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Zhang Y, Chen Z, Wang X, Yan R, Bao H, Chu X, Guo L, Wang X, Li Y, Mu Y, He Q, Zhang L, Zhang C, Zhou D, Ji D. Site-specific tethering nanobodies on recombinant adeno-associated virus vectors for retargeted gene therapy. Acta Biomater 2024:S1742-7061(24)00390-8. [PMID: 39025389 DOI: 10.1016/j.actbio.2024.07.023] [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: 04/01/2024] [Revised: 06/30/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024]
Abstract
Recombinant adeno-associated viruses (rAAVs) have been extensively studied for decades as carriers for delivering therapeutic genes. However, designing rAAV vectors with selective tropism for specific cell types and tissues has remained challenging. Here, we introduce a strategy for redirecting rAAV by attaching nanobodies with desired tropism at specific sites, effectively replacing the original tropism. To demonstrate this concept, we initially modified the genetic code of rAAV2 to introduce an azido-containing unnatural amino acid at a precise site within the capsid protein. Following a screening process, we identified a critical site (N587+1) where the introduction of unnatural amino acid eliminated the natural tropism of rAAV2. Subsequently, we successfully redirected rAAV2 by conjugating various nanobodies at the N587+1 site, using click and SpyTag-Spycatcher chemistries to form nanobody-AAV conjugates (NACs). By investigating the relationship between NACs quantity and effect and optimizing the linker between rAAV2 and the nanobody using a cathepsin B-susceptible valine-citrulline (VC) dipeptide, we significantly improved gene delivery efficiency both in vitro and in vivo. This enhancement can be attributed to the facilitated endosomal escape of rAAV2. Our method offers an exciting avenue for the rational modification of rAAV2 as a retargeting vehicle, providing a convenient platform for precisely engineering various rAAV2 vectors for both basic research and therapeutic applications. STATEMENT OF SIGNIFICANCE: AAVs hold great promise in the treatment of genetic diseases, but their clinical use has been limited by off-target transduction and efficiency. Here, we report a strategy to construct NACs by conjugating a nanobody or scFv to an rAAV capsid site, specifically via biorthogonal click chemistry and a spy-spycatcher reaction. We explored the structure-effect and quantity-effect relationships of NACs and then optimized the transduction efficiency by introducing a valine-citrulline peptide linker. This approach provides a biocompatible method for rational modification of rAAV as a retargeting platform without structural disruption of the virus or alteration of the binding capacity of the nanobody, with potential utility across a broad spectrum of applications in targeted imaging and gene delivery.
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Affiliation(s)
- Yuanjie Zhang
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Peking University Ningbo Institute of Marine Medicines, Ningbo, China.
| | - Zhiqian Chen
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Xiaoyang Wang
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Peking University Ningbo Institute of Marine Medicines, Ningbo, China.
| | - Rongding Yan
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Han Bao
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Xindang Chu
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Lingfeng Guo
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Xinchen Wang
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Yuanhao Li
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Peking University Ningbo Institute of Marine Medicines, Ningbo, China.
| | - Yu Mu
- Shenzhen Bay Laboratory, Gaoke International Innovation Center, Shenzhen, China.
| | - Qiuchen He
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Peking University Ningbo Institute of Marine Medicines, Ningbo, China.
| | - Lihe Zhang
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Chuanling Zhang
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Demin Zhou
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Shenzhen Bay Laboratory, Gaoke International Innovation Center, Shenzhen, China; Peking University Ningbo Institute of Marine Medicines, Ningbo, China.
| | - Dezhong Ji
- Peking University-Yunnan Baiiyao International Medical Research Center, ChemicalBiology Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Peking University Ningbo Institute of Marine Medicines, Ningbo, China.
