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Shi C, Zou W, Liu X, Zhang H, Li X, Fu G, Fei Q, Qian Q, Shang L. Programmable RNA N 6-methyladenosine editing with CRISPR/dCas13a in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1867-1880. [PMID: 38363049 PMCID: PMC11182597 DOI: 10.1111/pbi.14307] [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: 04/12/2023] [Revised: 10/07/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
N6-methyladenonsine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) and plays critical roles in mRNA processing and metabolism. However, perturbation of individual m6A modification to reveal its function and the phenotypic effects is still lacking in plants. Here, we describe the construction and characterization of programmable m6A editing tools by fusing the m6A writers, the core catalytic domain of the MTA and MTB complex, and the AlkB homologue 5 (ALKBH5) eraser, to catalytically dead Cas13a (dCas13a) to edit individual m6A sites on mRNAs. We demonstrated that our m6A editors could efficiently and specifically deposit and remove m6A modifications on specific RNA transcripts in both Nicotiana benthamiana and Arabidopsis thaliana. Moreover, we found that targeting SHORT-ROOT (SHR) transcripts with a methylation editor could significantly increase its m6A levels with limited off-target effects and promote its degradation. This leads to a boost in plant growth with enlarged leaves and roots, increased plant height, plant biomass, and total grain weight in Arabidopsis. Collectively, these findings suggest that our programmable m6A editing tools can be applied to study the functions of individual m6A modifications in plants, and may also have potential applications for future crop improvement.
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Affiliation(s)
- Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Wenli Zou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Xiaofang Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Zhengzhou Research Base, State Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
| | - Guiling Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- College of AgricultureShanxi Agricultural UniversityTaiyuanShanxiChina
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouZhejiangChina
- Yazhouwan National LaboratorySanya CityHainan ProvinceChina
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Yazhouwan National LaboratorySanya CityHainan ProvinceChina
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2
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Zhu H, Wang L, Wang Y, Jiang X, Qin Q, Song M, Huang Q. Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e. Cell Mol Life Sci 2024; 81:257. [PMID: 38874784 DOI: 10.1007/s00018-024-05263-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 06/15/2024]
Abstract
Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.
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Affiliation(s)
- Haixia Zhu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinyi Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qin Qin
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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3
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Chen Q, Wang X, Zhang Y, Tian M, Duan J, Zhang Y, Yin H. Minimizing the ratio of ionizable lipid in lipid nanoparticles for in vivo base editing. Natl Sci Rev 2024; 11:nwae135. [PMID: 38770531 PMCID: PMC11104531 DOI: 10.1093/nsr/nwae135] [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: 11/12/2023] [Revised: 02/22/2024] [Accepted: 04/02/2024] [Indexed: 05/22/2024] Open
Abstract
Lipid nanoparticles (LNPs) have gained clinical approval as carriers for both siRNA and mRNA. Among the crucial components of LNPs, ionizable lipids play a pivotal role in determining the efficiency of RNA delivery. In this study, we synthesized a series of ionizable lipids, denoted as HTO, with a higher count of hydroxyl groups compared to SM-102. Remarkably, LNPs based on HTO12 lipid demonstrated comparable mRNA delivery efficiency and biosafety to those based on SM-102. However, the former reduced the ratio of ionizable lipid/total lipids to mRNA in LNPs by 2.5 times compared to SM-102. The HTO12 LNP efficiently encapsulated adenine base editor mRNA and sgRNA targeting Pcsk9, leading to substantial gene editing within the liver of mice and effective reduction of the target protein. Our study underscores that ionizable lipids with multiple hydroxyl groups may facilitate an improved lipid-to-mRNA ratio to minimize the dosage of ionizable lipids for in vivo delivery.
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Affiliation(s)
- Qiubing Chen
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Xuebin Wang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Yizhou Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Ming Tian
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Junyi Duan
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Ying Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Hao Yin
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
- RNA Institute, Wuhan University, Wuhan 430071, China
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Olivi L, Bagchus C, Pool V, Bekkering E, Speckner K, Offerhaus H, Wu W, Depken M, Martens KA, Staals RJ, Hohlbein J. Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a. Nucleic Acids Res 2024; 52:5241-5256. [PMID: 38647045 PMCID: PMC11109954 DOI: 10.1093/nar/gkae283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
CRISPR-Cas systems have widely been adopted as genome editing tools, with two frequently employed Cas nucleases being SpyCas9 and LbCas12a. Although both nucleases use RNA guides to find and cleave target DNA sites, the two enzymes differ in terms of protospacer-adjacent motif (PAM) requirements, guide architecture and cleavage mechanism. In the last years, rational engineering led to the creation of PAM-relaxed variants SpRYCas9 and impLbCas12a to broaden the targetable DNA space. By employing their catalytically inactive variants (dCas9/dCas12a), we quantified how the protein-specific characteristics impact the target search process. To allow quantification, we fused these nucleases to the photoactivatable fluorescent protein PAmCherry2.1 and performed single-particle tracking in cells of Escherichia coli. From our tracking analysis, we derived kinetic parameters for each nuclease with a non-targeting RNA guide, strongly suggesting that interrogation of DNA by LbdCas12a variants proceeds faster than that of SpydCas9. In the presence of a targeting RNA guide, both simulations and imaging of cells confirmed that LbdCas12a variants are faster and more efficient in finding a specific target site. Our work demonstrates the trade-off of relaxing PAM requirements in SpydCas9 and LbdCas12a using a powerful framework, which can be applied to other nucleases to quantify their DNA target search.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Cleo Bagchus
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Victor Pool
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ezra Bekkering
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Konstantin Speckner
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hidde Offerhaus
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Wen Y Wu
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Koen J A Martens
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
- Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, The Netherlands
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5
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Chen F, Zhang C, Xue J, Wang F, Li Z. Molecular mechanism for target RNA recognition and cleavage of Cas13h. Nucleic Acids Res 2024:gkae324. [PMID: 38661236 DOI: 10.1093/nar/gkae324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
RNA-targeting type VI CRISPR-Cas effectors are widely used in RNA applications. Cas13h is a recently identified subtype of Cas13 ribonuclease, with strong RNA cleavage activity and robust in vivo RNA knockdown efficiency. However, little is known regarding its biochemical properties and working mechanisms. Biochemical characterization of Cas13h1 indicated that it lacks in vitro pre-crRNA processing activity and adopts a central seed. The cleavage activity of Cas13h1 is enhanced by a R(G/A) 5'-PFS, and inhibited by tag:anti-tag RNA pairing. We determined the structures of Cas13h1-crRNA binary complex at 3.1 Å and Cas13h1-crRNA-target RNA ternary complex at 3.0 Å. The ternary complex adopts an elongated architecture, and encodes a nucleotide-binding pocket within Helical-2 domain to recognize the guanosine at the 5'-end of the target RNA. Base pairing between crRNA guide and target RNA disrupts Cas13h1-guide interactions, leading to dramatic movement of HEPN domains. Upon target RNA engagement, Cas13h1 adopts a complicated activation mechanism, including separation of HEPN catalytic residues and destabilization of the active site loop and NTD domain, to get activated. Collectively, these insights expand our understanding into Cas13 effectors.
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Affiliation(s)
- Fugen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jialin Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Feng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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6
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Vondracek K, Altpeter F, Liu T, Lee S. Advances in genomics and genome editing for improving strawberry ( Fragaria ×ananassa). Front Genet 2024; 15:1382445. [PMID: 38706796 PMCID: PMC11066249 DOI: 10.3389/fgene.2024.1382445] [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: 02/05/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.
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Affiliation(s)
- Kaitlyn Vondracek
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Fredy Altpeter
- University of Florida, Agronomy Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Tie Liu
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
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7
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Ren CY, Liu YS, He YS, Zhang LP, Rao JH, Rao Y, Chen JH. Engineered CBEs based on Macaca fascicularis A3A with improved properties for precise genome editing. Cell Rep 2024; 43:113878. [PMID: 38431844 DOI: 10.1016/j.celrep.2024.113878] [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: 06/27/2023] [Revised: 11/20/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Cytidine deaminase defines the properties of cytosine base editors (CBEs) for C-to-T conversion. Replacing the cytidine deaminase rat APOBEC1 (rA1) in CBEs with a human APOBEC3A (hA3A) improves CBE properties. However, the potential CBE application of macaque A3A orthologs remains undetermined. Our current study develops and evaluates engineered CBEs based on Macaca fascicularis A3A (mA3A). Here, we demonstrate that BE4-mA3A and its RNA-editing-derived variants exhibit improved CBE properties, except for DNA off-target activity, compared to BE3-rA1 and BE4-rA1. Unexpectedly, deleting Ser-Val-Arg (SVR) in BE4-mA3A dramatically reduces DNA and RNA off-target activities and improves editing accuracy, with on-target efficiency unaffected. In contrast, a chimeric BE4-hA3A-SVR+ shows editing efficiency increased by about 50%, with other properties unaffected. Our findings demonstrate that mA3A-based CBEs could provide prototype options with advantages over rA1- and hA3A-based CBEs for further optimization, highlighting the importance of the SVR motif in defining CBE intrinsic properties.
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Affiliation(s)
- Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan-Shan Liu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
| | - Yu-Shan He
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Lin-Pei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jun-Hua Rao
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Xinshijie Eye Hospital, Wuxi, China.
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8
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Lv Y, Luo X, Xie Z, Qiu J, Yang J, Deng Y, Long R, Tang G, Zhang C, Zuo J. Prospects and challenges of CAR-T cell therapy combined with ICIs. Front Oncol 2024; 14:1368732. [PMID: 38571495 PMCID: PMC10989075 DOI: 10.3389/fonc.2024.1368732] [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: 01/11/2024] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
Immune checkpoint molecules are a group of molecules expressed on the surface of immune cells that primarily regulate their immune homeostasis. Chimeric antigen receptor (CAR) T cell therapy is an immunotherapeutic technology that realizes tumor-targeted killing by constructing synthetic T cells expressing specific antigens through biotechnology. Currently, CAR-T cell therapy has achieved good efficacy in non-solid tumors, but its treatment of solid tumors has not yielded the desired results. Immune checkpoint inhibitors (ICIs) combined with CAR-T cell therapy is a novel combination therapy with high expectations to defeat solid tumors. This review addresses the challenges and expectations of this combination therapy in the treatment of solid tumors.
