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Meng X, Mao H, Wan M, Lu L, Chen Z, Zhang L. Mitochondrial homeostasis in odontoblast: Physiology, pathogenesis and targeting strategies. Life Sci 2024:122797. [PMID: 38917871 DOI: 10.1016/j.lfs.2024.122797] [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: 02/17/2024] [Revised: 04/15/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024]
Abstract
Caries and pulpitis remain a major global disease burden and affect the quality of life of patients. Odontoblasts are key players in the progression of caries and pulpitis, not only secreting and mineralizing to form dentin, but also acting as a wall of defense to initiate immune defenses. Mitochondrion is an information processor for numerous cellular activities, and dysregulation of mitochondrion homeostasis not only affects cellular metabolism but also triggers a wide range of diseases. Elucidating mitochondrial homeostasis in odontoblasts can help deepen scholars' understanding of odontoblast-associated diseases. Articles on mitochondrial homeostasis in odontoblasts were evaluated for information pertinent to include in this narrative review. This narrative review focused on understanding the complex interplay between mitochondrial homeostasis in odontoblasts under physiological and pathological conditions. Furthermore, mitochondria-centered therapeutic strategies (including mitochondrial base editing, targeting platforms, and mitochondrial transplantation) were emphasized by resolving key genes that regulate mitochondrial function. Mitochondria are involved in odontoblast differentiation and function, and act as mitochondrial danger-associated molecular patterns (mtDAMPs) to mediate odontoblast pathological progression. Novel mitochondria-centered therapeutic strategies are particularly attractive as emerging therapeutic approaches for the maintenance of mitochondrial homeostasis. It is expected to probe key events of odontoblast differentiation and advance the clinical resolution of dentin formation and mineralization disorders and odontoblast-related diseases.
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Affiliation(s)
- Xiang Meng
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China.
| | - Hanqing Mao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China.
| | - Minting Wan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China.
| | - Linxin Lu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China.
| | - Zhi Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; Department of Endodontics, School and Hospital of Stomatology, Wuhan University, HongShan District, LuoYu Road No. 237, Wuhan 430079, China.
| | - Lu Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; Department of Endodontics, School and Hospital of Stomatology, Wuhan University, HongShan District, LuoYu Road No. 237, Wuhan 430079, China.
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2
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Feola M, Pulicani S, Tkach D, Boyne A, Hong R, Mayer L, Duclert A, Duchateau P, Juillerat A. Comprehensive analysis of the editing window of C-to-T TALE base editors. Sci Rep 2024; 14:12870. [PMID: 38834632 PMCID: PMC11150444 DOI: 10.1038/s41598-024-63203-8] [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: 12/14/2023] [Accepted: 05/27/2024] [Indexed: 06/06/2024] Open
Abstract
One of the most recent advances in the genome editing field has been the addition of "TALE Base Editors", an innovative platform for cell therapy that relies on the deamination of cytidines within double strand DNA, leading to the formation of an uracil (U) intermediate. These molecular tools are fusions of transcription activator-like effector domains (TALE) for specific DNA sequence binding, split-DddA deaminase halves that will, upon catalytic domain reconstitution, initiate the conversion of a cytosine (C) to a thymine (T), and an uracil glycosylase inhibitor (UGI). We developed a high throughput screening strategy capable to probe key editing parameters in a precisely defined genomic context in cellulo, excluding or minimizing biases arising from different microenvironmental and/or epigenetic contexts. Here we aimed to further explore how target composition and TALEB architecture will impact the editing outcomes. We demonstrated how the nature of the linker between TALE array and split DddAtox head allows us to fine tune the editing window, also controlling possible bystander activity. Furthermore, we showed that both the TALEB architecture and spacer length separating the two TALE DNA binding regions impact the target TC editing dependence by the surrounding bases, leading to more restrictive or permissive editing profiles.
