
- Clinical Laboratory, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 311100, China
| | - Zhaohui Qiao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Yongming Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of life science, Fudan University, Shanghai 200438, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200438, China
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of life science, Fudan University, Shanghai 200438, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 200438, China
- International Human Phenome Institutes, Shanghai 200438, China
| |
Collapse
|
14
|
Duan Z, Zhang X, Zhang JT, Li S, Liu R, Sun J, Zhao Q, Jia N, Jia N, Zhu JK. Molecular basis for DNA cleavage by the hypercompact Cas12j-SF05. Cell Discov 2023; 9:117. [PMID: 37990011 PMCID: PMC10663539 DOI: 10.1038/s41421-023-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/07/2023] [Indexed: 11/23/2023] Open
Affiliation(s)
- Zhiqiang Duan
- Bellagen Biotechnology Co. Ltd., Jinan, Shandong, China
| | - Xi Zhang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jun-Tao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shanshan Li
- Bellagen Biotechnology Co. Ltd., Jinan, Shandong, China
| | - Ruiheng Liu
- Bellagen Biotechnology Co. Ltd., Jinan, Shandong, China
| | - Jie Sun
- Bellagen Biotechnology Co. Ltd., Jinan, Shandong, China
| | - Qingzhi Zhao
- Bellagen Biotechnology Co. Ltd., Jinan, Shandong, China
| | - Nannan Jia
- Bellagen Biotechnology Co. Ltd., Jinan, Shandong, China
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China.
- Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, Guangdong, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, China.
| |
Collapse
|
15
|
Zhao R, Luo W, Wu Y, Zhang L, Liu X, Li J, Yang Y, Wang L, Wang L, Han X, Wang Z, Zhang J, Lv K, Chen T, Xie G. Unmodificated stepless regulation of CRISPR/Cas12a multi-performance. Nucleic Acids Res 2023; 51:10795-10807. [PMID: 37757856 PMCID: PMC10602922 DOI: 10.1093/nar/gkad748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
As CRISPR technology is promoted to more fine-divided molecular biology applications, its inherent performance finds it increasingly difficult to cope with diverse needs in these different fields, and how to more accurately control the performance has become a key issue to develop CRISPR technology to a new stage. Herein, we propose a CRISPR/Cas12a regulation strategy based on the powerful programmability of nucleic acid nanotechnology. Unlike previous difficult and rigid regulation of core components Cas nuclease and crRNA, only a simple switch of different external RNA accessories is required to change the reaction kinetics or thermodynamics, thereby finely and almost steplessly regulating multi-performance of CRISPR/Cas12a including activity, speed, specificity, compatibility, programmability and sensitivity. In particular, the significantly improved specificity is expected to mark advance the accuracy of molecular detection and the safety of gene editing. In addition, this strategy was applied to regulate the delayed activation of Cas12a, overcoming the compatibility problem of the one-pot assay without any physical separation or external stimulation, and demonstrating great potential for fine-grained control of CRISPR. This simple but powerful CRISPR regulation strategy without any component modification has pioneering flexibility and versatility, and will unlock the potential for deeper applications of CRISPR technology in many finely divided fields.
Collapse
Affiliation(s)
- Rong Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - You Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Xin Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Junjie Li
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Jianhong Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Ke Lv
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Tingmei Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, PR China
| |
Collapse
|
16
|
Kocsisova Z, Coneva V. Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration. Front Genome Ed 2023; 5:1209586. [PMID: 37545761 PMCID: PMC10398581 DOI: 10.3389/fgeed.2023.1209586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.
Collapse
|
17
|
Qian Y, Wang D, Niu W, Zhao D, Li J, Liu Z, Gao X, Han Y, Lai L, Li Z. A new compact adenine base editor generated through deletion of HNH and REC2 domain of SpCas9. BMC Biol 2023; 21:155. [PMID: 37434184 PMCID: PMC10337206 DOI: 10.1186/s12915-023-01644-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/06/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Adenine base editors (ABEs) are promising therapeutic gene editing tools that can efficiently convert targeted A•T to G•C base pairs in the genome. However, the large size of commonly used ABEs based on SpCas9 hinders its delivery in vivo using certain vectors such as adeno-associated virus (AAV) during preclinical applications. Despite a number of approaches having previously been attempted to overcome that challenge, including split Cas9-derived and numerous domain-deleted versions of editors, whether base editor (BE) and prime editor (PE) systems can also allow deletion of those domains remains to be proven. In this study, we present a new small ABE (sABE) with significantly reduced size. RESULTS We discovered that ABE8e can tolerate large single deletions in the REC2 (Δ174-296) and HNH (Δ786-855) domains of SpCas9, and these deletions can be stacked together to create a new sABE. The sABE showed higher precision than the original ABE8e, with proximally shifted protospacer adjacent motif (PAM) editing windows (A3- A15), and comparable editing efficiencies to 8e-SaCas9-KKH. The sABE system efficiently generated A-G mutations at disease-relevant loci (T1214C in GAA and A494G in MFN2) in HEK293T cells and several canonical Pcsk9 splice sites in N2a cells. Moreover, the sABE enabled in vivo delivery in a single adeno-associated virus (AAV) vector with slight efficiency. Furthermore, we also successfully edited the genome of mouse embryos by microinjecting mRNA and sgRNA of sABE system into zygotes. CONCLUSIONS We have developed a substantially smaller sABE system that expands the targeting scope and offers higher precision of genome editing. Our findings suggest that the sABE system holds great therapeutic potential in preclinical applications.
Collapse
Affiliation(s)
- Yuqiang Qian
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Di Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Wenchao Niu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Ding Zhao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Jinze Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Zhiquan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Xun Gao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yang Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China.
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China.
| |
Collapse
|