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Affiliation(s)
- Yufan Lv
- The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xinyu Luo
- The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Zhuoyi Xie
- Transformation Research Lab, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jieya Qiu
- Transformation Research Lab, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jinsai Yang
- Computer Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yuqi Deng
- Transformation Research Lab, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Rou Long
- Transformation Research Lab, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Guiyang Tang
- Transformation Research Lab, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Chaohui Zhang
- The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Jianhong Zuo
- The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Transformation Research Lab, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Computer Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Third Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
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9
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Walton RT, Qin Y, Blainey PC. CROPseq-multi: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585235. [PMID: 38558968 PMCID: PMC10979941 DOI: 10.1101/2024.03.17.585235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Forward genetic screens seek to dissect complex biological systems by systematically perturbing genetic elements and observing the resulting phenotypes. While standard screening methodologies introduce individual perturbations, multiplexing perturbations improves the performance of single-target screens and enables combinatorial screens for the study of genetic interactions. Current tools for multiplexing perturbations are incompatible with pooled screening methodologies that require mRNA-embedded barcodes, including some microscopy and single cell sequencing approaches. Here, we report the development of CROPseq-multi, a CROPseq1-inspired lentiviral system to multiplex Streptococcus pyogenes (Sp) Cas9-based perturbations with mRNA-embedded barcodes. CROPseq-multi has equivalent per-guide activity to CROPseq and low lentiviral recombination frequencies. CROPseq-multi is compatible with enrichment screening methodologies and optical pooled screens, and is extensible to screens with single-cell sequencing readouts. For optical pooled screens, an optimized and multiplexed in situ detection protocol improves barcode detection efficiency 10-fold, enables detection of recombination events, and increases decoding efficiency 3-fold relative to CROPseq. CROPseq-multi is a widely applicable multiplexing solution for diverse SpCas9-based genetic screening approaches.
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Affiliation(s)
- Russell T. Walton
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Yue Qin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul C. Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
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10
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Wang LL, Wu CQ, Zhang QL, Wang Y, Liu Y, Yang WJ, Ye SL, Tian Y, Xu L. Chemically Cross-Linked Hammerhead Ribozyme as an Efficient RNA Interference Tool. J Am Chem Soc 2024; 146:6665-6674. [PMID: 38412223 DOI: 10.1021/jacs.3c12702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
RNA-cleaving ribozymes are promising candidates as general tools of RNA interference (RNAi) in gene manipulation. However, compared with other RNA systems, such as siRNA and CRISPR technologies, the ribozyme tools are still far from broad applications on RNAi due to their poor performance in the cellular context. In this work, we report an efficient RNAi tool based on chemically modified hammerhead ribozyme (HHR). By the introduction of an intramolecular linkage into the minimal HHR to reconstruct the distal interaction within the tertiary ribozyme structure, this cross-linked HHR exhibits efficient RNA substrate cleavage activities with almost no sequence constraint. Cellular experiments suggest that both exogenous and endogenous RNA expression can be dramatically knocked down by this HHR tool with levels comparable to those of siRNA. Unlike the widely applied protein-recruiting RNA systems (siRNA and CRISPR), this ribozyme tool functions solely on RNA itself with great simplicity, which may provide a new approach for gene manipulation in both fundamental and translational studies.
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Affiliation(s)
- Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
- School of Pharmacy and Medical Technology, Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine of Fujian Province, Putian University, Putian 351100, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen-Jian Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Sen-Lin Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yongqiang Tian
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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11
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Knauer C, Haltern H, Schoger E, Kügler S, Roos L, Zelarayán LC, Hasenfuss G, Zimmermann WH, Wollnik B, Cyganek L. Preclinical evaluation of CRISPR-based therapies for Noonan syndrome caused by deep-intronic LZTR1 variants. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102123. [PMID: 38333672 PMCID: PMC10851011 DOI: 10.1016/j.omtn.2024.102123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
Gene variants in LZTR1 are implicated to cause Noonan syndrome associated with a severe and early-onset hypertrophic cardiomyopathy. Mechanistically, LZTR1 deficiency results in accumulation of RAS GTPases and, as a consequence, in RAS-MAPK signaling hyperactivity, thereby causing the Noonan syndrome-associated phenotype. Despite its epidemiological relevance, pharmacological as well as invasive therapies remain limited. Here, personalized CRISPR-Cas9 gene therapies might offer a novel alternative for a curative treatment in this patient cohort. In this study, by utilizing a patient-specific screening platform based on iPSC-derived cardiomyocytes from two Noonan syndrome patients, we evaluated different clinically translatable therapeutic approaches using small Cas9 orthologs targeting a deep-intronic LZTR1 variant to cure the disease-associated molecular pathology. Despite high editing efficiencies in cardiomyocyte cultures transduced with lentivirus or all-in-one adeno-associated viruses, we observed crucial differences in editing outcomes in proliferative iPSCs vs. non-proliferative cardiomyocytes. While editing in iPSCs rescued the phenotype, the same editing approaches did not robustly restore LZTR1 function in cardiomyocytes, indicating critical differences in the activity of DNA double-strand break repair mechanisms between proliferative and non-proliferative cell types and highlighting the importance of cell type-specific screens for testing CRISPR-Cas9 gene therapies.
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Affiliation(s)
- Carolin Knauer
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
| | - Henrike Haltern
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
| | - Eric Schoger
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Sebastian Kügler
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Lennart Roos
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Laura C. Zelarayán
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Department of Cardiology and Angiology, University of Giessen, 35390 Giessen, Germany
| | - Gerd Hasenfuss
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Wolfram-Hubertus Zimmermann
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 37075 Göttingen, Germany
- DZNE (German Center for Neurodegenerative Diseases), 37075 Göttingen, Germany
| | - Bernd Wollnik
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 37075 Göttingen, Germany
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12
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Jiang H, Tang M, Xu Z, Wang Y, Li M, Zheng S, Zhu J, Lin Z, Zhang M. CRISPR/Cas9 system and its applications in nervous system diseases. Genes Dis 2024; 11:675-686. [PMID: 37692518 PMCID: PMC10491921 DOI: 10.1016/j.gendis.2023.03.017] [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: 11/28/2022] [Accepted: 03/05/2023] [Indexed: 09/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is an acquired immune system of many bacteria and archaea, comprising CRISPR loci, Cas genes, and its associated proteins. This system can recognize exogenous DNA and utilize the Cas9 protein's nuclease activity to break DNA double-strand and to achieve base insertion or deletion by subsequent DNA repair. In recent years, multiple laboratory and clinical studies have revealed the therapeutic role of the CRISPR/Cas9 system in neurological diseases. This article reviews the CRISPR/Cas9-mediated gene editing technology and its potential for clinical application against neurological diseases.
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Affiliation(s)
- Haibin Jiang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mengyan Tang
- The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zidi Xu
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yanan Wang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mopu Li
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Shuyin Zheng
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jianghu Zhu
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Zhenlang Lin
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Min Zhang
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
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13
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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14
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Zhang Z, Baxter AE, Ren D, Qin K, Chen Z, Collins SM, Huang H, Komar CA, Bailer PF, Parker JB, Blobel GA, Kohli RM, Wherry EJ, Berger SL, Shi J. Efficient engineering of human and mouse primary cells using peptide-assisted genome editing. Nat Biotechnol 2024; 42:305-315. [PMID: 37095348 DOI: 10.1038/s41587-023-01756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023]
Abstract
Simple, efficient and well-tolerated delivery of CRISPR genome editing systems into primary cells remains a major challenge. Here we describe an engineered Peptide-Assisted Genome Editing (PAGE) CRISPR-Cas system for rapid and robust editing of primary cells with minimal toxicity. The PAGE system requires only a 30-min incubation with a cell-penetrating Cas9 or Cas12a and a cell-penetrating endosomal escape peptide to achieve robust single and multiplex genome editing. Unlike electroporation-based methods, PAGE gene editing has low cellular toxicity and shows no significant transcriptional perturbation. We demonstrate rapid and efficient editing of primary cells, including human and mouse T cells, as well as human hematopoietic progenitor cells, with editing efficiencies upwards of 98%. PAGE provides a broadly generalizable platform for next-generation genome engineering in primary cells.
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Affiliation(s)
- Zhen Zhang
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA
| | - Diqiu Ren
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kunhua Qin
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA
| | - Sierra M Collins
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hua Huang
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chad A Komar
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter F Bailer
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jared B Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gerd A Blobel
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rahul M Kohli
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Shelley L Berger
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Junwei Shi
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Oser MG, MacPherson D, Oliver TG, Sage J, Park KS. Genetically-engineered mouse models of small cell lung cancer: the next generation. Oncogene 2024; 43:457-469. [PMID: 38191672 PMCID: PMC11180418 DOI: 10.1038/s41388-023-02929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024]
Abstract
Small cell lung cancer (SCLC) remains the most fatal form of lung cancer, with patients in dire need of new and effective therapeutic approaches. Modeling SCLC in an immunocompetent host is essential for understanding SCLC pathogenesis and ultimately discovering and testing new experimental therapeutic strategies. Human SCLC is characterized by near universal genetic loss of the RB1 and TP53 tumor suppressor genes. Twenty years ago, the first genetically-engineered mouse model (GEMM) of SCLC was generated using conditional deletion of both Rb1 and Trp53 in the lungs of adult mice. Since then, several other GEMMs of SCLC have been developed coupling genomic alterations found in human SCLC with Rb1 and Trp53 deletion. Here we summarize how GEMMs of SCLC have contributed significantly to our understanding of the disease in the past two decades. We also review recent advances in modeling SCLC in mice that allow investigators to bypass limitations of the previous generation of GEMMs while studying new genes of interest in SCLC. In particular, CRISPR/Cas9-mediated somatic gene editing can accelerate how new genes of interest are functionally interrogated in SCLC tumorigenesis. Notably, the development of allograft models and precancerous precursor models from SCLC GEMMs provides complementary approaches to GEMMs to study tumor cell-immune microenvironment interactions and test new therapeutic strategies to enhance response to immunotherapy. Ultimately, the new generation of SCLC models can accelerate research and help develop new therapeutic strategies for SCLC.
