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Castillo SR, Simone BW, Clark KJ, Devaux P, Ekker SC. Unconstrained Precision Mitochondrial Genome Editing with αDdCBEs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593977. [PMID: 38798498 PMCID: PMC11118498 DOI: 10.1101/2024.05.13.593977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
DddA-derived cytosine base editors (DdCBEs) enable the targeted introduction of C•G-to-T•A conversions in mitochondrial DNA (mtDNA). DdCBEs are often deployed as pairs, with each arm comprised of a transcription activator-like effector (TALE), a split double-stranded DNA deaminase half, and a uracil glycosylase inhibitor. This pioneering technology has helped improve our understanding of cellular processes involving mtDNA and has paved the way for the development of models and therapies for genetic disorders caused by pathogenic mtDNA variants. Nonetheless, given the intrinsic properties of TALE proteins, several target sites in human mtDNA remain out of reach to DdCBEs and other TALE-based technologies. Specifically, due to the conventional requirement for a thymine immediately upstream of the TALE target sequences (i.e., the 5'-T constraint), over 150 loci in the human mitochondrial genome are presumed to be inaccessible to DdCBEs. Previous attempts at circumventing this constraint, either by developing monomeric DdCBEs or utilizing DNA-binding domains alternative to TALEs, have resulted in suboptimal specificity profiles with reduced therapeutic potential. Here, aiming to challenge and elucidate the relevance of the 5'-T constraint in the context of DdCBE-mediated mtDNA editing, and to expand the range of motifs that are editable by this technology, we generated αDdCBEs that contain modified TALE proteins engineered to recognize all 5' bases. Notably, 5'-T-noncompliant, canonical DdCBEs efficiently edited mtDNA at diverse loci. However, DdCBEs were frequently outperformed by αDdCBEs, which consistently displayed significant improvements in activity and specificity, regardless of the 5'-most bases of their TALE binding sites. Furthermore, we showed that αDdCBEs are compatible with DddA tox and its derivatives DddA6, and DddA11, and we validated TALE shifting with αDdCBEs as an effective approach to optimize base editing outcomes at a single target site. Overall, αDdCBEs enable efficient, specific, and unconstrained mitochondrial base editing.
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2
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Zhang D, Pries V, Boch J. Targeted C•G-to-T•A base editing with TALE-cytosine deaminases in plants. BMC Biol 2024; 22:99. [PMID: 38679734 PMCID: PMC11057107 DOI: 10.1186/s12915-024-01895-0] [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: 10/20/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND TALE-derived DddA-based cytosine base editors (TALE-DdCBEs) can perform efficient base editing of mitochondria and chloroplast genomes. They use transcription activator-like effector (TALE) arrays as programmable DNA-binding domains and a split version of the double-strand DNA cytidine deaminase (DddA) to catalyze C•G-to-T•A editing. This technology has not been optimized for use in plant cells. RESULTS To systematically investigate TALE-DdCBE architectures and editing rules, we established a β-glucuronidase reporter for transient assays in Nicotiana benthamiana. We show that TALE-DdCBEs function with distinct spacer lengths between the DNA-binding sites of their two TALE parts. Compared to canonical DddA, TALE-DdCBEs containing evolved DddA variants (DddA6 or DddA11) showed a significant improvement in editing efficiency in Nicotiana benthamiana and rice. Moreover, TALE-DdCBEs containing DddA11 have broader sequence compatibility for non-TC target editing. We have successfully regenerated rice with C•G-to-T•A conversions in their chloroplast genome, as well as N. benthamiana with C•G-to-T•A editing in the nuclear genome using TALE-DdCBE. We also found that the spontaneous assembly of split DddA halves can cause undesired editing by TALE-DdCBEs in plants. CONCLUSIONS Altogether, our results refined the targeting scope of TALE-DdCBEs and successfully applied them to target the chloroplast and nuclear genomes. Our study expands the base editing toolbox in plants and further defines parameters to optimize TALE-DdCBEs for high-fidelity crop improvement.
