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Fang M, Allen A, Luo C, Finn JD. Unlocking the potential of iPSC-derived immune cells: engineering iNK and iT cells for cutting-edge immunotherapy. Front Immunol 2024; 15:1457629. [PMID: 39281684 PMCID: PMC11392856 DOI: 10.3389/fimmu.2024.1457629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 08/14/2024] [Indexed: 09/18/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) have emerged as a revolutionary tool in cell therapies due to their ability to differentiate into various cell types, unlimited supply, and potential as off-the-shelf cell products. New advances in iPSC-derived immune cells have generated potent iNK and iT cells which showed robust killing of cancer cells in animal models and clinical trials. With the advent of advanced genome editing technologies that enable the development of highly engineered cells, here we outline 12 strategies to engineer iPSCs to overcome limitations and challenges of current cell-based immunotherapies, including safety switches, stealth edits, avoiding graft-versus-host disease (GvHD), targeting, reduced lymphodepletion, efficient differentiation, increased in vivo persistence, stemness, metabolic fitness, homing/trafficking, and overcoming suppressive tumor microenvironment and stromal cell barrier. With the development of advanced genome editing techniques, it is now possible to insert large DNA sequences into precise genomic locations without the need for DNA double strand breaks, enabling the potential for multiplexed knock out and insertion. These technological breakthroughs have made it possible to engineer complex cell therapy products at unprecedented speed and efficiency. The combination of iPSC derived iNK, iT and advanced gene editing techniques provides new opportunities and could lead to a new era for next generation of cell immunotherapies.
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Affiliation(s)
- Minggang Fang
- Cell Therapy, Tome Biosciences, Watertown, MA, United States
| | - Alexander Allen
- Cell Therapy, Tome Biosciences, Watertown, MA, United States
| | - Chong Luo
- Cell Therapy, Tome Biosciences, Watertown, MA, United States
| | - Jonathan D Finn
- Cell Therapy, Tome Biosciences, Watertown, MA, United States
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2
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Park A, Lee JY. Adenoviral Vector System: A Comprehensive Overview of Constructions, Therapeutic Applications and Host Responses. J Microbiol 2024; 62:491-509. [PMID: 39037484 DOI: 10.1007/s12275-024-00159-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024]
Abstract
Adenoviral vectors are crucial for gene therapy and vaccine development, offering a platform for gene delivery into host cells. Since the discovery of adenoviruses, first-generation vectors with limited capacity have evolved to third-generation vectors flacking viral coding sequences, balancing safety and gene-carrying capacity. The applications of adenoviral vectors for gene therapy and anti-viral treatments have expanded through the use of in vitro ligation and homologous recombination, along with gene editing advancements such as CRISPR-Cas9. Current research aims to maintain the efficacy and safety of adenoviral vectors by addressing challenges such as pre-existing immunity against adenoviral vectors and developing new adenoviral vectors from rare adenovirus types and non-human species. In summary, adenoviral vectors have great potential in gene therapy and vaccine development. Through continuous research and technological advancements, these vectors are expected to lead to the development of safer and more effective treatments.
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Affiliation(s)
- Anyeseu Park
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Jeong Yoon Lee
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.
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3
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Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol 2024:10.1038/s41587-024-02240-0. [PMID: 38773305 DOI: 10.1038/s41587-024-02240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 04/10/2024] [Indexed: 05/23/2024]
Abstract
Base editors (BEs) enable efficient, programmable installation of point mutations while avoiding the use of double-strand breaks. Simultaneous application of two or more different BEs, such as an adenine BE (which converts A·T base pairs to G·C) and a cytosine BE (which converts C·G base pairs to T·A), is not feasible because guide RNA crosstalk results in non-orthogonal editing, with all BEs modifying all target loci. Here we engineer both adenine BEs and cytosine BEs that can be orthogonally multiplexed by using RNA aptamer-coat protein systems to recruit the DNA-modifying enzymes directly to the guide RNAs. We generate four multiplexed orthogonal BE systems that enable rates of precise co-occurring edits of up to 7.1% in the same DNA strand without enrichment or selection strategies. The addition of a fluorescent enrichment strategy increases co-occurring edit rates up to 24.8% in human cells. These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 variants, function well in multiple cell types, have equivalent or reduced off-target propensities compared with their parental systems and can model disease-relevant point mutation combinations.