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2
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Zheng Z, Wu X, Wang Y, Yang X, Chen H, Shen Y, Yang Y, Xia Q. Attenuating RNA Viruses with Expanded Genetic Codes to Evoke Adjustable Immune Response in PylRS-tRNACUAPyl Transgenic Mice. Vaccines (Basel) 2023; 11:1606. [PMID: 37897007 PMCID: PMC10610612 DOI: 10.3390/vaccines11101606] [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: 07/30/2023] [Revised: 09/03/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
Ribonucleic acid (RNA) viruses pose heavy burdens on public-health systems. Synthetic biology holds great potential for artificially controlling their replication, a strategy that could be used to attenuate infectious viruses but is still in the exploratory stage. Herein, we used the genetic-code expansion technique to convert Enterovirus 71 (EV71), a prototypical RNA virus, into a controllable EV71 strain carrying the unnatural amino acid (UAA) Nε-2-azidoethyloxycarbonyl-L-lysine (NAEK), which we termed an EV71-NAEK virus. After NAEK supplementation, EV71-NAEK could recapitulate an authentic NAEK time- and dose-dependent infection in vitro, which could serve as a novel method to manipulate virulent viruses in conventional laboratories. We further validated the prophylactic effect of EV71-NAEK in two mouse models. In susceptible parent mice, vaccination with EV71-NAEK elicited a strong immune response and protected their neonatal offspring from lethal challenges similar to that of commercial vaccines. Meanwhile, in transgenic mice harboring a PylRS-tRNACUAPyl pair, substantial elements of genetic-code expansion technology, EV71-NAEK evoked an adjustable neutralizing-antibody response in a strictly external NAEK dose-dependent manner. These findings suggested that EV71-NAEK could be the basis of a feasible immunization program for populations with different levels of immunity. Moreover, we expanded the strategy to generate controllable coxsackieviruses for conceptual verification. In combination, these results could underlie a competent strategy for attenuating viruses and priming the immune system via artificial control, which might be a promising direction for the development of amenable vaccine candidates and be broadly applied to other RNA viruses.
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Affiliation(s)
| | | | | | | | | | | | | | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; (Z.Z.); (X.W.); (Y.W.); (X.Y.); (H.C.); (Y.S.); (Y.Y.)
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3
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Ma XY, Hill BD, Hoang T, Wen F. Virus-inspired strategies for cancer therapy. Semin Cancer Biol 2022; 86:1143-1157. [PMID: 34182141 PMCID: PMC8710185 DOI: 10.1016/j.semcancer.2021.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 01/27/2023]
Abstract
The intentional use of viruses for cancer therapy dates back over a century. As viruses are inherently immunogenic and naturally optimized delivery vehicles, repurposing viruses for drug delivery, tumor antigen presentation, or selective replication in cancer cells represents a simple and elegant approach to cancer treatment. While early virotherapy was fraught with harsh side effects and low response rates, virus-based therapies have recently seen a resurgence due to newfound abilities to engineer and tune oncolytic viruses, virus-like particles, and virus-mimicking nanoparticles for improved safety and efficacy. However, despite their great potential, very few virus-based therapies have made it through clinical trials. In this review, we present an overview of virus-inspired approaches for cancer therapy, discuss engineering strategies to enhance their mechanisms of action, and highlight their application for overcoming the challenges of traditional cancer therapies.
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Affiliation(s)
- Xiao Yin Ma
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Brett D Hill
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Trang Hoang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States.
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4
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Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 478] [Impact Index Per Article: 239.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
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5
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Giannakoulias S, Shringari SR, Ferrie JJ, Petersson EJ. Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine. Sci Rep 2021; 11:18406. [PMID: 34526629 PMCID: PMC8443755 DOI: 10.1038/s41598-021-97965-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/17/2021] [Indexed: 11/08/2022] Open
Abstract
The incorporation of unnatural amino acids (Uaas) has provided an avenue for novel chemistries to be explored in biological systems. However, the successful application of Uaas is often hampered by site-specific impacts on protein yield and solubility. Although previous efforts to identify features which accurately capture these site-specific effects have been unsuccessful, we have developed a set of novel Rosetta Custom Score Functions and alternative Empirical Score Functions that accurately predict the effects of acridon-2-yl-alanine (Acd) incorporation on protein yield and solubility. Acd-containing mutants were simulated in PyRosetta, and machine learning (ML) was performed using either the decomposed values of the Rosetta energy function, or changes in residue contacts and bioinformatics. Using these feature sets, which represent Rosetta score function specific and bioinformatics-derived terms, ML models were trained to predict highly abstract experimental parameters such as mutant protein yield and solubility and displayed robust performance on well-balanced holdouts. Model feature importance analyses demonstrated that terms corresponding to hydrophobic interactions, desolvation, and amino acid angle preferences played a pivotal role in predicting tolerance of mutation to Acd. Overall, this work provides evidence that the application of ML to features extracted from simulated structural models allow for the accurate prediction of diverse and abstract biological phenomena, beyond the predictivity of traditional modeling and simulation approaches.