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Affiliation(s)
- Dingbo Zhang
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Vanessa Pries
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Jens Boch
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany.
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Fauser F, Kadam BN, Arangundy-Franklin S, Davis JE, Vaidya V, Schmidt NJ, Lew G, Xia DF, Mureli R, Ng C, Zhou Y, Scarlott NA, Eshleman J, Bendaña YR, Shivak DA, Reik A, Li P, Davis GD, Miller JC. Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells. Nat Commun 2024; 15:1181. [PMID: 38360922 PMCID: PMC10869815 DOI: 10.1038/s41467-024-45100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.
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Affiliation(s)
| | | | | | | | | | | | - Garrett Lew
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | - Danny F Xia
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | - Colman Ng
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | | | | | | | | | | | - Patrick Li
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
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Lin JY, Liu YC, Tseng YH, Chan MT, Chang CC. TALE-based organellar genome editing and gene expression in plants. PLANT CELL REPORTS 2024; 43:61. [PMID: 38336900 DOI: 10.1007/s00299-024-03150-w] [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: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
KEY MESSAGE TALE-based editors provide an alternative way to engineer the organellar genomes in plants. We update and discuss the most recent developments of TALE-based organellar genome editing in plants. Gene editing tools have been widely used to modify the nuclear genomes of plants for various basic research and biotechnological applications. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 editing platform is the most commonly used technique because of its ease of use, fast speed, and low cost; however, it encounters difficulty when being delivered to plant organelles for gene editing. In contrast, protein-based editing technologies, such as transcription activator-like effector (TALE)-based tools, could be easily delivered, expressed, and targeted to organelles in plants via Agrobacteria-mediated nuclear transformation. Therefore, TALE-based editors provide an alternative way to engineer the organellar genomes in plants since the conventional chloroplast transformation method encounters technical challenges and is limited to certain species, and the direct transformation of mitochondria in higher plants is not yet possible. In this review, we update and discuss the most recent developments of TALE-based organellar genome editing in plants.
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Affiliation(s)
- Jer-Young Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yu-Chang Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
| | - Yan-Hao Tseng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan.
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Ching-Chun Chang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
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5
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Cho SI, Lim K, Hong S, Lee J, Kim A, Lim CJ, Ryou S, Lee JM, Mok YG, Chung E, Kim S, Han S, Cho SM, Kim J, Kim EK, Nam KH, Oh Y, Choi M, An TH, Oh KJ, Lee S, Lee H, Kim JS. Engineering TALE-linked deaminases to facilitate precision adenine base editing in mitochondrial DNA. Cell 2024; 187:95-109.e26. [PMID: 38181745 DOI: 10.1016/j.cell.2023.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
DddA-derived cytosine base editors (DdCBEs) and transcription activator-like effector (TALE)-linked deaminases (TALEDs) catalyze targeted base editing of mitochondrial DNA (mtDNA) in eukaryotic cells, a method useful for modeling of mitochondrial genetic disorders and developing novel therapeutic modalities. Here, we report that A-to-G-editing TALEDs but not C-to-T-editing DdCBEs induce tens of thousands of transcriptome-wide off-target edits in human cells. To avoid these unwanted RNA edits, we engineered the substrate-binding site in TadA8e, the deoxy-adenine deaminase in TALEDs, and created TALED variants with fine-tuned deaminase activity. Our engineered TALED variants not only reduced RNA off-target edits by >99% but also minimized off-target mtDNA mutations and bystander edits at a target site. Unlike wild-type versions, our TALED variants were not cytotoxic and did not cause developmental arrest of mouse embryos. As a result, we obtained mice with pathogenic mtDNA mutations, associated with Leigh syndrome, which showed reduced heart rates.