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Affiliation(s)
- Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Tatum S Simonson
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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4
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Kaur N, Pati PK. Retron Library Recombineering: Next Powerful Tool for Genome Editing after CRISPR/Cas. ACS Synth Biol 2024; 13:1019-1025. [PMID: 38480006 DOI: 10.1021/acssynbio.3c00667] [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: 04/20/2024]
Abstract
Retron library recombineering (RLR) is a powerful tool in the field of genome editing that exceeds the scope and specificity of the CRISPR/Cas technique. In RLR, single-stranded DNA produced in vivo by harnessing the in-built potential of bacterial retrons is used for replication-dependent genome editing. RLR introduces several genomic variations at once, resulting in pooled and barcoded variant libraries, thus permitting multiplexed applications. Retron-generated RT-DNA has already shown promise for use in genome editing. Thus, this new tool will result in fresh, intriguing, and surprising developments in molecular biology and its juncture with other disciplines of research, including medicine, agriculture, and microbiology. In this review, we discuss the current state of this brand-new tool that could eventually boost genome editing research.
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Affiliation(s)
- Navdeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
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5
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Zhang C, Yang S, Quansah E, Zhang Z, Da W, Wang B. The dCas9-based genome editing in Plasmodium yoelii. mSphere 2024; 9:e0009524. [PMID: 38411120 DOI: 10.1128/msphere.00095-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Genetic editing is a powerful tool for functional characterization of genes in various organisms. With its simplicity and specificity, the CRISPR-Cas9 technology has become a popular editing tool, which introduces site-specific DNA double-strand breaks (DSBs), and then leverages the endogenous repair pathway for DSB repair via homology-directed repair (HDR) or the more error-prone non-homologous end joining (NHEJ) pathways. However, in the Plasmodium parasites, the lack of a typical NHEJ pathway selects for DSB repair through the HDR pathway when a homologous DNA template is available. The AT-rich nature of the Plasmodium genome exacerbates this drawback by making it difficult to clone longer homologous repair DNA templates. To circumvent these challenges, we adopted the hybrid catalytically inactive Cas9 (dCas9)-microbial single-stranded annealing proteins (SSAP) editor to the Plasmodium genome. In Plasmodium yoelii, we demonstrated the use of the dCas9-SSAP, as the cleavage-free gene editor, by targeted gene deletion and gene tagging, even using shorter homologous DNA templates. This dCas9-SSAP method with a shorter DNA template, which did not require DSBs, independent of HDR and NHEJ, would be a great addition to the existing genetic toolbox and could be deployed for the functional characterization of genes in Plasmodium, contributing to improving the ability of the malaria research community in characterizing more than half of genes with unknown functions.IMPORTANCEMalaria caused by Plasmodium parasites infection remains a serious threat to human health, with an estimated 249 million malaria cases and 608,000 deaths worldwide in 2022, according to the latest report from the World Health Organization (WHO). Here, we demonstrated the use of dCas9-single-stranded annealing protein, as the cleavage-free gene editor in Plasmodium yoelii, by targeted deletion and gene tagging, even using shorter homologous DNA templates. This method with a shorter DNA template, which did not require DSBs, independent of HDR and NHEJ, showing the potential significance in greatly improving our ability to elucidate gene functions, would contribute to assisting the malaria research community in deciphering more than half of genes with unknown functions to identify new drug and vaccine targets.