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Affiliation(s)
- Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St, Philadelphia, PA, 19104, USA
| | - Sumant R Shringari
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St, Philadelphia, PA, 19104, USA
| | - John J Ferrie
- Department of Molecular & Cell Biology, University of California, Berkeley, 475B Li Ka Shing Center, Berkeley, CA, 94720, USA.
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St, Philadelphia, PA, 19104, USA.
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6
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Hao R, Ma K, Ru Y, Li D, Song G, Lu B, Liu H, Li Y, Zhang J, Wu C, Zhang G, Hu H, Luo J, Zheng H. Amber codon is genetically unstable in generation of premature termination codon (PTC)-harbouring Foot-and-mouth disease virus (FMDV) via genetic code expansion. RNA Biol 2021; 18:2330-2341. [PMID: 33849391 DOI: 10.1080/15476286.2021.1907055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The foot-and-mouth disease virus (FMDV) is the causative agent of FMD, a highly infectious and devastating viral disease of domestic and wild cloven-hoofed animals. FMD affects livestock and animal products' national and international trade, causing severe economic losses and social consequences. Currently, inactivated vaccines play a vital role in FMD control, but they have several limitations. The genetic code expansion technology provides powerful strategies for generating premature termination codon (PTC)-harbouring virus as a live but replication-incompetent viral vaccine. However, this technology has not been explored for the design and development of new FMD vaccines. In this study, we first expanded the genetic code of the FMDV genome via a transgenic cell line containing an orthogonal translation machinery. We demonstrated that the transgenic cells stably integrated the orthogonal pyltRNA/pylRS pair into the genome and enabled efficient, homogeneous incorporation of unnatural amino acids into target proteins in mammalian cells. Next, we constructed 129 single-PTC FMDV mutants and four dual-PTC FMDV mutants after considering the tolerance, location, and potential functions of those mutated sites. Amber stop codons individually substituted the selected amino acid codons in four viral proteins (3D, L, VP1, and VP4) of FMDV. We successfully rescued PTC-FMDV mutants, but the amber codon unexpectedly showed a highly degree of mutation rate during PTC-FMDV packaging and replication. Our findings highlight that the genetic code expansion technology for the generation of PTC-FMD vaccines needs to be further improved and that the genetic stability of amber codons during the packaging and replication of FMDV is a concern.
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Affiliation(s)
- Rongzeng Hao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kun Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yi Ru
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Gaoyuan Song
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingzhou Lu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huanan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yajun Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jiaoyan Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunping Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guicai Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haitao Hu
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development and Institute for Human Infections and Immunity, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
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7
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Wang Y, Li S, Tian Z, Sun J, Liang S, Zhang B, Bai L, Zhang Y, Zhou X, Xiao S, Zhang Q, Zhang L, Zhang C, Zhou D. Generation of a caged lentiviral vector through an unnatural amino acid for photo-switchable transduction. Nucleic Acids Res 2019; 47:e114. [PMID: 31361892 PMCID: PMC6821241 DOI: 10.1093/nar/gkz659] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 07/06/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022] Open
Abstract
Application of viral vectors in gene delivery is attracting widespread attention but is hampered by the absence of control over transduction, which may lead to non-selective transduction with adverse side effects. To overcome some of these limitations, we proposed an unnatural amino acid aided caging–uncaging strategy for controlling the transduction capability of a viral vector. In this proof-of-principle study, we first expanded the genetic code of the lentiviral vector to incorporate an azido-containing unnatural amino acid (Nϵ-2-azidoethyloxycarbonyl-l-lysine, NAEK) site specifically within a lentiviral envelope protein. Screening of the resultant vectors indicated that NAEK incorporation at Y77 and Y116 was capable of inactivating viral transduction upon click conjugation with a photo-cleavable chemical molecule (T1). Exposure of the chimeric viral vector (Y77-T1) to UVA light subsequently removed the photo-caging group and restored the transduction capability of lentiviral vector both in vitro and in vivo. Our results indicate that the use of the photo-uncage activation procedure can reverse deactivated lentiviral vectors and thus enable regulation of viral transduction in a switchable manner. The methods presented here may be a general approach for generating various switchable vectors that respond to different stimulations and adapt to different viral vectors.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Shuai Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenyu Tian
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jiaqi Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Shuobin Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bo Zhang
- Center for Translational Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lu Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuanjie Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xueying Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Sulong Xiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qiang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chuanling Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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8