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Hu J, Sun Y, Li B, Liu Z, Wang Z, Gao Q, Guo M, Liu G, Zhao KT, Gao C. Strand-preferred base editing of organellar and nuclear genomes using CyDENT. Nat Biotechnol 2024; 42:936-945. [PMID: 37640945 DOI: 10.1038/s41587-023-01910-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Transcription-activator-like effector (TALE)-based tools for base editing of nuclear and organellar DNA rely on double-stranded DNA deaminases, which edit substrate bases on both strands of DNA, reducing editing precision. Here, we present CyDENT base editing, a CRISPR-free, strand-selective, modular base editor. CyDENT comprises a pair of TALEs fused with a FokI nickase, a single-strand-specific cytidine deaminase and an exonuclease to generate a single-stranded DNA substrate for deamination. We demonstrate effective base editing in nuclear, mitochondrial and chloroplast genomes. At certain mitochondrial sites, we show editing efficiencies of 14% and strand specificity of 95%. Furthermore, by exchanging the CyDENT deaminase with one that prefers editing GC motifs, we demonstrate up to 20% mitochondrial base editing at sites that are otherwise inaccessible to editing by other methods. The modular nature of CyDENT enables a suite of bespoke base editors for various applications.
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Affiliation(s)
- Jiacheng Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | - Guanwen Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | | | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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4
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Moraes CT. Tools for editing the mammalian mitochondrial genome. Hum Mol Genet 2024; 33:R92-R99. [PMID: 38779768 DOI: 10.1093/hmg/ddae037] [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: 01/17/2024] [Revised: 02/28/2024] [Accepted: 03/03/2024] [Indexed: 05/25/2024] Open
Abstract
The manipulation of animal mitochondrial genomes has long been a challenge due to the lack of an effective transformation method. With the discovery of specific gene editing enzymes, designed to target pathogenic mitochondrial DNA mutations (often heteroplasmic), the selective removal or modification of mutant variants has become a reality. Because mitochondria cannot efficiently import RNAs, CRISPR has not been the first choice for editing mitochondrial genes. However, the last few years witnessed an explosion in novel and optimized non-CRISPR approaches to promote double-strand breaks or base-edit of mtDNA in vivo. Engineered forms of specific nucleases and cytidine/adenine deaminases form the basis for these techniques. I will review the newest developments that constitute the current toolbox for animal mtDNA gene editing in vivo, bringing these approaches not only to the exploration of mitochondrial function, but also closer to clinical use.
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Affiliation(s)
- Carlos T Moraes
- Miller School of Medicine, University of Miami, 1600 NW 10th Ave, room 7044, Miami, FL 33136, United States
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Arimura SI, Nakazato I. Genome Editing of Plant Mitochondrial and Chloroplast Genomes. PLANT & CELL PHYSIOLOGY 2024; 65:477-483. [PMID: 38113380 PMCID: PMC11094758 DOI: 10.1093/pcp/pcad162] [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: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Plastids (including chloroplasts) and mitochondria are remnants of endosymbiotic bacteria, yet they maintain their own genomes, which encode vital components for photosynthesis and respiration, respectively. Organellar genomes have distinctive features, such as being present as multicopies, being mostly inherited maternally, having characteristic genomic structures and undergoing frequent homologous recombination. To date, it has proven to be challenging to modify these genomes. For example, while CRISPR/Cas9 is a widely used system for editing nuclear genes, it has not yet been successfully applied to organellar genomes. Recently, however, precise gene-editing technologies have been successfully applied to organellar genomes. Protein-based enzymes, especially transcription activator-like effector nucleases (TALENs) and artificial enzymes utilizing DNA-binding domains of TALENs (TALEs), have been successfully used to modify these genomes by harnessing organellar-targeting signals. This short review introduces and discusses the use of targeted nucleases and base editors in organellar genomes, their effects and their potential applications in plant science and breeding.