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Affiliation(s)
- Chao Zhang
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Shijie Yang
- The Second Clinical Medical College, Anhui Medical University, Hefei, China
| | - Elvis Quansah
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Ziyu Zhang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Weiran Da
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Bingjie Wang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
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Chen X, Du J, Yun S, Xue C, Yao Y, Rao S. Recent advances in CRISPR-Cas9-based genome insertion technologies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102138. [PMID: 38379727 PMCID: PMC10878794 DOI: 10.1016/j.omtn.2024.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Programmable genome insertion (or knock-in) is vital for both fundamental and translational research. The continuously expanding number of CRISPR-based genome insertion strategies demonstrates the ongoing development in this field. Common methods for site-specific genome insertion rely on cellular double-strand breaks repair pathways, such as homology-directed repair, non-homologous end-joining, and microhomology-mediated end joining. Recent advancements have further expanded the toolbox of programmable genome insertion techniques, including prime editing, integrase coupled with programmable nuclease, and CRISPR-associated transposon. These tools possess their own capabilities and limitations, promoting tremendous efforts to enhance editing efficiency, broaden targeting scope and improve editing specificity. In this review, we first summarize recent advances in programmable genome insertion techniques. We then elaborate on the cons and pros of each technique to assist researchers in making informed choices when using these tools. Finally, we identify opportunities for future improvements and applications in basic research and therapeutics.
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Affiliation(s)
- Xinwen Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingjing Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shaowei Yun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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7
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Deng M, Wu Y, Lv X, Liu L, Li J, Du G, Chen J, Liu Y. Heterologous Single-Strand DNA-Annealing and Binding Protein Enhance CRISPR-Based Genome Editing Efficiency in Komagataella phaffii. ACS Synth Biol 2023; 12:3443-3453. [PMID: 37881961 DOI: 10.1021/acssynbio.3c00494] [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: 10/27/2023]
Abstract
The industrial yeast Komagataella phaffii is a highly effective platform for heterologous protein production, owing to its high protein expression and secretion capacity. Heterologous genes and proteins are involved in multiple processes, including transcription, translation, protein folding, modification, transportation, and degradation; however, engineering these proteins and genes is challenging due to inefficient genome editing techniques. We employed Pseudomonas aeruginosa phage single-stranded DNA-annealing protein (SSAP) PapRecT and P. aeruginosa single-stranded DNA-binding protein (SSB) PaSSB to introduce SSAP-SSB-based homology recombination, which facilitated K. phaffii CRISPR-based genome engineering. Specifically, a host-independent method was developed by expressing sgRNA with PapRecT-PaSSB in a single plasmid, with which only a 50 bp short homologous arm (HA) reached a 100% positive rate for CRISPR-based gene insertion, reaching 18 colony-forming units (CFU) per μg of donor DNA. Single deletion using 1000 bp HA attained 100%, reaching 68 CFUs per μg of donor DNA. Using this efficient CRISPR-based genome editing tool, we integrated three genes (INO4, GAL4-like, and PAB1) at three different loci for overexpression to realize the collaborative regulation of human-lactalbumin (α-LA) production. Specifically, we strengthened phospholipid biosynthesis to facilitate endoplasmic reticulum membrane formation and enhanced recombinant protein transcription and translation by overexpressing transcription and translation factors. The final production of α-LA in the 3 L fermentation reached 113.4 mg L-1, two times higher than that of the strain without multiple site gene editing, which is the highest reported titer in K. phaffii. The CRISPR-based genome editing method developed in this study is suitable for the synergistic multiple-site engineering of protein and biochemical biosynthesis pathways to improve the biomanufacturing efficiency.
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Affiliation(s)
- Mengting Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
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Han W, Li Z, Guo Y, He K, Li W, Xu C, Ge L, He M, Yin X, Zhou J, Li C, Yao D, Bao J, Liang H. Efficient precise integration of large DNA sequences with 3'-overhang dsDNA donors using CRISPR/Cas9. Proc Natl Acad Sci U S A 2023; 120:e2221127120. [PMID: 37216515 PMCID: PMC10235934 DOI: 10.1073/pnas.2221127120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
CRISPR/Cas9 genome-editing tools have tremendously boosted our capability of manipulating the eukaryotic genomes in biomedical research and innovative biotechnologies. However, the current approaches that allow precise integration of gene-sized large DNA fragments generally suffer from low efficiency and high cost. Herein, we developed a versatile and efficient approach, termed LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in), by utilizing specially designed 3'-overhang double-stranded DNA (odsDNA) donors harboring 50-nt homology arm. The length of the 3'-overhangs of odsDNA is specified by the five consecutive phosphorothioate modifications. Compared with existing methods, LOCK allows highly efficient targeted insertion of kilobase-sized DNA fragments into the mammalian genomes with low cost and low off-target effects, yielding >fivefold higher knock-in frequencies than conventional homologous recombination-based approaches. This newly designed LOCK approach based on homology-directed repair is a powerful tool suitable for gene-sized fragment integration that is urgently needed for genetic engineering, gene therapies, and synthetic biology.