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Affiliation(s)
- Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - David MacPherson
- Division of Human Biology, Fred Hutch Cancer Center, Seattle, WA, 98109, USA
| | - Trudy G Oliver
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, 27708, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, 22903, USA.
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16
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Tang N, Wu Z, Gao Y, Chen W, Wang Z, Su M, Ji W, Ji Q. Molecular Basis and Genome Editing Applications of a Compact Eubacterium ventriosum CRISPR-Cas9 System. ACS Synth Biol 2024; 13:269-281. [PMID: 38061052 DOI: 10.1021/acssynbio.3c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
CRISPR-Cas9 systems have been widely harnessed for diverse genome editing applications because of their ease of use and high efficiency. However, the large molecular sizes and strict PAM requirements of commonly used CRISPR-Cas9 systems restrict their broad applications in therapeutics. Here, we report the molecular basis and genome editing applications of a novel compact type II-A Eubacterium ventriosum CRISPR-Cas9 system (EvCas9) with 1107 residues and distinct 5'-NNGDGN-3' (where D represents A, T, or G) PAM specificity. We determine the cryo-EM structure of EvCas9 in a complex with an sgRNA and a target DNA, revealing the detailed PAM recognition and sgRNA and target DNA association mechanisms. Additionally, we demonstrate the robust genome editing capacity of EvCas9 in bacteria and human cells with superior fidelity compared to SaCas9 and SpCas9, and we engineer it to be efficient base editors by fusing a cytidine or adenosine deaminase. Collectively, our results facilitate further understanding of CRISPR-Cas9 working mechanisms and expand the compact CRISPR-Cas9 toolbox.
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Affiliation(s)
- Na Tang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhaowei Wu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zixiao Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengjiao Su
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenxin Ji
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- 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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17
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Ping N, Hara-Kuge S, Yagi Y, Kazama T, Nakamura T. Translational enhancement of target endogenous mRNA in mammalian cells using programmable RNA-binding pentatricopeptide repeat proteins. Sci Rep 2024; 14:251. [PMID: 38167853 PMCID: PMC10762265 DOI: 10.1038/s41598-023-50776-z] [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: 07/31/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
Programmable protein scaffolds are invaluable in the development of genome engineering tools. The pentatricopeptide repeat (PPR) protein is an attractive platform for RNA manipulation because of its programmable RNA-binding selectivity, which is determined by the combination of amino acid species at three specific sites in the PPR motif. Translation is a key RNA regulatory step that determines the final gene expression level and is involved in various human diseases. In this study, designer PPR protein was used to develop a translational enhancement technique by fusion with the translation initiation factor eIF4G. The results showed that the PPR-eIF4G fusion protein could activate the translation of endogenous c-Myc and p53 mRNAs and control cell fate, indicating that PPR-based translational enhancement is a versatile technique applicable to various endogenous mRNAs in mammalian cells. In addition, the translational enhancement was dependent on both the target position and presence of eIF4G, suggesting the presence of an unknown translation activation mechanism.
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Affiliation(s)
- Ning Ping
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | - Sayuri Hara-Kuge
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | | | - Tomohiko Kazama
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | - Takahiro Nakamura
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
- EditForce, Inc., Fukuoka, 819-0395, Japan.
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18
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Taharabaru T, Kihara T, Obata A, Onodera R, Wen Y, Li J, Motoyama K, Higashi T. Cyclodextrin-based tailored polyrotaxanes for highly efficient delivery of the genome-editing molecule. Carbohydr Polym 2024; 323:121443. [PMID: 37940259 DOI: 10.1016/j.carbpol.2023.121443] [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: 07/19/2023] [Revised: 09/10/2023] [Accepted: 09/27/2023] [Indexed: 11/10/2023]
Abstract
Direct cytosolic delivery of the Cas9 ribonucleoprotein is the most promising method for inducing CRISPR-Cas9 genome editing in mammalian cells. Recently, we focused the movable properties of cyclodextrin-based polyrotaxanes (PRXs), which consist of numerous cyclodextrins threaded onto the axile molecule with bulky endcaps at both ends of the axile molecule, and developed aminated PRXs as multistep transformable carriers for Cas9 ribonucleoprotein, ensuring efficient complexation, cellular internalization, endosomal escape, release, and nuclear localization. This study reports the structural fine-tuning and structure-property relationship of multistep transformable PRXs for more efficient Cas9 ribonucleoprotein delivery. Among various PRXs, PRX derivatives with a longer molecular length (35 kDa polyethylene glycol as the axile molecule) and a low total degree of substitution (1.5 amino groups/α-cyclodextrins), as well as the modified ratio of two modified amines (cystamine and diethylenetriamine) = ≈1:1, exhibited the highest genome-editing efficacy and intracellular dynamics control. These structural properties are important for efficient endosomal escape and Cas9 RNP release. Furthermore, ligand-modified-β-CD, which can endow the ligand through complexation with PRX termini, improved the cellular uptake and genome-editing effects of the optimized PRX/Cas9 RNP in target cells. Thus, structural fine-tuning and the addition of ligand-modified-β-cyclodextrin enabled efficient genome editing by the Cas9 RNP.
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Affiliation(s)
- Toru Taharabaru
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Department of Biomedical Engineering, National University of Singapore, 15 Kent Ridge Crescent, Singapore 119276, Singapore
| | - Takuya Kihara
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Airi Obata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Risako Onodera
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yuting Wen
- Department of Biomedical Engineering, National University of Singapore, 15 Kent Ridge Crescent, Singapore 119276, Singapore
| | - Jun Li
- Department of Biomedical Engineering, National University of Singapore, 15 Kent Ridge Crescent, Singapore 119276, Singapore
| | - Keiichi Motoyama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Taishi Higashi
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Priority Organization for Innovation and Excellence, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.
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19
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Hosseini SY, Mallick R, Mäkinen P, Ylä-Herttuala S. Navigating the prime editing strategy to treat cardiovascular genetic disorders in transforming heart health. Expert Rev Cardiovasc Ther 2024; 22:75-89. [PMID: 38494784 DOI: 10.1080/14779072.2024.2328642] [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: 10/18/2023] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
INTRODUCTION After understanding the genetic basis of cardiovascular disorders, the discovery of prime editing (PE), has opened new horizons for finding their cures. PE strategy is the most versatile editing tool to change cardiac genetic background for therapeutic interventions. The optimization of elements, prediction of efficiency, and discovery of the involved genes regulating the process have not been completed. The large size of the cargo and multi-elementary structure makes the in vivo heart delivery challenging. AREAS COVERED Updated from recent published studies, the fundamentals of the PEs, their application in cardiology, potentials, shortcomings, and the future perspectives for the treatment of cardiac-related genetic disorders will be discussed. EXPERT OPINION The ideal PE for the heart should be tissue-specific, regulatable, less immunogenic, high transducing, and safe. However, low efficiency, sup-optimal PE architecture, the large size of required elements, the unclear role of transcriptomics on the process, unpredictable off-target effects, and its context-dependency are subjects that need to be considered. It is also of great importance to see how beneficial or detrimental cell cycle or epigenomic modifier is to bring changes into cardiac cells. The PE delivery is challenging due to the size, multi-component properties of the editors and liver sink.
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Affiliation(s)
- Seyed Younes Hosseini
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Bacteriology and Virology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Rahul Mallick
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petri Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
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20
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Scott-Young M, Nielsen D, Riar S. Fundamentals of Mechanobiology and Potential Applications in Spinal Fusion. Int J Spine Surg 2023; 17:S61-S74. [PMID: 38135446 PMCID: PMC10753328 DOI: 10.14444/8562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Mechanobiology can help optimize spinal fusion by providing insights into the mechanical environment required for bone healing and fusion. This includes understanding the optimal loading conditions, the mechanical properties of implanted materials, and the effects of mechanical stimuli on the cells involved in bone formation. The present article reviews the evidence for surface technologies and implant modification of spinal cages in enhancing spinal fusion. METHODS Databases used included Embase, MEDLINE, Springer, and Cochrane Library. Relevant articles were identified using specific keywords and search fields. Only systematic reviews, meta-analyses, review articles, and original research articles in English were included. Two researchers independently performed the search and selection process. A flowchart of the search strategy and study selection method is provided in the article. RESULTS The studies indicate that surface modification can significantly enhance osseointegration and interbody fusion by promoting cellular adhesion, proliferation, differentiation, and mineralization. Various surface modification techniques such as coating, etching, nanotopography, and functionalization achieve this. Similarly, implant material modification can improve implant stability, biocompatibility, and bioactivity, leading to better fusion outcomes. Mechanobiology plays a vital role in this process by influencing the cellular response to mechanical cues and promoting bone formation. CONCLUSIONS The studies reviewed indicate that surface technologies and implant material modification are promising approaches for improving the success of spinal cage fusion. Mechanobiology is critical in this process by influencing the cellular response to mechanical signals and promoting bone growth.
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Affiliation(s)
- Matthew Scott-Young
- Faculty of Health Science and Medicine, Bond University, Gold Coast, Queensland, Australia
- Gold Coast Spine, Bond University, Gold Coast, Queensland, Australia
| | - David Nielsen
- Gold Coast Spine, Bond University, Gold Coast, Queensland, Australia
| | - Sukhman Riar
- Faculty of Health Science and Medicine, Bond University, Gold Coast, Queensland, Australia
- Gold Coast Spine, Bond University, Gold Coast, Queensland, Australia
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21
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Lye J, Delaney DS, Leith FK, Sardesai VS, McLenachan S, Chen FK, Atlas MD, Wong EYM. Recent Therapeutic Progress and Future Perspectives for the Treatment of Hearing Loss. Biomedicines 2023; 11:3347. [PMID: 38137568 PMCID: PMC10741758 DOI: 10.3390/biomedicines11123347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Up to 1.5 billion people worldwide suffer from various forms of hearing loss, with an additional 1.1 billion people at risk from various insults such as increased consumption of recreational noise-emitting devices and ageing. The most common type of hearing impairment is sensorineural hearing loss caused by the degeneration or malfunction of cochlear hair cells or spiral ganglion nerves in the inner ear. There is currently no cure for hearing loss. However, emerging frontier technologies such as gene, drug or cell-based therapies offer hope for an effective cure. In this review, we discuss the current therapeutic progress for the treatment of hearing loss. We describe and evaluate the major therapeutic approaches being applied to hearing loss and summarize the key trials and studies.