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Bauler M, Roberts JK, Wu CC, Fan B, Ferrara F, Yip BH, Diao S, Kim YI, Moore J, Zhou S, Wielgosz MM, Ryu B, Throm RE. Production of Lentiviral Vectors Using Suspension Cells Grown in Serum-free Media. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 17:58-68. [PMID: 31890741 PMCID: PMC6931067 DOI: 10.1016/j.omtm.2019.11.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/15/2019] [Indexed: 02/09/2023]
Abstract
Lentiviral vectors are increasingly utilized in cell and gene therapy applications because they efficiently transduce target cells such as hematopoietic stem cells and T cells. Large-scale production of current Good Manufacturing Practices-grade lentiviral vectors is limited because of the adherent, serum-dependent nature of HEK293T cells used in the manufacturing process. To optimize large-scale clinical-grade lentiviral vector production, we developed an improved production scheme by adapting HEK293T cells to grow in suspension using commercially available and chemically defined serum-free media. Lentiviral vectors with titers equivalent to those of HEK293T cells were produced from SJ293TS cells using optimized transfection conditions that reduced the required amount of plasmid DNA by 50%. Furthermore, purification of SJ293TS-derived lentiviral vectors at 1 L yielded a recovery of 55% ± 14% (n = 138) of transducing units in the starting material, more than a 2-fold increase over historical yields from adherent HEK293T serum-dependent lentiviral vector preparations. SJ293TS cells were stable to produce lentiviral vectors over 4 months of continuous culture. SJ293TS-derived lentiviral vectors efficiently transduced primary hematopoietic stem cells and T cells from healthy donors. Overall, our SJ293TS cell line enables high-titer vector production in serum-free conditions while reducing the amount of input DNA required, resulting in a highly efficient manufacturing option.
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Affiliation(s)
- Matthew Bauler
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jessica K Roberts
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chang-Chih Wu
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Baochang Fan
- Therapeutics Production and Quality, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Francesca Ferrara
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bon Ham Yip
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shiyong Diao
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Young-In Kim
- Experimental Cell Therapeutics Lab, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer Moore
- Experimental Cell Therapeutics Lab, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheng Zhou
- Experimental Cell Therapeutics Lab, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Matthew M Wielgosz
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Byoung Ryu
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert E Throm
- Vector Development and Production Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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9
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Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
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Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
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10
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Chen G, Katrekar D, Mali P. RNA-Guided Adenosine Deaminases: Advances and Challenges for Therapeutic RNA Editing. Biochemistry 2019; 58:1947-1957. [PMID: 30943016 DOI: 10.1021/acs.biochem.9b00046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Targeted transcriptome engineering, in contrast to genome engineering, offers a complementary and potentially tunable and reversible strategy for cellular engineering. In this regard, adenosine to inosine (A-to-I) RNA base editing was recently engineered to make programmable base conversions on target RNAs. Similar to the DNA base editing technology, A-to-I RNA editing may offer an attractive alternative in a therapeutic setting, especially for the correction of point mutations. This Perspective introduces five currently characterized RNA editing systems and serves as a reader's guide for implementing an appropriate RNA editing strategy for applications in research or therapeutics.
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Affiliation(s)
- Genghao Chen
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093-0412 , United States
| | - Dhruva Katrekar
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093-0412 , United States
| | - Prashant Mali
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093-0412 , United States
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11
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Hostetler ZM, Ferrie JJ, Bornstein MR, Sungwienwong I, Petersson EJ, Kohli RM. Systematic Evaluation of Soluble Protein Expression Using a Fluorescent Unnatural Amino Acid Reveals No Reliable Predictors of Tolerability. ACS Chem Biol 2018; 13:2855-2861. [PMID: 30216041 PMCID: PMC6195468 DOI: 10.1021/acschembio.8b00696] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Improvements in genetic code expansion have made preparing proteins with diverse functional groups almost routine. Nonetheless, unnatural amino acids (Uaas) pose theoretical burdens on protein solubility, and determinants of position-specific tolerability to Uaas remain underexplored. To broadly examine associations, we systematically assessed the effect of substituting the fluorescent Uaa, acridonylalanine, at more than 50 chemically, evolutionarily, and structurally diverse residues in two bacterial proteins: LexA and RecA. Surprisingly, properties that ostensibly contribute to Uaa tolerability-such as conservation, hydrophobicity, or accessibility-demonstrated no consistent correlations with resulting protein solubility. Instead, solubility is closely dependent on the location of the substitution within the overall tertiary structure, suggesting that intrinsic properties of protein domains, and not individual positions, are stronger determinants of Uaa tolerability. Consequently, those who seek to install Uaas in new target proteins should consider broadening, rather than narrowing, the types of residues screened for Uaa incorporation.