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Affiliation(s)
- Shin-ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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Lam BL. Leber hereditary optic neuropathy gene therapy. Curr Opin Ophthalmol 2024; 35:244-251. [PMID: 38117686 PMCID: PMC10959684 DOI: 10.1097/icu.0000000000001028] [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] [Indexed: 12/22/2023]
Abstract
PURPOSE OF REVIEW To discuss relevant clinical outcomes, challenges, and future opportunities of gene therapy in Leber hereditary optic neuropathy (LHON). RECENT FINDINGS Results of G11778A LHON Phase 3 randomized clinical trials with unilateral intravitreal rAAV2/2-ND4 allotopic gene therapy show good safety and unexpected bilateral partial improvements of BCVA (best-corrected visual acuity) with mean logMAR BCVA improvements of up to near ∼0.3 logMAR (3 lines) in the treated eyes and ∼0.25 logMAR (2.5 lines) in the sham-treated or placebo-treated fellow eyes. Final mean BCVA levels after gene therapy were in the range of ∼1.3 logMAR (20/400) bilaterally. SUMMARY Bilateral partial improvement with unilateral LHON gene therapy was unanticipated and may be due to treatment efficacy, natural history, learning effect, and other mediators. The overall efficacy is limited given the final BCVA levels. The sequential progressive visual loss and varied occurrence of spontaneous partial improvement in LHON confound trial results. Future clinical trials with randomization of patients to a group not receiving gene therapy in either eye would help to assess treatment effect. Promising future LHON gene therapy strategies include mitochondrially-targeted-sequence adeno-associated virus ('MTS-AAV') for direct delivery of the wild-type mitochondrial DNA into the mitochondria and CRISPR-free, RNA-free mitochondrial base editing systems. Signs of anatomical optic nerve damage and objective retinal ganglion cell dysfunction are evident in the asymptomatic eyes of LHON patients experiencing unilateral visual loss, indicating the therapeutic window is narrowing before onset of visual symptoms. Future treatment strategies utilizing mitochondrial base editing in LHON carriers without optic neuropathy holds the promise of a more advantageous approach to achieve optimal visual outcome by reducing disease penetrance and mitigating retinal ganglion cell loss when optic neuropathy develops.
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Affiliation(s)
- Byron L Lam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
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7
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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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Qiu J, Wu H, Xie Q, Zhou Y, Gao Y, Liu J, Jiang X, Suo L, Kuang Y. Harnessing accurate mitochondrial DNA base editing mediated by DdCBEs in a predictable manner. Front Bioeng Biotechnol 2024; 12:1372211. [PMID: 38655388 PMCID: PMC11035818 DOI: 10.3389/fbioe.2024.1372211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction: Mitochondrial diseases caused by mtDNA have no effective cures. Recently developed DddA-derived cytosine base editors (DdCBEs) have potential therapeutic implications in rescuing the mtDNA mutations. However, the performance of DdCBEs relies on designing different targets or improving combinations of split-DddA halves and orientations, lacking knowledge of predicting the results before its application. Methods: A series of DdCBE pairs for wide ranges of aC or tC targets was constructed, and transfected into Neuro-2a cells. The mutation rate of targets was compared to figure out the potential editing rules. Results: It is found that DdCBEs mediated mtDNA editing is predictable: 1) aC targets have a concentrated editing window for mtDNA editing in comparison with tC targets, which at 5'C8-11 (G1333) and 5'C10-13 (G1397) for aC target, while 5'C4-13 (G1333) and 5'C5-14 (G1397) for tC target with 16bp spacer. 2) G1333 mediated C>T conversion at aC targets in DddA-half-specific manner, while G1333 and G1397 mediated C>T conversion are DddA-half-prefer separately for tC and aC targets. 3) The nucleotide adjacent to the 3' end of aC motif affects mtDNA editing. Finally, by the guidance of these rules, a cell model harboring a pathogenic mtDNA mutation was constructed with high efficiency and no bystander effects. Discussion: In summary, this discovery helps us conceive the optimal strategy for accurate mtDNA editing, avoiding time- and effort-consuming optimized screening jobs.