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Affiliation(s)
- Joey Lye
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Derek S. Delaney
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Fiona K. Leith
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Varda S. Sardesai
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
| | - Samuel McLenachan
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia; (S.M.); (F.K.C.)
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Fred K. Chen
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia; (S.M.); (F.K.C.)
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
- Vitroretinal Surgery, Royal Perth Hospital, Perth, WA 6000, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC 3002, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Marcus D. Atlas
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Elaine Y. M. Wong
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA 6009, Australia; (J.L.); (D.S.D.); (F.K.L.); (V.S.S.); (M.D.A.)
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
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22
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Engfer ZJ, Lewandowski D, Dong Z, Palczewska G, Zhang J, Kordecka K, Płaczkiewicz J, Panas D, Foik AT, Tabaka M, Palczewski K. Distinct mouse models of Stargardt disease display differences in pharmacological targeting of ceramides and inflammatory responses. Proc Natl Acad Sci U S A 2023; 120:e2314698120. [PMID: 38064509 PMCID: PMC10723050 DOI: 10.1073/pnas.2314698120] [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: 08/24/2023] [Accepted: 10/25/2023] [Indexed: 12/17/2023] Open
Abstract
Mutations in many visual cycle enzymes in photoreceptors and retinal pigment epithelium (RPE) cells can lead to the chronic accumulation of toxic retinoid byproducts, which poison photoreceptors and the underlying RPE if left unchecked. Without a functional ATP-binding cassette, sub-family A, member 4 (ABCA4), there is an elevation of all-trans-retinal and prolonged buildup of all-trans-retinal adducts, resulting in a retinal degenerative disease known as Stargardt-1 disease. Even in this monogenic disorder, there is significant heterogeneity in the time to onset of symptoms among patients. Using a combination of molecular techniques, we studied Abca4 knockout (simulating human noncoding disease variants) and Abca4 knock-in mice (simulating human misfolded, catalytically inactive protein variants), which serve as models for Stargardt-1 disease. We compared the two strains to ascertain whether they exhibit differential responses to agents that affect cytokine signaling and/or ceramide metabolism, as alterations in either of these pathways can exacerbate retinal degenerative phenotypes. We found different degrees of responsiveness to maraviroc, a known immunomodulatory CCR5 antagonist, and to the ceramide-lowering agent AdipoRon, an agonist of the ADIPOR1 and ADIPOR2 receptors. The two strains also display different degrees of transcriptional deviation from matched WT controls. Our phenotypic comparison of the two distinct Abca4 mutant-mouse models sheds light on potential therapeutic avenues previously unexplored in the treatment of Stargardt disease and provides a surrogate assay for assessing the effectiveness for genome editing.
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Affiliation(s)
- Zachary J. Engfer
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - Dominik Lewandowski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Zhiqian Dong
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Grazyna Palczewska
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Jianye Zhang
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
| | - Katarzyna Kordecka
- Ophthalmic Biology Group, International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Jagoda Płaczkiewicz
- Ophthalmic Biology Group, International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Damian Panas
- International Centre for Translational Eye Research, Warsaw01-224, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Andrzej T. Foik
- Ophthalmic Biology Group, International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw01-224, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA92697
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
- Department of Chemistry, University of California, Irvine, CA92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697
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23
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Nandy K, Babu D, Rani S, Joshi G, Ijee S, George A, Palani D, Premkumar C, Rajesh P, Vijayanand S, David E, Murugesan M, Velayudhan SR. Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression. Sci Rep 2023; 13:21953. [PMID: 38081875 PMCID: PMC10713686 DOI: 10.1038/s41598-023-42174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.
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Affiliation(s)
- Krittika Nandy
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Dinesh Babu
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Sonam Rani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Gaurav Joshi
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Anila George
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Chitra Premkumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Praveena Rajesh
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Mohankumar Murugesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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24
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Huang X, Zhang W. Overcoming T Cell Exhaustion in Tumor Microenvironment via Immune Checkpoint Modulation with Nano-Delivery Systems for Enhanced Immunotherapy. SMALL METHODS 2023:e2301326. [PMID: 38040834 DOI: 10.1002/smtd.202301326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/12/2023] [Indexed: 12/03/2023]
Abstract
Immune checkpoint blockade (ICB) therapy for tumors has arisen in growing interest. However, the low response rate of tumors to ICB is mainly attributed to the inhibitory infiltration of immune cells in the tumor microenvironment (TME). Despite the promising benefits of ICB, the therapeutic effects of antibodies are dependent on a high dose and long-term usage in the clinic, thereby leading to immune-related adverse effects. Accordingly, ICB combined with nano-delivery systems could be used to overcome T cell exhaustion, which reduces the side effects and the usage of antibodies with higher response rates in patients. In this review, the authors aim to overcome T cell exhaustion in TME via immune checkpoint modulation with nano-delivery systems for enhanced immunotherapy. Several strategies are summarized to combine ICB and nano-delivery systems to further enhance immunotherapy: a) expressing immune checkpoint on the surface of nano-delivery systems; b) loading immune checkpoint inhibitors into nano-delivery systems; c) loading gene-editing technology into nano-delivery systems; and d) nano-delivery systems mediated immune checkpoint modulation. Taken together, ICB combined with nano-delivery systems might be a promising strategy to overcome T cell exhaustion in TME for enhanced immunotherapy.
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Affiliation(s)
- Xin Huang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weiyue Zhang
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
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25
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Angelopoulou L, Stylianopoulou E, Tegopoulos K, Farmakioti I, Grigoriou M, Skavdis G. A PCR-Induced Mutagenesis-Restriction Fragment Length Polymorphism Method for the Detection of CRISPR-Induced Indels. CRISPR J 2023; 6:514-526. [PMID: 38052051 DOI: 10.1089/crispr.2023.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
As CRISPR-based technologies are widely used for knocking out genes in cell lines and organisms, there is a need for the development of reliable, cost-effective, and fast methods that identify fully mutated clones. In this context, we present a novel strategy named PCR-induced mutagenesis-restriction fragment length polymorphism (PIM-RFLP), which is based on the well-documented robustness and simplicity of the classical PCR-RFLP approach. PIM-RFLP allows the assessment of the editing efficiency in pools of edited cells and the effective identification of fully mutated single-cell clones. It is based on the creation by mutagenic PCR of a restriction enzyme degenerate cleavage site in the PCR product of the wild-type allele, which can then be distinguished from the indel-containing alleles following the standard RFLP procedure. PIM-RFLP is highly accessible, can be executed in a single day, and appears to outperform Sanger sequencing deconvolution algorithms in the detection of fully mutated clones.
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Affiliation(s)
- Lydia Angelopoulou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Electra Stylianopoulou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Tegopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Farmakioti
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Grigoriou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Skavdis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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26
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Chen Y, Paramo MI, Zhang Y, Yao L, Shah SR, Jin Y, Zhang J, Pan X, Yu H. Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants. Annu Rev Genet 2023; 57:201-222. [PMID: 37562413 DOI: 10.1146/annurev-genet-030723-120717] [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: 08/12/2023]
Abstract
Despite accumulating evidence implicating noncoding variants in human diseases, unraveling their functionality remains a significant challenge. Systematic annotations of the regulatory landscape and the growth of sequence variant data sets have fueled the development of tools and methods to identify causal noncoding variants and evaluate their regulatory effects. Here, we review the latest advances in the field and discuss potential future research avenues to gain a more in-depth understanding of noncoding regulatory variants.
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Affiliation(s)
- You Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Mauricio I Paramo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Yingying Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Li Yao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Sagar R Shah
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Yiyang Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Junke Zhang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Xiuqi Pan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
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27
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Bustos FJ, Pandian S, Haensgen H, Zhao JP, Strouf H, Heidenreich M, Swiech L, Deverman BE, Gradinaru V, Zhang F, Constantine-Paton M. Removal of a partial genomic duplication restores synaptic transmission and behavior in the MyosinVA mutant mouse Flailer. BMC Biol 2023; 21:232. [PMID: 37957716 PMCID: PMC10644554 DOI: 10.1186/s12915-023-01714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Copy number variations, and particularly duplications of genomic regions, have been strongly associated with various neurodegenerative conditions including autism spectrum disorder (ASD). These genetic variations have been found to have a significant impact on brain development and function, which can lead to the emergence of neurological and behavioral symptoms. Developing strategies to target these genomic duplications has been challenging, as the presence of endogenous copies of the duplicate genes often complicates the editing strategies. RESULTS Using the ASD and anxiety mouse model Flailer, which contains a partial genomic duplication working as a dominant negative for MyoVa, we demonstrate the use of DN-CRISPRs to remove a 700 bp genomic region in vitro and in vivo. Importantly, DN-CRISPRs have not been used to remove genomic regions using sgRNA with an offset greater than 300 bp. We found that editing the flailer gene in primary cortical neurons reverts synaptic transport and transmission defects. Moreover, long-term depression (LTD), disrupted in Flailer animals, is recovered after gene editing. Delivery of DN-CRISPRs in vivo shows that local delivery to the ventral hippocampus can rescue some of the mutant behaviors, while intracerebroventricular delivery, completely recovers the Flailer animal phenotype associated to anxiety and ASD. CONCLUSIONS Our results demonstrate the potential of DN-CRISPR to efficiently remove larger genomic duplications, working as a new gene therapy approach for treating neurodegenerative diseases.