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Affiliation(s)
- Sung-Ik Cho
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kayeong Lim
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Seongho Hong
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
| | - Jaesuk Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Annie Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | | | | | - Ji Min Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Geun Mok
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; GreenGene Inc., Seoul 08790, Republic of Korea
| | - Eugene Chung
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Sanghun Kim
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Seunghun Han
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sang-Mi Cho
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jieun Kim
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea
| | - Eun-Kyoung Kim
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Yeji Oh
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Minkyung Choi
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Tae Hyeon An
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seonghyun Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea; Edgene, Inc., Seoul 08790, Republic of Korea; Department of MetaBioHealth, Sungkyunkwan University (SKKU), Suwon, Republic of Korea; Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon, Republic of Korea.
| | - Hyunji Lee
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Medicine, Korea University College of Medicine, Seoul 02708, Republic of Korea.
| | - Jin-Soo Kim
- Edgene, Inc., Seoul 08790, Republic of Korea; NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore.
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6
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Lim K. Mitochondrial genome editing: strategies, challenges, and applications. BMB Rep 2024; 57:19-29. [PMID: 38178652 PMCID: PMC10828433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
Mitochondrial DNA (mtDNA), a multicopy genome found in mitochondria, is crucial for oxidative phosphorylation. Mutations in mtDNA can lead to severe mitochondrial dysfunction in tissues and organs with high energy demand. MtDNA mutations are closely associated with mitochondrial and age-related disease. To better understand the functional role of mtDNA and work toward developing therapeutics, it is essential to advance technology that is capable of manipulating the mitochondrial genome. This review discusses ongoing efforts in mitochondrial genome editing with mtDNA nucleases and base editors, including the tools, delivery strategies, and applications. Future advances in mitochondrial genome editing to address challenges regarding their efficiency and specificity can achieve the promise of therapeutic genome editing. [BMB Reports 2024; 57(1): 19-29].
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Affiliation(s)
- Kayeong Lim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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7
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Gao Y, Guo L, Wang F, Wang Y, Li P, Zhang D. Development of mitochondrial gene-editing strategies and their potential applications in mitochondrial hereditary diseases: a review. Cytotherapy 2024; 26:11-24. [PMID: 37930294 DOI: 10.1016/j.jcyt.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
Mitochondrial DNA (mtDNA) is a critical genome contained within the mitochondria of eukaryotic cells, with many copies present in each mitochondrion. Mutations in mtDNA often are inherited and can lead to severe health problems, including various inherited diseases and premature aging. The lack of efficient repair mechanisms and the susceptibility of mtDNA to damage exacerbate the threat to human health. Heteroplasmy, the presence of different mtDNA genotypes within a single cell, increases the complexity of these diseases and requires an effective editing method for correction. Recently, gene-editing techniques, including programmable nucleases such as restriction endonuclease, zinc finger nuclease, transcription activator-like effector nuclease, clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated 9 and base editors, have provided new tools for editing mtDNA in mammalian cells. Base editors are particularly promising because of their high efficiency and precision in correcting mtDNA mutations. In this review, we discuss the application of these techniques in mitochondrial gene editing and their limitations. We also explore the potential of base editors for mtDNA modification and discuss the opportunities and challenges associated with their application in mitochondrial gene editing. In conclusion, this review highlights the advancements, limitations and opportunities in current mitochondrial gene-editing technologies and approaches. Our insights aim to stimulate the development of new editing strategies that can ultimately alleviate the adverse effects of mitochondrial hereditary diseases.
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Affiliation(s)
- Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Linlin Guo
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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8
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Kim JS, Chen J. Base editing of organellar DNA with programmable deaminases. Nat Rev Mol Cell Biol 2024; 25:34-45. [PMID: 37794167 DOI: 10.1038/s41580-023-00663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
Abstract
Mitochondria and chloroplasts are organelles that include their own genomes, which encode key genes for ATP production and carbon dioxide fixation, respectively. Mutations in mitochondrial DNA can cause diverse genetic disorders and are also linked to ageing and age-related diseases, including cancer. Targeted editing of organellar DNA should be useful for studying organellar genes and developing novel therapeutics, but it has been hindered by lack of efficient tools in living cells. Recently, CRISPR-free, protein-only base editors, such as double-stranded DNA deaminase toxin A-derived cytosine base editors (DdCBEs) and adenine base editors (ABEs), have been developed, which enable targeted organellar DNA editing in human cell lines, animals and plants. In this Review, we present programmable deaminases developed for base editing of organellar DNA in vitro and discuss mitochondrial DNA editing in animals, and plastid genome (plastome) editing in plants. We also discuss precision and efficiency limitations of these tools and propose improvements for therapeutic, agricultural and environmental applications.