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Affiliation(s)
| | | | | | | | | | | | | | - Lun Suo
- Department of Assisted Reproduction, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanping Kuang
- Department of Assisted Reproduction, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Vaisvila R, Johnson SR, Yan B, Dai N, Bourkia BM, Chen M, Corrêa IR, Yigit E, Sun Z. Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme. Mol Cell 2024; 84:854-866.e7. [PMID: 38402612 DOI: 10.1016/j.molcel.2024.01.027] [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: 07/06/2023] [Revised: 11/02/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Deaminases have important uses in modification detection and genome editing. However, the range of applications is limited by the small number of characterized enzymes. To expand the toolkit of deaminases, we developed an in vitro approach that bypasses a major hurdle with their toxicity in cells. We assayed 175 putative cytosine deaminases on a variety of substrates and found a broad range of activity on double- and single-stranded DNA in various sequence contexts, including CpG-specific deaminases and enzymes without sequence preference. We also characterized enzyme selectivity across six DNA modifications and reported enzymes that do not deaminate modified cytosines. The detailed analysis of diverse deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed SEM-seq, a non-destructive single-enzyme methylation sequencing method using a modification-sensitive double-stranded DNA deaminase. The streamlined protocol enables accurate, base-resolution methylome mapping of scarce biological material, including cell-free DNA and 10 pg input DNA.
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Affiliation(s)
| | - Sean R Johnson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Bo Yan
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Nan Dai
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Billal M Bourkia
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Minyong Chen
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Ivan R Corrêa
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Erbay Yigit
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Zhiyi Sun
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA.
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10
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Yi Z, Zhang X, Tang W, Yu Y, Wei X, Zhang X, Wei W. Strand-selective base editing of human mitochondrial DNA using mitoBEs. Nat Biotechnol 2024; 42:498-509. [PMID: 37217751 PMCID: PMC10940147 DOI: 10.1038/s41587-023-01791-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023]
Abstract
A number of mitochondrial diseases in humans are caused by point mutations that could be corrected by base editors, but delivery of CRISPR guide RNAs into the mitochondria is difficult. In this study, we present mitochondrial DNA base editors (mitoBEs), which combine a transcription activator-like effector (TALE)-fused nickase and a deaminase for precise base editing in mitochondrial DNA. Combining mitochondria-localized, programmable TALE binding proteins with the nickase MutH or Nt.BspD6I(C) and either the single-stranded DNA-specific adenine deaminase TadA8e or the cytosine deaminase ABOBEC1 and UGI, we achieve A-to-G or C-to-T base editing with up to 77% efficiency and high specificity. We find that mitoBEs are DNA strand-selective mitochondrial base editors, with editing results more likely to be retained on the nonnicked DNA strand. Furthermore, we correct pathogenic mitochondrial DNA mutations in patient-derived cells by delivering mitoBEs encoded in circular RNAs. mitoBEs offer a precise, efficient DNA editing tool with broad applicability for therapy in mitochondrial genetic diseases.
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Affiliation(s)
- Zongyi Yi
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Changping Laboratory, Beijing, P.R. China
| | - Xiaoxue Zhang
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Wei Tang
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Ying Yu
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
| | - Xiaoxu Wei
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Xue Zhang
- Changping Laboratory, Beijing, P.R. China
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China.
- Changping Laboratory, Beijing, P.R. China.