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Affiliation(s)
- Fernando J Bustos
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de La Vida, Universidad Andres Bello, Santiago, Chile.
| | - Swarna Pandian
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Henny Haensgen
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de La Vida, Universidad Andres Bello, Santiago, Chile
| | - Jian-Ping Zhao
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haley Strouf
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Lukasz Swiech
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin E Deverman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Feng Zhang
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Martha Constantine-Paton
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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28
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Chen C, Wang Z, Qin Y. CRISPR/Cas9 system: recent applications in immuno-oncology and cancer immunotherapy. Exp Hematol Oncol 2023; 12:95. [PMID: 37964355 PMCID: PMC10647168 DOI: 10.1186/s40164-023-00457-4] [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: 08/01/2023] [Accepted: 11/08/2023] [Indexed: 11/16/2023] Open
Abstract
Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is essentially an adaptive immunity weapon in prokaryotes against foreign DNA. This system inspires the development of genome-editing technology in eukaryotes. In biomedicine research, CRISPR has offered a powerful platform to establish tumor-bearing models and screen potential targets in the immuno-oncology field, broadening our insights into cancer genomics. In translational medicine, the versatile CRISPR/Cas9 system exhibits immense potential to break the current limitations of cancer immunotherapy, thereby expanding the feasibility of adoptive cell therapy (ACT) in treating solid tumors. Herein, we first explain the principles of CRISPR/Cas9 genome editing technology and introduce CRISPR as a tool in tumor modeling. We next focus on the CRISPR screening for target discovery that reveals tumorigenesis, immune evasion, and drug resistance mechanisms. Moreover, we discuss the recent breakthroughs of genetically modified ACT using CRISPR/Cas9. Finally, we present potential challenges and perspectives in basic research and clinical translation of CRISPR/Cas9. This review provides a comprehensive overview of CRISPR/Cas9 applications that advance our insights into tumor-immune interaction and lay the foundation to optimize cancer immunotherapy.
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Affiliation(s)
- Chen Chen
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zehua Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanru Qin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Bexte T, Reindl LM, Ullrich E. Nonviral technologies can pave the way for CAR-NK cell therapy. J Leukoc Biol 2023; 114:475-486. [PMID: 37403203 DOI: 10.1093/jleuko/qiad074] [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: 12/03/2022] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
Natural killer cells are a promising platform for cancer immunotherapy. Natural killer cells have high intrinsic killing capability, and the insertion of a chimeric antigen receptor can further enhance their antitumor potential. In first-in-human trials, chimeric antigen receptor-natural killer cells demonstrated strong clinical activity without therapy-induced side effects. The applicability of natural killer cells as an "off-the-shelf" product makes them highly attractive for gene-engineered cell therapies. Traditionally, viral transduction has been used for gene editing; however, the use of viral vectors remains a safety concern and is associated with high costs and regulatory requirements. Here, we review the current landscape of nonviral approaches for chimeric antigen receptor-natural killer cell generation. This includes transfection of vector particles and electroporation of mRNA and DNA vectors, resulting in transient modification and chimeric antigen receptor expression. In addition, using nonviral transposon technologies, natural killer cells can be stably modified ensuring long-lasting chimeric antigen receptor expression. Finally, we discuss CRISPR/Cas9 tools to edit key genes for natural killer cell functionality.
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Affiliation(s)
- Tobias Bexte
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Lisa Marie Reindl
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
| | - Evelyn Ullrich
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Frankfurt/Mainz; Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Zhang YR, Yin TL, Zhou LQ. CRISPR/Cas9 technology: applications in oocytes and early embryos. J Transl Med 2023; 21:746. [PMID: 37875936 PMCID: PMC10594749 DOI: 10.1186/s12967-023-04610-9] [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: 07/12/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
CRISPR/Cas9, a highly versatile genome-editing tool, has garnered significant attention in recent years. Despite the unique characteristics of oocytes and early embryos compared to other cell types, this technology has been increasing used in mammalian reproduction. In this comprehensive review, we elucidate the fundamental principles of CRISPR/Cas9-related methodologies and explore their wide-ranging applications in deciphering molecular intricacies during oocyte and early embryo development as well as in addressing associated diseases. However, it is imperative to acknowledge the limitations inherent to these technologies, including the potential for off-target effects, as well as the ethical concerns surrounding the manipulation of human embryos. Thus, a judicious and thoughtful approach is warranted. Regardless of these challenges, CRISPR/Cas9 technology undeniably represents a formidable tool for genome and epigenome manipulation within oocytes and early embryos. Continuous refinements in this field are poised to fortify its future prospects and applications.
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Affiliation(s)
- Yi-Ran Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tai-Lang Yin
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China.
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Nakamura S, Morohoshi K, Inada E, Sato Y, Watanabe S, Saitoh I, Sato M. Recent Advances in In Vivo Somatic Cell Gene Modification in Newborn Pups. Int J Mol Sci 2023; 24:15301. [PMID: 37894981 PMCID: PMC10607593 DOI: 10.3390/ijms242015301] [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: 08/31/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Germline manipulation at the zygote stage using the CRISPR/Cas9 system has been extensively employed for creating genetically modified animals and maintaining established lines. However, this approach requires a long and laborious task. Recently, many researchers have attempted to overcome these limitations by generating somatic mutations in the adult stage through tail vein injection or local administration of CRISPR reagents, as a new strategy called "in vivo somatic cell genome editing". This approach does not require manipulation of early embryos or strain maintenance, and it can test the results of genome editing in a short period. The newborn is an ideal stage to perform in vivo somatic cell genome editing because it is immune-privileged, easily accessible, and only a small amount of CRISPR reagents is required to achieve somatic cell genome editing throughout the entire body, owing to its small size. In this review, we summarize in vivo genome engineering strategies that have been successfully demonstrated in newborns. We also report successful in vivo genome editing through the neonatal introduction of genome editing reagents into various sites in newborns (as exemplified by intravenous injection via the facial vein), which will be helpful for creating models for genetic diseases or treating many genetic diseases.
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Affiliation(s)
- Shingo Nakamura
- Division of Biomedical Engineering, National Defense Medical College Research Institute, Tokorozawa 359-8513, Japan;
| | - Kazunori Morohoshi
- Division of Biomedical Engineering, National Defense Medical College Research Institute, Tokorozawa 359-8513, Japan;
| | - Emi Inada
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan;
| | - Yoko Sato
- Graduate School of Public Health, Shizuoka Graduate University of Public Health, Aoi-ku, Shizuoka 420-0881, Japan;
| | - Satoshi Watanabe
- Institute of Livestock and Grassland Science, NARO, Tsukuba 305-0901, Japan;
| | - Issei Saitoh
- Department of Pediatric Dentistry, Asahi University School of Dentistry, Mizuho 501-0296, Japan;
| | - Masahiro Sato
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan;
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Lin YW, Lin TT, Chen CH, Wang RH, Lin YH, Tseng TY, Zhuang YJ, Tang SY, Lin YC, Pang JY, Chakravarthy RD, Lin HC, Tzou SC, Chao JI. Enhancing Efficacy of Albumin-Bound Paclitaxel for Human Lung and Colorectal Cancers through Autophagy Receptor Sequestosome 1 (SQSTM1)/p62-Mediated Nanodrug Delivery and Cancer therapy. ACS NANO 2023; 17:19033-19051. [PMID: 37737568 DOI: 10.1021/acsnano.3c04739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Selective autophagy is a defense mechanism by which foreign pathogens and abnormal substances are processed to maintain cellular homeostasis. Sequestosome 1 (SQSTM1)/p62, a vital selective autophagy receptor, recruits ubiquitinated cargo to form autophagosomes for lysosomal degradation. Nab-PTX is an albumin-bound paclitaxel nanoparticle used in clinical cancer therapy. However, the role of SQSTM1 in regulating the delivery and efficacy of nanodrugs remains unclear. Here we showed that SQSTM1 plays a crucial role in Nab-PTX drug delivery and efficacy in human lung and colorectal cancers. Nab-PTX induces SQSTM1 phosphorylation at Ser403, which facilitates its incorporation into the selective autophagy of nanoparticles, known as nanoparticulophagy. Nab-PTX increased LC3-II protein expression, which triggered autophagosome formation. SQSTM1 enhanced Nab-PTX recognition to form autophagosomes, which were delivered to lysosomes for albumin degradation, thereby releasing PTX to induce mitotic catastrophe and apoptosis. Knockout of SQSTM1 downregulated Nab-PTX-induced mitotic catastrophe, apoptosis, and tumor inhibition in vitro and in vivo and inhibited Nab-PTX-induced caspase 3 activation via a p53-independent pathway. Ectopic expression of SQSTM1 by transfection of an SQSTM1-GFP vector restored the drug efficacy of Nab-PTX. Importantly, SQSTM1 is highly expressed in advanced lung and colorectal tumors and is associated with poor overall survival in clinical patients. Targeting SQSTM1 may provide an important strategy to improve nanodrug efficacy in clinical cancer therapy. This study demonstrates the enhanced efficacy of Nab-PTX for human lung and colorectal cancers via SQSTM1-mediated nanodrug delivery.
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Affiliation(s)
- Yu-Wei Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Tzu-Ting Lin
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chien-Hung Chen
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Rou-Hsin Wang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ya-Hui Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Tzu-Yen Tseng
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yan-Jun Zhuang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Sheng-Yueh Tang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yen-Cheng Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jiun-Yu Pang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Rajan Deepan Chakravarthy
- Department of Materials Science and Engineering, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Hsin-Chieh Lin
- Department of Materials Science and Engineering, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Shey-Cherng Tzou
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jui-I Chao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
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Yan Q, Shi S, Ge Y, Wan S, Li M, Li M. UCHL1 alleviates apoptosis in chondrocytes via upregulation of HIF‑1α‑mediated mitophagy. Int J Mol Med 2023; 52:99. [PMID: 37681473 PMCID: PMC10555477 DOI: 10.3892/ijmm.2023.5302] [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: 05/18/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Stem cell‑based tissue engineering has shown significant potential for rapid restoration of injured cartilage tissues. Stem cells frequently undergo apoptosis because of the prevalence of oxidative stress and inflammation in the microenvironment at the sites of injury. Our previous study demonstrated that stabilization of hypoxia‑inducible factor 1α (HIF‑1α) is key to resisting apoptosis in chondrocytes. Recently, it was reported that Ubiquitin C‑terminal hydrolase L1 (UCHL1) can stabilize HIF‑1α by abrogating the ubiquitination process. However, the effect of UCHL1 on apoptosis in chondrocytes remains unclear. Herein, adipose‑derived stem cells were differentiated into chondrocytes. Next, the CRISPR activation (CRISPRa) system, LDN‑57444 (LDM; a specific inhibitor for UCHL1), KC7F2 (a specific inhibitor for HIF‑1α), and 3‑methyladenine (a specific inhibitor for mitophagy) were used to activate or block UCHL1, HIF‑1α, and mitophagy. Mitophagy, apoptosis, and mitochondrial function in chondrocytes were detected using immunofluorescence, TUNEL staining, and flow cytometry. Moreover, the oxygen consumption rate of chondrocytes was measured using the Seahorse XF 96 Extracellular Flux Analyzer. UCHL1 expression was increased in hypoxia, which in turn regulated mitophagy and apoptosis in the chondrocytes. Further studies revealed that UCHL1 mediated hypoxia‑regulated mitophagy in the chondrocytes. The CRISPRa module was utilized to activate UCHL1 effectively for 7 days; endogenous activation of UCHL1 accelerated mitophagy, inhibited apoptosis, and maintained mitochondrial function in the chondrocytes, which was mediated by HIF‑1α. Taken together, UCHL1 could block apoptosis in chondrocytes via upregulation of HIF‑1α-mediated mitophagy and maintain mitochondrial function. These results indicate the potential of UCHL1 activation using the CRISPRa system for the regeneration of cartilage tissue.