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Affiliation(s)
- Jin-Soo Kim
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore.
- Edgene, Seoul, South Korea.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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9
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Zhang M, Zhu Z, Xun G, Zhao H. To Cut or not to Cut: Next-generation Genome Editors for Precision Genome Engineering. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023; 28:100489. [PMID: 37593347 PMCID: PMC10430874 DOI: 10.1016/j.cobme.2023.100489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Since the original report of repurposing the CRISPR/Cas9 system for genome engineering, the past decade has witnessed profound improvement in our ability to efficiently manipulate the mammalian genome. However, significant challenges lie ahead that hinder the translation of CRISPR-based gene editing technologies into safe and effective therapeutics. The CRISPR systems often have a limited target scope due to PAM restrictions, and the off-target activity also poses serious risks for therapeutic applications. Moreover, the first-generation genome editors typically achieve desired genomic modifications by inducing double-strand breaks (DSBs) at target site(s). Despite being highly efficient, this "cut and fix" strategy is less favorable in clinical settings due to drawbacks associated with the nuclease-induced DSBs. In this review, we focus on recent advances that help address these challenges, including the engineering and discovery of novel CRISPR/Cas systems with improved functionalities and the development of DSB-free genome editors.
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Affiliation(s)
- Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhixin Zhu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Guanhua Xun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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10
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Yin L, Shi K, Aihara H. Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Nat Struct Mol Biol 2023; 30:1153-1159. [PMID: 37460895 PMCID: PMC10442228 DOI: 10.1038/s41594-023-01034-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T-G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.
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Affiliation(s)
- Lulu Yin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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11
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Liang Y, Chen F, Wang K, Lai L. Base editors: development and applications in biomedicine. Front Med 2023; 17:359-387. [PMID: 37434066 DOI: 10.1007/s11684-023-1013-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/19/2023] [Indexed: 07/13/2023]
Abstract
Base editor (BE) is a gene-editing tool developed by combining the CRISPR/Cas system with an individual deaminase, enabling precise single-base substitution in DNA or RNA without generating a DNA double-strand break (DSB) or requiring donor DNA templates in living cells. Base editors offer more precise and secure genome-editing effects than other conventional artificial nuclease systems, such as CRISPR/Cas9, as the DSB induced by Cas9 will cause severe damage to the genome. Thus, base editors have important applications in the field of biomedicine, including gene function investigation, directed protein evolution, genetic lineage tracing, disease modeling, and gene therapy. Since the development of the two main base editors, cytosine base editors (CBEs) and adenine base editors (ABEs), scientists have developed more than 100 optimized base editors with improved editing efficiency, precision, specificity, targeting scope, and capacity to be delivered in vivo, greatly enhancing their application potential in biomedicine. Here, we review the recent development of base editors, summarize their applications in the biomedical field, and discuss future perspectives and challenges for therapeutic applications.
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Affiliation(s)
- Yanhui Liang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
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12
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Kar B, Castillo SR, Sabharwal A, Clark KJ, Ekker SC. Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities. Int J Mol Sci 2023; 24:ijms24065798. [PMID: 36982871 PMCID: PMC10056815 DOI: 10.3390/ijms24065798] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are critical organelles that form networks within our cells, generate energy dynamically, contribute to diverse cell and organ function, and produce a variety of critical signaling molecules, such as cortisol. This intracellular microbiome can differ between cells, tissues, and organs. Mitochondria can change with disease, age, and in response to the environment. Single nucleotide variants in the circular genomes of human mitochondrial DNA are associated with many different life-threatening diseases. Mitochondrial DNA base editing tools have established novel disease models and represent a new possibility toward personalized gene therapies for the treatment of mtDNA-based disorders.