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11
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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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12
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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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13
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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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14
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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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15
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Wei Y, Jin M, Huang S, Yao F, Ren N, Xu K, Li S, Gao P, Zhou Y, Chen Y, Yang H, Li W, Xu C, Zhang M, Wang X. Enhanced C-To-T and A-To-G Base Editing in Mitochondrial DNA with Engineered DdCBE and TALED. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304113. [PMID: 37984866 PMCID: PMC10797475 DOI: 10.1002/advs.202304113] [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: 06/21/2023] [Revised: 10/26/2023] [Indexed: 11/22/2023]
Abstract
Mitochondrial base editing with DddA-derived cytosine base editor (DdCBE) is limited in the accessible target sequences and modest activity. Here, the optimized DdCBE tools is presented with improved editing activity and expanded C-to-T targeting scope by fusing DddA11 variant with different cytosine deaminases with single-strand DNA activity. Compared to previous DdCBE based on DddA11 variant alone, fusion of the activation-induced cytidine deaminase (AID) from Xenopus laevis not only permits cytosine editing of 5'-GC-3' sequence, but also elevates editing efficiency at 5'-TC-3', 5'-CC-3', and 5'-GC-3' targets by up to 25-, 10-, and 6-fold, respectively. Furthermore, the A-to-G editing efficiency is significantly improved by fusing the evolved DddA6 variant with TALE-linked deoxyadenosine deaminase (TALED). Notably, the authors introduce the reported high-fidelity mutations in DddA and add nuclear export signal (NES) sequences in DdCBE and TALED to reduce off-target editing in the nuclear and mitochondrial genome while improving on-target editing efficiency in mitochondrial DNA (mtDNA). Finally, these engineered mitochondrial base editors are shown to be efficient in installing mtDNA mutations in human cells or mouse embryos for disease modeling. Collectively, the study shows broad implications for the basic study and therapeutic applications of optimized DdCBE and TALED.
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Affiliation(s)
- Yinghui Wei
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
- School of Future Technology on Bio‐BreedingCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated HospitalInstitute of Neuroscience, and Fujian Key Laboratory of Molecular NeurologyFujian Medical UniversityFuzhouFujian350004China
| | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Fangyao Yao
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Ningxin Ren
- HuidaGene Therapeutics Co., Ltd.Shanghai200131China
| | - Kun Xu
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Shangpu Li
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Pengfei Gao
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Yingsi Zhou
- HuidaGene Therapeutics Co., Ltd.Shanghai200131China
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
- School of Future Technology on Bio‐BreedingCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Hui Yang
- HuidaGene Therapeutics Co., Ltd.Shanghai200131China
- Shanghai Center for Brain Science and Brain‐Inspired IntelligenceShanghai201602China
| | - Wen Li
- International Peace Maternity and Child Health HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200030China
| | - Chunlong Xu
- Shanghai Center for Brain Science and Brain‐Inspired IntelligenceShanghai201602China
| | - Meiling Zhang
- International Peace Maternity and Child Health HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200030China
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio‐Breeding of Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
- School of Future Technology on Bio‐BreedingCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
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16
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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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17
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Xiang J, Xu W, Wu J, Luo Y, Yang B, Chen J. Nucleoside deaminases: the key players in base editing toolkit. BIOPHYSICS REPORTS 2023; 9:325-337. [PMID: 38524700 PMCID: PMC10960570 DOI: 10.52601/bpr.2023.230029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/28/2023] [Indexed: 03/26/2024] Open
Abstract
The development of nucleoside deaminase-containing base editors realized targeted single base change with high efficiency and precision. Such nucleoside deaminases include adenosine and cytidine deaminases, which can catalyze adenosine-to-inosine (A-to-I) and cytidine-to-uridine (C-to-U) conversion respectively. These nucleoside deaminases are under the spotlight because of their vast application potential in gene editing. Recent advances in the engineering of current nucleoside deaminases and the discovery of new nucleoside deaminases greatly broaden the application scope and improve the editing specificity of base editors. In this review, we cover current knowledge about the deaminases used in base editors, including their key structural features, working mechanisms, optimization, and evolution.