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Affiliation(s)
- Qiqian Yan
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong 510280
- Guangdong Academy of Stomatology, Guangzhou, Guangdong 510180, P.R. China
| | - Shanwei Shi
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong 510280
- Guangdong Academy of Stomatology, Guangzhou, Guangdong 510180, P.R. China
| | - Yang Ge
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong 510280
- Guangdong Academy of Stomatology, Guangzhou, Guangdong 510180, P.R. China
| | - Shuangquan Wan
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong 510280
- Guangdong Academy of Stomatology, Guangzhou, Guangdong 510180, P.R. China
| | - Mingfei Li
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong 510280
- Guangdong Academy of Stomatology, Guangzhou, Guangdong 510180, P.R. China
| | - Maoquan Li
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong 510280
- Guangdong Academy of Stomatology, Guangzhou, Guangdong 510180, P.R. China
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Mahmood MA. Efficient A·T-to-C·G Base Editing via Adenine Transversion Editors. Cell Reprogram 2023; 25:187-189. [PMID: 37725011 DOI: 10.1089/cell.2023.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
Generating A-to-C transversions to correct defective alleles or introduce novel alleles has posed significant challenges. However, two recent studies focusing on adenine transversions have achieved successful A-to-C transversions in mouse embryos and plant cell. These remarkable accomplishments notably broaden the range of base editing and their applications both in fundamental research and in therapeutics.
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Affiliation(s)
- Muhammad Arslan Mahmood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, Australia
- Department of Biological Sciences, University of Sialkot, Sialkot, Pakistan
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Rabaan AA, Al Fares MA, Almaghaslah M, Alpakistany T, Al Kaabi NA, Alshamrani SA, Alshehri AA, Almazni IA, Saif A, Hakami AR, Khamis F, Alfaresi M, Alsalem Z, Alsoliabi ZA, Al Amri KAS, Hassoueh AK, Mohapatra RK, Arteaga-Livias K, Alissa M. Application of CRISPR-Cas System to Mitigate Superbug Infections. Microorganisms 2023; 11:2404. [PMID: 37894063 PMCID: PMC10609045 DOI: 10.3390/microorganisms11102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Multidrug resistance in bacterial strains known as superbugs is estimated to cause fatal infections worldwide. Migration and urbanization have resulted in overcrowding and inadequate sanitation, contributing to a high risk of superbug infections within and between different communities. The CRISPR-Cas system, mainly type II, has been projected as a robust tool to precisely edit drug-resistant bacterial genomes to combat antibiotic-resistant bacterial strains effectively. To entirely opt for its potential, advanced development in the CRISPR-Cas system is needed to reduce toxicity and promote efficacy in gene-editing applications. This might involve base-editing techniques used to produce point mutations. These methods employ designed Cas9 variations, such as the adenine base editor (ABE) and the cytidine base editor (CBE), to directly edit single base pairs without causing DSBs. The CBE and ABE could change a target base pair into a different one (for example, G-C to A-T or C-G to A-T). In this review, we addressed the limitations of the CRISPR/Cas system and explored strategies for circumventing these limitations by applying diverse base-editing techniques. Furthermore, we also discussed recent research showcasing the ability of base editors to eliminate drug-resistant microbes.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia
| | - Manar Almaghaslah
- Infectious Disease Division, Department of Internal Medicine, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Tariq Alpakistany
- Bacteriology Department, Public Health Laboratory, Taif 26521, Saudi Arabia
| | - Nawal A Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Saleh A Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ibrahim Abdullah Almazni
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62223, Saudi Arabia
| | - Abdulrahim R Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62223, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases Unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Mubarak Alfaresi
- Department of Pathology and Laboratory Medicine, Zayed Military Hospital, Abu Dhabi 3740, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
| | - Zainab Alsalem
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | | | - Amal K Hassoueh
- Pharmacy Department, King Saud Medical City, Riyadh 7790, Saudi Arabia
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, India
| | - Kovy Arteaga-Livias
- Escuela de Medicina-Filial Ica, Universidad Privada San Juan Bautista, Ica 11000, Peru
- Escuela de Medicina, Universidad Nacional Hermilio Valdizán, Huanuco 10000, Peru
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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Zheng X, Huang C, Lin Y, Han B, Chen Y, Li C, Li J, Ding Y, Song X, Wang W, Liang W, Wu J, Wu J, Gao J, Wei C, Zhang X, Tu Z, Yan S. Generation of inactivated IL2RG and RAG1 monkeys with severe combined immunodeficiency using base editing. Signal Transduct Target Ther 2023; 8:327. [PMID: 37661226 PMCID: PMC10475462 DOI: 10.1038/s41392-023-01544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 09/05/2023] Open
Abstract
Severe combined immunodeficiency (SCID) encompasses a range of inherited disorders that lead to a profound deterioration of the immune system. Among the pivotal genes associated with SCID, RAG1 and IL2RG play crucial roles. IL2RG is essential for the development, differentiation, and functioning of T, B, and NK cells, while RAG1 critically contributes to adaptive immunity by facilitating V(D)J recombination during the maturation of lymphocytes. Animal models carrying mutations in these genes exhibit notable deficiencies in their immune systems. Non-human primates (NHPs) are exceptionally well-suited models for biomedical research due to their genetic and physiological similarities to humans. Cytosine base editors (CBEs) serve as powerful tools for precisely and effectively modifying single-base mutations in the genome. Their successful implementation has been demonstrated in human cells, mice, and crop species. This study outlines the creation of an immunodeficient monkey model by deactivating both the IL2RG and RAG1 genes using the CBE4max system. The base-edited monkeys exhibited a severely compromised immune system characterized by lymphopenia, atrophy of lymphoid organs, and a deficiency of mature T cells. Furthermore, these base-edited monkeys were capable of hosting and supporting the growth of human breast cancer cells, leading to tumor formation. In summary, we have successfully developed an immunodeficient monkey model with the ability to foster tumor growth using the CBE4max system. These immunodeficiency monkeys show tremendous potential as valuable tools for advancing biomedical and translational research.
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Affiliation(s)
- Xiao Zheng
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Chunhui Huang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Yingqi Lin
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Bofeng Han
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Yizhi Chen
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Caijuan Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Jiawei Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Yongyan Ding
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Xichen Song
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Wei Wang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Weien Liang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jianhao Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jiaxi Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jiale Gao
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Chengxi Wei
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Xudong Zhang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Zhuchi Tu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China.
| | - Sen Yan
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China.
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China.
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Alinejad T, Modarressi S, Sadri Z, Hao Z, Chen CS. Diagnostic applications and therapeutic option of Cascade CRISPR/Cas in the modulation of miRNA in diverse cancers: promises and obstacles. J Cancer Res Clin Oncol 2023; 149:9557-9575. [PMID: 37222810 PMCID: PMC10423114 DOI: 10.1007/s00432-023-04747-6] [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: 12/14/2022] [Accepted: 04/03/2023] [Indexed: 05/25/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas technology is a molecular tool specific to sequences for engineering genomes. Among diverse clusters of Cas proteins, the class 2/type II CRISPR/Cas9 system, despite several challenges, such as off-target effects, editing efficiency, and efficient delivery, has shown great promise for driver gene mutation discovery, high-throughput gene screening, epigenetic modulation, nucleic acid detection, disease modeling, and more importantly for therapeutic purposes. CRISPR-based clinical and experimental methods have applications across a wide range of areas, especially for cancer research and, possibly, anticancer therapy. On the other hand, given the influential role of microRNAs (miRNAs) in the regulations of cellular division, carcinogenicity, tumorigenesis, migration/invasion, and angiogenesis in diverse normal and pathogenic cellular processes, in different stages of cancer, miRNAs are either oncogenes or tumor suppressors, according to what type of cancer they are involved in. Hence, these noncoding RNA molecules are conceivable biomarkers for diagnosis and therapeutic targets. Moreover, they are suggested to be adequate predictors for cancer prediction. Conclusive evidence proves that CRISPR/Cas system can be applied to target small non-coding RNAs. However, the majority of studies have highlighted the application of the CRISPR/Cas system for targeting protein-coding regions. In this review, we specifically discuss diverse applications of CRISPR-based tools for probing miRNA gene function and miRNA-based therapeutic involvement in different types of cancers.