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Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Yijun Guo
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Kaining He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Wenqing Li
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Caoling Xu
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Lishuang Ge
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Chengxu Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Jianqiang Bao
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
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9
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Li J, Zhang C, He Y, Li S, Yan L, Li Y, Zhu Z, Xia L. Plant base editing and prime editing: The current status and future perspectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:444-467. [PMID: 36479615 DOI: 10.1111/jipb.13425] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Precise replacement of an allele with an elite allele controlling an important agronomic trait in a predefined manner by gene editing technologies is highly desirable in crop improvement. Base editing and prime editing are two newly developed precision gene editing systems which can introduce the substitution of a single base and install the desired short indels to the target loci in the absence of double-strand breaks and donor repair templates, respectively. Since their discoveries, various strategies have been attempted to optimize both base editor (BE) and prime editor (PE) in order to improve the precise editing efficacy, specificity, and expand the targeting scopes. Here, we summarize the latest development of various BEs and PEs, as well as their applications in plants. Based on these progresses, we recommend the appropriate BEs and PEs for both basic plant research and crop improvement. Moreover, we propose the perspectives for further optimization of these two editors. We envision that both BEs and PEs will become the routine and customized precise gene editing tools for both plant biological research and crop improvement in the near future.
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Affiliation(s)
- Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Chen Zhang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yubing He
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Lei Yan
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yucai Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ziwei Zhu
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
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10
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Finney M, Romanowski J, Adelman ZN. Strategies to improve homology-based repair outcomes following CRISPR-based gene editing in mosquitoes: lessons in how to keep any repair disruptions local. Virol J 2022; 19:128. [PMID: 35908059 PMCID: PMC9338592 DOI: 10.1186/s12985-022-01859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
Programmable gene editing systems such as CRISPR-Cas have made mosquito genome engineering more practical and accessible, catalyzing the development of cutting-edge genetic methods of disease vector control. This progress, however, has been limited by the low efficiency of homology-directed repair (HDR)-based sequence integration at DNA double-strand breaks (DSBs) and a lack of understanding about DSB repair in mosquitoes. Innovative efforts to optimize HDR sequence integration by inhibiting non-homologous end joining or promoting HDR have been performed in mammalian systems, however many of these approaches have not been applied to mosquitoes. Here, we review some of the most relevant steps of DNA DSB repair choice and highlight promising approaches that influence this choice to enhance HDR in the context of mosquito gene editing.
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Affiliation(s)
- Micaela Finney
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Joseph Romanowski
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Zach N Adelman
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA.
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11
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Wang C, Xia Q, Zhang Q, Qu Y, Su S, Cheng JKW, Hughes NW, Cong L. CRISPR-Cas12a System With Synergistic Phage Recombination Proteins for Multiplex Precision Editing in Human Cells. Front Cell Dev Biol 2022; 9:719705. [PMID: 35774104 PMCID: PMC9237396 DOI: 10.3389/fcell.2021.719705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
The development of CRISPR-based gene-editing technologies has brought an unprecedented revolution in the field of genome engineering. Cas12a, a member of the Class 2 Type V CRISPR-associated endonuclease family distinct from Cas9, has been repurposed and developed into versatile gene-editing tools with distinct PAM recognition sites and multiplexed gene targeting capability. However, with current CRISPR/Cas12a technologies, it remains a challenge to perform efficient and precise genome editing of long sequences in mammalian cells. To address this limitation, we utilized phage recombination enzymes and developed an efficient CRISPR/Cas12a tool for multiplexed precision editing in mammalian cells. Through protein engineering, we were able to recruit phage recombination proteins to Cas12a to enhance its homology-directed repair efficiencies. Our phage-recombination-assisted Cas12a system achieved up to 3-fold improvements for kilobase-scale knock-ins in human cells without compromising the specificity of the enzyme. The performance of this system compares favorably against Cas9 references, the commonly used enzyme for gene-editing tasks, with improved specificity. Additionally, we demonstrated multi-target editing with similar improved activities thanks to the RNA-processing activity of the Cas12a system. This compact, multi-target editing tool has the potential to assist in understanding multi-gene interactions. In particular, it paves the way for a gene therapy method for human diseases that complements existing tools and is suitable for polygenic disorders and diseases requiring long-sequence corrections.