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Affiliation(s)
- Jiangchao Xiang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenchao Xu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yaxin Luo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Bei Yang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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18
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Affiliation(s)
- Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
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19
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Cheng K, Li C, Jin J, Qian X, Guo J, Shen L, Dai Y, Zhang X, Li Z, Guan Y, Zhou F, Tang J, Zhang J, Shen B, Lou X. Engineering RsDddA as mitochondrial base editor with wide target compatibility and enhanced activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102028. [PMID: 37744175 PMCID: PMC10514076 DOI: 10.1016/j.omtn.2023.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Double-stranded DNA-specific cytidine deaminase (DddA) base editors hold great promise for applications in bio-medical research, medicine, and biotechnology. Strict sequence preference on spacing region presents a challenge for DddA editors to reach their full potential. To overcome this sequence-context constraint, we analyzed a protein dataset and identified a novel DddAtox homolog from Ruminococcus sp. AF17-6 (RsDddA). We engineered RsDddA for mitochondrial base editing in a mammalian cell line and demonstrated RsDddA-derived cytosine base editors (RsDdCBE) offered a broadened NC sequence compatibility and exhibited robust editing efficiency. Moreover, our results suggest the average frequencies of mitochondrial genome-wide off-target editing arising from RsDdCBE are comparable to canonical DdCBE and its variants.
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Affiliation(s)
- Kai Cheng
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cao Li
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiachuan Jin
- Center for Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xuezhen Qian
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiayin Guo
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Limini Shen
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - YiChen Dai
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xue Zhang
- Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou, Zhejiang, China
| | - Zhanwei Li
- Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou, Zhejiang, China
| | - Yichun Guan
- Center for Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fei Zhou
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Medical College of Soochow University, Suzhou, China
| | - Jin Tang
- Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou, Zhejiang, China
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou, Zhejiang, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Lou
- Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou, Zhejiang, China
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20
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Veloso Ribeiro Franco L, Barros MH. Biolistic transformation of the yeast Saccharomyces cerevisiae mitochondrial DNA. IUBMB Life 2023; 75:972-982. [PMID: 37470229 DOI: 10.1002/iub.2769] [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: 04/26/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023]
Abstract
The insertion of genes into mitochondria by biolistic transformation is currently only possible in the yeast Saccharomyces cerevisiae and the algae Chlamydomonas reinhardtii. The fact that S. cerevisiae mitochondria can exist with partial (ρ- mutants) or complete deletions (ρ0 mutants) of mitochondrial DNA (mtDNA), without requiring a specific origin of replication, enables the propagation of exogenous sequences. Additionally, mtDNA in this organism undergoes efficient homologous recombination, making it well-suited for genetic manipulation. In this review, we present a summarized historical overview of the development of biolistic transformation and discuss iconic applications of the technique. We also provide a detailed example on how to obtain transformants with recombined foreign DNA in their mitochondrial genome.
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Affiliation(s)
| | - Mario H Barros
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de Sao Paulo, Sao Paulo, Brazil
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21
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Chen X, Chen M, Zhu Y, Sun H, Wang Y, Xie Y, Ji L, Wang C, Hu Z, Guo X, Xu Z, Zhang J, Yang S, Liang D, Shen B. Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor. Commun Biol 2023; 6:1116. [PMID: 37923818 PMCID: PMC10624837 DOI: 10.1038/s42003-023-05500-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
Pathogenic mutations in mitochondrial DNA cause severe and often lethal multi-system symptoms in primary mitochondrial defects. However, effective therapies for these defects are still lacking. Strategies such as employing mitochondrially targeted restriction enzymes or programmable nucleases to shift the ratio of heteroplasmic mutations and allotopic expression of mitochondrial protein-coding genes have limitations in treating mitochondrial homoplasmic mutations, especially in non-coding genes. Here, we conduct a proof of concept study applying a screened DdCBE pair to correct the homoplasmic m.A4300G mutation in induced pluripotent stem cells derived from a patient with hypertrophic cardiomyopathy. We achieve efficient G4300A correction with limited off-target editing, and successfully restore mitochondrial function in corrected induced pluripotent stem cell clones. Our study demonstrates the feasibility of using DdCBE to treat primary mitochondrial defects caused by homoplasmic pathogenic mitochondrial DNA mutations.