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Affiliation(s)
- Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Santiago R Castillo
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, MN 55905, USA
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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13
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Papaioannou NY, Patsali P, Naiisseh B, Papasavva PL, Koniali L, Kurita R, Nakamura Y, Christou S, Sitarou M, Mussolino C, Cathomen T, Kleanthous M, Lederer CW. High-efficiency editing in hematopoietic stem cells and the HUDEP-2 cell line based on in vitro mRNA synthesis. Front Genome Ed 2023; 5:1141618. [PMID: 36969374 PMCID: PMC10030607 DOI: 10.3389/fgeed.2023.1141618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Introduction: Genome editing tools, such as CRISPR/Cas, TALE nucleases and, more recently, double-strand-break-independent editors, have been successfully used for gene therapy and reverse genetics. Among various challenges in the field, tolerable and efficient delivery of editors to target cells and sites, as well as independence from commercially available tools for flexibility and fast adoption of new editing technology are the most pressing. For many hematopoietic research applications, primary CD34+ cells and the human umbilical cord-derived progenitor erythroid 2 (HUDEP-2) cell line are highly informative substrates and readily accessible for in vitro manipulation. Moreover, ex vivo editing of CD34+ cells has immediate therapeutic relevance. Both cell types are sensitive to standard transfection procedures and reagents, such as lipofection with plasmid DNA, calling for more suitable methodology in order to achieve high efficiency and tolerability of editing with editors of choice. These challenges can be addressed by RNA delivery, either as a mixture of guide RNA and mRNA for CRISRP/Cas-based systems or as a mixture of mRNAs for TALENs. Compared to ribonucleoproteins or proteins, RNA as vector creates flexibility by removing dependence on commercial availability or laborious in-house preparations of novel editor proteins. Compared to DNA, RNA is less toxic and by obviating nuclear transcription and export of mRNA offers faster kinetics and higher editing efficiencies. Methods: Here, we detail an in vitro transcription protocol based on plasmid DNA templates with the addition of Anti-Reverse Cap Analog (ARCA) using T7 RNA polymerase, and poly (A) tailing using poly (A) polymerase, combined with nucleofection of HUDEP-2 and patient-derived CD34+ cells. Our protocol for RNA-based delivery employs widely available reagents and equipment and can easily be adopted for universal in vitro delivery of genome editing tools. Results and Discussion: Drawing on a common use case, we employ the protocol to target a β-globin mutation and to reactivate γ-globin expression as two potential therapies for β-hemoglobinopathies, followed by erythroid differentiation and functional analyses. Our protocol allows high editing efficiencies and unimpaired cell viability and differentiation, with scalability, suitability for functional assessment of editing outcomes and high flexibility in the application to different editors.
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Affiliation(s)
- Nikoletta Y. Papaioannou
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Basma Naiisseh
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Panayiota L. Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lola Koniali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Soteroula Christou
- Thalassaemia Centre, State Health Services Organisation of Cyprus, Nicosia, Cyprus
| | - Maria Sitarou
- Thalassaemia Centre, State Health Services Organisation of Cyprus, Larnaca, Cyprus
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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14
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Tolle I, Tiranti V, Prigione A. Modeling mitochondrial DNA diseases: from base editing to pluripotent stem-cell-derived organoids. EMBO Rep 2023; 24:e55678. [PMID: 36876467 PMCID: PMC10074100 DOI: 10.15252/embr.202255678] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/12/2023] [Accepted: 02/15/2023] [Indexed: 03/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) diseases are multi-systemic disorders caused by mutations affecting a fraction or the entirety of mtDNA copies. Currently, there are no approved therapies for the majority of mtDNA diseases. Challenges associated with engineering mtDNA have in fact hindered the study of mtDNA defects. Despite these difficulties, it has been possible to develop valuable cellular and animal models of mtDNA diseases. Here, we describe recent advances in base editing of mtDNA and the generation of three-dimensional organoids from patient-derived human-induced pluripotent stem cells (iPSCs). Together with already available modeling tools, the combination of these novel technologies could allow determining the impact of specific mtDNA mutations in distinct human cell types and might help uncover how mtDNA mutation load segregates during tissue organization. iPSC-derived organoids could also represent a platform for the identification of treatment strategies and for probing the in vitro effectiveness of mtDNA gene therapies. These studies have the potential to increase our mechanistic understanding of mtDNA diseases and may open the way to highly needed and personalized therapeutic interventions.