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Affiliation(s)
- Chengkun Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Qiong Xia
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Qianhe Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Yuanhao Qu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Stephen Su
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Jason K. W. Cheng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Nicholas W. Hughes
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Le Cong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
- Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, United States
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12
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Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. NATURE REVIEWS. METHODS PRIMERS 2022; 2:37. [PMID: 37073402 PMCID: PMC10108624 DOI: 10.1038/s43586-022-00130-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rosana S. Molina
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
| | - Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Amanuella A. Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Beatriz Alvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Daeje Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Haiqi Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juan Hurtado
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qiong Zhang
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge Donato García-García
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona 2514, Nuevo Mexico, C.P. 45138, Zapopan, Jalisco, Mexico
| | - Zachary J. Heins
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Patrick J. Almhjell
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad S. Khalil
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92617, USA
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13
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Validation Study to Determine the Accuracy of Widespread Promoterless EGFP Reporter at Assessing CRISPR/Cas9-Mediated Homology Directed Repair. Curr Issues Mol Biol 2022; 44:1688-1700. [PMID: 35723374 PMCID: PMC9164083 DOI: 10.3390/cimb44040116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
An accurate visual reporter system to assess homology-directed repair (HDR) is a key prerequisite for evaluating the efficiency of Cas9-mediated precise gene editing. Herein, we tested the utility of the widespread promoterless EGFP reporter to assess the efficiency of CRISPR/Cas9-mediated homologous recombination by fluorescence expression. We firstly established a promoterless EGFP reporter donor targeting the porcine GAPDH locus to study CRISPR/Cas9-mediated homologous recombination in porcine cells. Curiously, EGFP was expressed at unexpectedly high levels from the promoterless donor in porcine cells, with or without Cas9/sgRNA. Even higher EGFP expression was detected in human cells and those of other species when the porcine donor was transfected alone. Therefore, EGFP could be expressed at certain level in various cells transfected with the promoterless EGFP reporter alone, making it a low-resolution reporter for measuring Cas9-mediated HDR events. In summary, the widespread promoterless EGFP reporter could not be an ideal measurement for HDR screening and there is an urgent need to develop a more reliable, high-resolution HDR screening system to better explore strategies of increasing the efficiency of Cas9-mediated HDR in mammalian cells.
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14
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dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nat Cell Biol 2022; 24:268-278. [PMID: 35145221 PMCID: PMC8843813 DOI: 10.1038/s41556-021-00836-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022]
Abstract
Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9–SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9–SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9–SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering. Wang, Qu et al. developed a genome-editing system, utilizing catalytically inactive Cas9 fused to microbial single-strand annealing proteins, for kilobase-scale insertion in human cells without introducing DNA nicks or breaks.
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15
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Abstract
Retrons are bacterial genetic elements involved in anti-phage defense. They have the unique ability to reverse transcribe RNA into multicopy single-stranded DNA (msDNA) that remains covalently linked to their template RNA. Retrons coupled with CRISPR-Cas9 in yeast have been shown to improve the efficiency of precise genome editing via homology-directed repair (HDR). In human cells, HDR editing efficiency has been limited by challenges associated with delivering extracellular donor DNA encoding the desired mutation. In this study, we tested the ability of retrons to produce msDNA as donor DNA and facilitate HDR by tethering msDNA to guide RNA in HEK293T and K562 cells. Through heterologous reconstitution of retrons from multiple bacterial species with the CRISPR-Cas9 system, we demonstrated HDR rates of up to 11.4%. Overall, our findings represent the first step in extending retron-based precise gene editing to human cells.
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Affiliation(s)
- Bin Zhao
- Department of Biology, Stanford University, Stanford, California, USA
| | - Shi-An A. Chen
- Department of Biology, Stanford University, Stanford, California, USA
| | - Jiwoo Lee
- Department of Biology, Stanford University, Stanford, California, USA
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, California, USA
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