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Affiliation(s)
- Tahereh Alinejad
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, 325015 Zhejiang People’s Republic of China
| | - Shabnam Modarressi
- Department of Food Microbiology, Faculty of Science, University of Copenhagen, 1958 Frederiksberg C. Copenhagen, Denmark
| | - Zahra Sadri
- The Department of Biological Science, Molecular and Cell Biology, Dedman College of Humanities and Sciences Southern Methodist University (SMU), Dallas, TX USA
| | - Zuo Hao
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, 325015 Zhejiang People’s Republic of China
| | - Cheng Shui Chen
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, 325015 Zhejiang People’s Republic of China
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Yin G, Wang XH, Sun Y. Recent advances in CRISPR-Cas system for the treatment of genetic hearing loss. AMERICAN JOURNAL OF STEM CELLS 2023; 12:37-50. [PMID: 37736272 PMCID: PMC10509501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023]
Abstract
Genetic hearing loss has emerged as a significant public health concern that demands attention. Among the various treatment strategies, gene therapy based on gene editing technology is considered the most promising approach for addressing genetic hearing loss by repairing or eliminating mutated genes. The advent of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has revolutionized gene therapy through its remarkable gene editing capabilities. This system has been extensively employed in mammalian gene editing and is currently being evaluated through clinical trials. Against this backdrop, this review aims to provide an overview of recent advances in utilizing the CRISPR-Cas system to treat genetic hearing loss. Additionally, we delve into the primary challenges and prospects associated with the current application of this system in addressing genetic hearing loss.
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Affiliation(s)
- Ge Yin
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Xiao-Hui Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and RegenerationWuhan 430022, Hubei, China
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
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Chacko L, Chaudhary A, Singh B, Dewanjee S, Kandimalla R. CRISPR-Cas9 in Alzheimer's disease: Therapeutic trends, modalities, and challenges. Drug Discov Today 2023; 28:103652. [PMID: 37290639 DOI: 10.1016/j.drudis.2023.103652] [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: 04/06/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with no known cure, which has prompted the exploration of novel therapeutic approaches. The clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) tool has generated significant interest for its potential in AD therapeutics by correcting faulty genes. Our report comprehensively reviews emerging applications for CRISPR-Cas9 in developing in vitro and in vivo models for AD research and therapeutics. We further assess its ability to identify and validate genetic markers and potential therapeutic targets for AD. Moreover, we review the current challenges and delivery strategies for the in vivo application of CRISPR-Cas9 in AD therapeutics.
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Affiliation(s)
- Leena Chacko
- BioAnalytical Lab, Meso Scale Discovery, 1601 Research Blvd, Rockville, MD, USA
| | - Anupama Chaudhary
- Orinin-BioSystems, LE-52, Lotus Road 4, CHD City, Karnal, Haryana 132 001, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute (IVRI), Regional Station, Palampur, Himachal Pradesh 176 061, India
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700 032, India.
| | - Ramesh Kandimalla
- Department of Biochemistry, Kakatiya Medical College, Warangal 506 007, Telangana, India; Department of Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad 500 007, India.
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Ogunnaike M, Das S, Raut SS, Sultana A, Nayan MU, Ganesan M, Edagwa BJ, Osna NA, Poluektova LY. Chronic Hepatitis B Infection: New Approaches towards Cure. Biomolecules 2023; 13:1208. [PMID: 37627273 PMCID: PMC10452112 DOI: 10.3390/biom13081208] [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: 06/07/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection leads to the development of cirrhosis and hepatocellular carcinoma. Lifelong treatment with nucleotides/nucleoside antiviral agents is effective at suppressing HBV replication, however, adherence to daily therapy can be challenging. This review discusses recent advances in the development of long-acting formulations for HBV treatment and prevention, which could potentially improve adherence. Promising new compounds that target distinct steps of the virus life cycle are summarized. In addition to treatments that suppress viral replication, curative strategies are focused on the elimination of covalently closed circular DNA and the inactivation of the integrated viral DNA from infected hepatocytes. We highlight promising long-acting antivirals and genome editing strategies for the elimination or deactivation of persistent viral DNA products in development.
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Affiliation(s)
- Mojisola Ogunnaike
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Srijanee Das
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Samiksha S. Raut
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
| | - Ashrafi Sultana
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
| | - Mohammad Ullah Nayan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
| | - Murali Ganesan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Benson J. Edagwa
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
| | - Natalia A. Osna
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Larisa Y. Poluektova
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.O.); (S.D.); (S.S.R.); (A.S.); (M.U.N.); (M.G.)
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Choi EH, Suh S, Sears AE, Hołubowicz R, Kedhar SR, Browne AW, Palczewski K. Genome editing in the treatment of ocular diseases. Exp Mol Med 2023; 55:1678-1690. [PMID: 37524870 PMCID: PMC10474087 DOI: 10.1038/s12276-023-01057-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/14/2023] [Indexed: 08/02/2023] Open
Abstract
Genome-editing technologies have ushered in a new era in gene therapy, providing novel therapeutic strategies for a wide range of diseases, including both genetic and nongenetic ocular diseases. These technologies offer new hope for patients suffering from previously untreatable conditions. The unique anatomical and physiological features of the eye, including its immune-privileged status, size, and compartmentalized structure, provide an optimal environment for the application of these cutting-edge technologies. Moreover, the development of various delivery methods has facilitated the efficient and targeted administration of genome engineering tools designed to correct specific ocular tissues. Additionally, advancements in noninvasive ocular imaging techniques and electroretinography have enabled real-time monitoring of therapeutic efficacy and safety. Herein, we discuss the discovery and development of genome-editing technologies, their application to ocular diseases from the anterior segment to the posterior segment, current limitations encountered in translating these technologies into clinical practice, and ongoing research endeavors aimed at overcoming these challenges.
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Affiliation(s)
- Elliot H Choi
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Susie Suh
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Avery E Sears
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Rafał Hołubowicz
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Sanjay R Kedhar
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Andrew W Browne
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA.
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA.
- Department of Chemistry, University of California, Irvine, CA, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
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Wang JH, Wu SJ, Li Y, Zhao Y, Liu ZM, Deng SL, Lian ZX. Improving the Efficiency of Precise Genome Editing with CRISPR/Cas9 to Generate Goats Overexpressing Human Butyrylcholinesterase. Cells 2023; 12:1818. [PMID: 37508483 PMCID: PMC10378061 DOI: 10.3390/cells12141818] [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: 05/02/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The CRISPR/Cas9 system is widely used for genome editing in livestock production, although off-target effects can occur. It is the main method to produce genome-edited goats by somatic cell nuclear transfer (SCNT) of CRISPR/Cas9-mediated genome-edited primary goat fetal fibroblast cells (GFFs). Improving the double-strand break (DSB) efficiency of Cas9 in primary cells would improve the homologous repair (HR) efficiency. The low efficiency of HR remains a major hurdle in CRISPR/Cas9-mediated precise genome editing, increasing the work required to screen the genome-edited primary cell clones. In this study, we modified several essential parameters that affect the efficiency of the CRISPR/Cas9-mediated knock-in GFF cloning system, including establishing a high-efficiency transfection system for primary cells via nucleofection and optimizing homology arm (HA) length during HR. Here, we specifically inserted a recombinant human butyrylcholinesterase gene (rhBChE) into the goat fibroblast growth factor (FGF)-5 locus through the CRISPR/Cas9 system, thereby achieving simultaneous rhBChE insertion and FGF5 knock-out. First, this study introduced the Cas9, FGF5 knock-out small guide RNA, and rhBChE knock-in donors into GFFs by electroporation and obtained positive cell clones without off-target effects. Then, we demonstrated the expression of rhBChE in GFF clones and verified its function. Finally, we obtained a CRISPR/Cas9-mediated rhBChE-overexpression goat.
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Affiliation(s)
- Jia-Hao Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Su-Jun Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yan Li
- Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing 100071, China;
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhi-Mei Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shou-Long Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Zheng-Xing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Elhawary NA, AlJahdali IA, Abumansour IS, Azher ZA, Falemban AH, Madani WM, Alosaimi W, Alghamdi G, Sindi IA. Phenotypic variability to medication management: an update on fragile X syndrome. Hum Genomics 2023; 17:60. [PMID: 37420260 DOI: 10.1186/s40246-023-00507-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
This review discusses the discovery, epidemiology, pathophysiology, genetic etiology, molecular diagnosis, and medication-based management of fragile X syndrome (FXS). It also highlights the syndrome's variable expressivity and common comorbid and overlapping conditions. FXS is an X-linked dominant disorder associated with a wide spectrum of clinical features, including but not limited to intellectual disability, autism spectrum disorder, language deficits, macroorchidism, seizures, and anxiety. Its prevalence in the general population is approximately 1 in 5000-7000 men and 1 in 4000-6000 women worldwide. FXS is associated with the fragile X messenger ribonucleoprotein 1 (FMR1) gene located at locus Xq27.3 and encodes the fragile X messenger ribonucleoprotein (FMRP). Most individuals with FXS have an FMR1 allele with > 200 CGG repeats (full mutation) and hypermethylation of the CpG island proximal to the repeats, which silences the gene's promoter. Some individuals have mosaicism in the size of the CGG repeats or in hypermethylation of the CpG island, both produce some FMRP and give rise to milder cognitive and behavioral deficits than in non-mosaic individuals with FXS. As in several monogenic disorders, modifier genes influence the penetrance of FMR1 mutations and FXS's variable expressivity by regulating the pathophysiological mechanisms related to the syndrome's behavioral features. Although there is no cure for FXS, prenatal molecular diagnostic testing is recommended to facilitate early diagnosis. Pharmacologic agents can reduce some behavioral features of FXS, and researchers are investigating whether gene editing can be used to demethylate the FMR1 promoter region to improve patient outcomes. Moreover, clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 and developed nuclease defective Cas9 (dCas9) strategies have promised options of genome editing in gain-of-function mutations to rewrite new genetic information into a specified DNA site, are also being studied.