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Affiliation(s)
- Isabella Tolle
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Valeria Tiranti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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15
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Chou CW, Hsu YC. Current development of patient-specific induced pluripotent stem cells harbouring mitochondrial gene mutations and their applications in the treatment of sensorineural hearing loss. Hear Res 2023; 429:108689. [PMID: 36649664 DOI: 10.1016/j.heares.2023.108689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Of all the human body's sensory systems, the auditory system is perhaps its most intricate. Hearing loss can result from even modest damage or cell death in the inner ear, and is the most common form of sensory loss. Human hearing is made possible by the sensory epithelium, the lateral wall, and auditory nerves. The most prominent functional cells in the sensory epithelium are outer hair cells (OHCs), inner hair cells (IHCs), and supporting cells. Different sound frequencies are processed by OHCs and IHCs in different cochlear regions, with those in the apex responsible for low frequencies and those in the basal region responsible for high frequencies. Hair cells can be damaged or destroyed by loud noise, aging process, genetic mutations, ototoxicity, infection, and illness. As such, they are a primary target for treating sensorineural hearing loss. Other areas known to affect hearing include spiral ganglion neurons (SGNs) in the auditory nerve. Age-related degradation of HCs and SGNs can also cause hearing loss. The aim of this review is to introduce the roles of mitochondria in human auditory system and the inner ear's main cell types and cellular functions, before going on to detail the likely health benefits of iPSC technology. We posit that patient-specific iPSCs with mitochondrial gene mutations will be an important aspect of regenerative medicine and will lead to significant progress in the treatment of SNHL.
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Affiliation(s)
- Chao-Wen Chou
- Department of Audiology and Speech-Language Pathology, Mackay Medical College, New Taipei City, Taiwan
| | - Yi-Chao Hsu
- Department of Audiology and Speech-Language Pathology, Mackay Medical College, New Taipei City, Taiwan; Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
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16
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Mok YG, Hong S, Bae SJ, Cho SI, Kim JS. Targeted A-to-G base editing of chloroplast DNA in plants. NATURE PLANTS 2022; 8:1378-1384. [PMID: 36456803 PMCID: PMC9788985 DOI: 10.1038/s41477-022-01279-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
Chloroplast DNA (cpDNA) encodes up to 315 (typically, 120-130) genes1, including those for essential components in photosystems I and II and the large subunit of RuBisCo, which catalyses CO2 fixation in plants. Targeted mutagenesis in cpDNA will be broadly useful for studying the functions of these genes in molecular detail and for developing crops and other plants with desired traits. Unfortunately, CRISPR-Cas9 and CRISPR-derived base editors, which enable targeted genetic modifications in nuclear DNA, are not suitable for organellar DNA editing2, owing to the difficulty of delivering guide RNA into organelles. CRISPR-free, protein-only base editors (including DddA-derived cytosine base editors3-8 and zinc finger deaminases9), originally developed for mitochondrial DNA editing in mammalian cells, can be used for C-to-T, rather than A-to-G, editing in cpDNA10-12. Here we show that heritable homoplasmic A-to-G edits can be induced in cpDNA, leading to phenotypic changes, using transcription activator-like effector-linked deaminases13.
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Affiliation(s)
- Young Geun Mok
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- GreenGene Inc., Seoul, Republic of Korea
| | - Sunghyun Hong
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- GreenGene Inc., Seoul, Republic of Korea
| | - Su-Ji Bae
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Sung-Ik Cho
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea.
- GreenGene Inc., Seoul, Republic of Korea.
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