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Affiliation(s)
- Xiaoxu Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Mingyue Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Yuqing Zhu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Haifeng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Yue Wang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Yuan Xie
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Lianfu Ji
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Cheng Wang
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China.
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
| | - Shiwei Yang
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China.
| | - Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China.
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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22
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Sun H, Wang Z, Shen L, Feng Y, Han L, Qian X, Meng R, Ji K, Liang D, Zhou F, Lou X, Zhang J, Shen B. Developing mitochondrial base editors with diverse context compatibility and high fidelity via saturated spacer library. Nat Commun 2023; 14:6625. [PMID: 37857619 PMCID: PMC10587121 DOI: 10.1038/s41467-023-42359-3] [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: 06/28/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) greatly facilitated the basic and therapeutic research of mitochondrial DNA mutation diseases. Here we devise a saturated spacer library and successfully identify seven DddA homologs by performing high-throughput sequencing based screen. DddAs of Streptomyces sp. BK438 and Lachnospiraceae bacterium sunii NSJ-8 display high deaminase activity with a strong GC context preference, and DddA of Ruminococcus sp. AF17-6 is highly compatible to AC context. We also find that different split sites result in wide divergence on off-target activity and context preference of DdCBEs derived from these DddA homologs. Additionally, we demonstrate the orthogonality between DddA and DddIA, and successfully minimize the nuclear off-target editing by co-expressing corresponding nuclear-localized DddIA. The current study presents a comprehensive and unbiased strategy for screening and characterizing dsDNA cytidine deaminases, and expands the toolbox for mtDNA editing, providing additional insights for optimizing dsDNA base editors.
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Affiliation(s)
- Haifeng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Zhaojun Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Limini Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Yeling Feng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Lu Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Xuezhen Qian
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Runde Meng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Kangming Ji
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Fei Zhou
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xin Lou
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311100, China.
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
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23
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Liu M, Ji W, Zhao X, Liu X, Hu JF, Cui J. Therapeutic potential of engineering the mitochondrial genome. Biochim Biophys Acta Mol Basis Dis 2023:166804. [PMID: 37429560 DOI: 10.1016/j.bbadis.2023.166804] [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: 04/20/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Mitochondrial diseases are a group of clinical disorders caused by mutations in the genes encoded by either the nuclear or the mitochondrial genome involved in mitochondrial oxidative phosphorylation. Disorders become evident when mitochondrial dysfunction reaches a cell-specific threshold. Similarly, the severity of disorders is related to the degree of gene mutation. Clinical treatments for mitochondrial diseases mainly rely on symptomatic management. Theoretically, replacing or repairing dysfunctional mitochondria to acquire and preserve normal physiological functions should be effective. Significant advances have been made in gene therapies, including mitochondrial replacement therapy, mitochondrial genome manipulation, nuclease programming, mitochondrial DNA editing, and mitochondrial RNA interference. In this paper, we review the recent progress in these technologies by focusing on advancements that overcome limitations.
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Affiliation(s)
- Mengmeng Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Wei Ji
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Xin Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Xiaoliang Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China.
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24
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Xu C, Huang P. Mitochondrial genome editing: Get aCcess to modeling broad disease mutations with engineered base editors. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:566-567. [PMID: 37200857 PMCID: PMC10185700 DOI: 10.1016/j.omtn.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Chunlong Xu
- Lingang Laboratory, Shanghai 200031, China
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 200031, China
- Corresponding author: Chunlong Xu, Lingang Laboratory, Shanghai 200031, China.
| | - Pengyu Huang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 201210, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
- Corresponding author: Pengyu Huang, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 201210, China.
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25
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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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26
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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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