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Affiliation(s)
- Nasser A Elhawary
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia.
| | - Imad A AlJahdali
- Department of Community Medicine, College of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Iman S Abumansour
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Zohor A Azher
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Alaa H Falemban
- Department of Pharmacology and Toxicology, College of Medicine, Umm Al-Qura University, Mecca, 24382, Saudi Arabia
| | - Wefaq M Madani
- Department of Hematology and Immunology, Faculty of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Wafaa Alosaimi
- Department of Hematology, Maternity and Children Hospital, Mecca, Saudi Arabia
| | - Ghydda Alghamdi
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Ikhlas A Sindi
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Preparatory Year Program, Batterjee Medical College, Jeddah, 21442, Saudi Arabia
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Qu J, Liu N, Gao L, Hu J, Sun M, Yu D. Development of CRISPR Cas9, spin-off technologies and their application in model construction and potential therapeutic methods of Parkinson's disease. Front Neurosci 2023; 17:1223747. [PMID: 37483347 PMCID: PMC10359996 DOI: 10.3389/fnins.2023.1223747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common degenerative diseases. It is most typically characterized by neuronal death following the accumulation of Lewis inclusions in dopaminergic neurons in the substantia nigra region, with clinical symptoms such as motor retardation, autonomic dysfunction, and dystonia spasms. The exact molecular mechanism of its pathogenesis has not been revealed up to now. And there is a lack of effective treatments for PD, which places a burden on patients, families, and society. CRISPR Cas9 is a powerful technology to modify target genomic sequence with rapid development. More and more scientists utilized this technique to perform research associated neurodegenerative disease including PD. However, the complexity involved makes it urgent to organize and summarize the existing findings to facilitate a clearer understanding. In this review, we described the development of CRISPR Cas9 technology and the latest spin-off gene editing systems. Then we focused on the application of CRISPR Cas9 technology in PD research, summarizing the construction of the novel PD-related medical models including cellular models, small animal models, large mammal models. We also discussed new directions and target molecules related to the use of CRISPR Cas9 for PD treatment from the above models. Finally, we proposed the view about the directions for the development and optimization of the CRISPR Cas9 technology system, and its application to PD and gene therapy in the future. All these results provided a valuable reference and enhanced in understanding for studying PD.
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Affiliation(s)
- Jiangbo Qu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Na Liu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Lu Gao
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Jia Hu
- School of Life Science and Technology, Weifang Medical University, Weifang, Shandong, China
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dongyi Yu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
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45
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Vardanyan VH, Wang Q, Kolomeisky AB. Dynamics of single-base editing: Theoretical analysis. J Chem Phys 2023; 158:245101. [PMID: 37347132 PMCID: PMC10908558 DOI: 10.1063/5.0157193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023] Open
Abstract
Recent experimental advances led to the development of DNA base editors (BEs) with single-nucleotide precision, which is critical for future progress in various scientific and technological fields. The molecular mechanisms of single-base discrimination, however, remain poorly understood. Using a recently developed stochastic approach, we theoretically investigated the dynamics of single-base editing. More specifically, transient and mean times to edit "TC" motifs by cytosine BEs are explicitly evaluated for correct (target) and incorrect (bystander) locations on DNA. In addition, the effect of mutations on the dynamics of the single-base edition is also analyzed. It is found that for most ranges of parameters, it is possible to temporarily separate target and bystander products of base editing, supporting the idea of dynamic selectivity as a method of improving the precision of single-base editing. We conclude that to improve the efficiency of single-base editing, selecting the probability or selecting the time requires different strategies. Physical-chemical arguments to explain the observed dynamic properties are presented. The theoretical analysis clarifies some important aspects of the molecular mechanisms of selective base editing.
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Affiliation(s)
| | - Qian Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
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Chen H, Liu X, Li L, Tan Q, Li S, Li L, Li C, Fu J, Lu Y, Wang Y, Sun Y, Luo ZG, Lu Z, Sun Q, Liu Z. CATI: an efficient gene integration method for rodent and primate embryos by MMEJ suppression. Genome Biol 2023; 24:146. [PMID: 37353834 DOI: 10.1186/s13059-023-02987-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substantial proportion of DNA repair during CRISPR-mediated gene editing. Using CasRx to downregulate a key MMEJ factor, Polymerase Q (Polq), we improve the targeted integration efficiency of linearized DNA fragments and single-strand oligonucleotides (ssODN) in mouse embryos and offspring. CasRX-assisted targeted integration (CATI) also leads to substantial improvements in HDR efficiency during the CRISPR/Cas9 editing of monkey embryos. We present a promising tool for generating monkey models and developing gene therapies for clinical trials.
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Affiliation(s)
- Hongyu Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Xingchen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Lanxin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qingtong Tan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Shiyan Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Li Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Chunyang Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jiqiang Fu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yong Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yidi Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zongyang Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
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Zimmermann A, Prieto-Vivas JE, Cautereels C, Gorkovskiy A, Steensels J, Van de Peer Y, Verstrepen KJ. A Cas3-base editing tool for targetable in vivo mutagenesis. Nat Commun 2023; 14:3389. [PMID: 37296137 PMCID: PMC10256805 DOI: 10.1038/s41467-023-39087-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
The generation of genetic diversity via mutagenesis is routinely used for protein engineering and pathway optimization. Current technologies for random mutagenesis often target either the whole genome or relatively narrow windows. To bridge this gap, we developed CoMuTER (Confined Mutagenesis using a Type I-E CRISPR-Cas system), a tool that allows inducible and targetable, in vivo mutagenesis of genomic loci of up to 55 kilobases. CoMuTER employs the targetable helicase Cas3, signature enzyme of the class 1 type I-E CRISPR-Cas system, fused to a cytidine deaminase to unwind and mutate large stretches of DNA at once, including complete metabolic pathways. The tool increases the number of mutations in the target region 350-fold compared to the rest of the genome, with an average of 0.3 mutations per kilobase. We demonstrate the suitability of CoMuTER for pathway optimization by doubling the production of lycopene in Saccharomyces cerevisiae after a single round of mutagenesis.
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Affiliation(s)
- Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Julian E Prieto-Vivas
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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48
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Huang X, Zhou J, Yang D, Zhang J, Xia X, Chen YE, Xu J. Decoding CRISPR-Cas PAM recognition with UniDesign. Brief Bioinform 2023; 24:bbad133. [PMID: 37078688 PMCID: PMC10199764 DOI: 10.1093/bib/bbad133] [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: 12/20/2022] [Revised: 02/09/2023] [Accepted: 03/16/2023] [Indexed: 04/21/2023] Open
Abstract
The critical first step in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (CRISPR-Cas) protein-mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the protein's PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR-Cas engineering to relax or tighten PAM requirements for subsequent applications. Here, we describe a universal computational protein design framework (UniDesign) for designing protein-nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM-PIAA interactions for eight Cas9 and two Cas12a proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs of all Cas proteins. In turn, given natural PAMs, the computationally redesigned PIAA residues largely recapitulated the native PIAAs (74% and 86% in terms of identity and similarity, respectively). These results demonstrate that UniDesign faithfully captures the mutual preference between natural PAMs and native PIAAs, suggesting it is a useful tool for engineering CRISPR-Cas and other nucleic acid-interacting proteins. UniDesign is open-sourced at https://github.com/tommyhuangthu/UniDesign.
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Affiliation(s)
- Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jun Zhou
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Xiaofeng Xia
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab 129, Wynnewood, PA 19096, USA
| | - Yuqing Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
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49
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Eisen B, Binah O. Modeling Duchenne Muscular Dystrophy Cardiomyopathy with Patients' Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Int J Mol Sci 2023; 24:ijms24108657. [PMID: 37240001 DOI: 10.3390/ijms24108657] [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: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle degenerative disease caused by mutations in the dystrophin gene, resulting in death by the end of the third decade of life at the latest. A key aspect of the DMD clinical phenotype is dilated cardiomyopathy, affecting virtually all patients by the end of the second decade of life. Furthermore, despite respiratory complications still being the leading cause of death, with advancements in medical care in recent years, cardiac involvement has become an increasing cause of mortality. Over the years, extensive research has been conducted using different DMD animal models, including the mdx mouse. While these models present certain important similarities to human DMD patients, they also have some differences which pose a challenge to researchers. The development of somatic cell reprograming technology has enabled generation of human induced pluripotent stem cells (hiPSCs) which can be differentiated into different cell types. This technology provides a potentially endless pool of human cells for research. Furthermore, hiPSCs can be generated from patients, thus providing patient-specific cells and enabling research tailored to different mutations. DMD cardiac involvement has been shown in animal models to include changes in gene expression of different proteins, abnormal cellular Ca2+ handling, and other aberrations. To gain a better understanding of the disease mechanisms, it is imperative to validate these findings in human cells. Furthermore, with the recent advancements in gene-editing technology, hiPSCs provide a valuable platform for research and development of new therapies including the possibility of regenerative medicine. In this article, we review the DMD cardiac-related research performed so far using human hiPSCs-derived cardiomyocytes (hiPSC-CMs) carrying DMD mutations.
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Affiliation(s)
- Binyamin Eisen
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Ofer Binah
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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50
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Leonard S, Benfante R. Unanswered questions in the regulation and function of the duplicated α7 nicotinic receptor gene CHRFAM7A. Pharmacol Res 2023; 192:106783. [PMID: 37164281 DOI: 10.1016/j.phrs.2023.106783] [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: 03/17/2023] [Revised: 04/20/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
The α7 nicotinic receptor (α7 nAChR) is an important entry point for Ca2+ into the cell, which has broad and important effects on gene expression and function. The gene (CHRNA7), mapping to chromosome (15q14), has been genetically linked to a large number of diseases, many of which involve defects in cognition. While numerous mutations in CHRNA7 are associated with mental illness and inflammation, an important control point may be the function of a recently discovered partial duplication CHRNA7, CHRFAM7A, that negatively regulates the function of the α7 receptor, through the formation of heteropentamers; other functions cannot be excluded. The deregulation of this human specific gene (CHRFAM7A) has been linked to neurodevelopmental, neurodegenerative, and inflammatory disorders and has important copy number variations. Much effort is being made to understand its function and regulation both in healthy and pathological conditions. However, many questions remain to be answered regarding its functional role, its regulation, and its role in the etiogenesis of neurological and inflammatory disorders. Missing knowledge on the pharmacology of the heteroreceptor has limited the discovery of new molecules capable of modulating its activity. Here we review the state of the art on the role of CHRFAM7A, highlighting unanswered questions to be addressed. A possible therapeutic approach based on genome editing protocols is also discussed.
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Affiliation(s)
- Sherry Leonard
- Department of Psychiatry - University of Colorado Anschutz, Aurora, Colorado, USA
| | - Roberta Benfante
- CNR - Institute of Neuroscience, Vedano al Lambro (MB), Italy; Dept. Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy; NeuroMI - Milan Center for Neuroscience, University of Milano Bicocca, Milan, Italy.
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