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Affiliation(s)
- Zachary M. Hostetler
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - John J. Ferrie
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Marc R. Bornstein
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Itthipol Sungwienwong
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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12
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Kelemen RE, Erickson SB, Chatterjee A. Synthesis at the interface of virology and genetic code expansion. Curr Opin Chem Biol 2018; 46:164-171. [PMID: 30086446 DOI: 10.1016/j.cbpa.2018.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/18/2018] [Accepted: 07/13/2018] [Indexed: 01/24/2023]
Abstract
How a virus efficiently invades its host cell and masterfully engineers its properties provides valuable lessons and resources for the emerging discipline of synthetic biology, which seeks to create engineered biological systems with novel functions. Recently, the toolbox of synthetic biology has also been enriched by the genetic code expansion technology, which has provided access to a large assortment of unnatural amino acids with novel chemical functionalities that can be site-specifically incorporated into proteins in living cells. The synergistic interplay of these two disciplines holds much promise to advance their individual progress, while creating new paradigms for synthetic biology. In this review we seek to provide an account of the recent advances at the interface of these two research areas.
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Affiliation(s)
- Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States
| | - Sarah B Erickson
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States.
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13
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Katrekar D, Moreno AM, Chen G, Worlikar A, Mali P. Oligonucleotide conjugated multi-functional adeno-associated viruses. Sci Rep 2018; 8:3589. [PMID: 29483550 PMCID: PMC5827683 DOI: 10.1038/s41598-018-21742-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/07/2018] [Indexed: 02/06/2023] Open
Abstract
Recombinant adeno-associated viruses (AAVs) are among the most commonly used vehicles for in vivo gene delivery. However, their tropism is limited, and additionally their efficacy can be negatively affected by prevalence of neutralizing antibodies in sera. Methodologies to systematically engineer AAV capsid properties would thus be of great relevance. In this regard, we develop here multi-functional AAVs by engineering precision tethering of oligonucleotides onto the AAV surface, and thereby enabling a spectrum of nucleic-acid programmable functionalities. Towards this, we engineered genetically encoded incorporation of unnatural amino acids (UAA) bearing bio-orthogonal chemical handles onto capsid proteins. Via these we enabled site-specific coupling of oligonucleotides onto the AAV capsid surface using facile click chemistry. The resulting oligo-AAVs could be sequence specifically labeled, and also patterned in 2D using DNA array substrates. Additionally, we utilized these oligo conjugations to engineer viral shielding by lipid-based cloaks that efficaciously protected the AAV particles from neutralizing serum. We confirmed these 'cloaked AAVs' retained full functionality via their ability to transduce a range of cell types, and also enable robust delivery of CRISPR-Cas9 effectors. Taken together, we anticipate this programmable oligo-AAV system will have broad utility in synthetic biology and AAV engineering applications.
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Affiliation(s)
- Dhruva Katrekar
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Ana M Moreno
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Genghao Chen
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Atharv Worlikar
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, CA, USA.
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14
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Zhang C, Zhou X, Yao T, Tian Z, Zhou D. Precision Fluorescent Labeling of an Adeno-Associated Virus Vector to Monitor the Viral Infection Pathway. Biotechnol J 2018; 13:e1700374. [DOI: 10.1002/biot.201700374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 12/04/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Chuanling Zhang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; Beijing 100191 China
| | - Xueying Zhou
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; Beijing 100191 China
| | - Tianzhuo Yao
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; Beijing 100191 China
| | - Zhenyu Tian
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; Beijing 100191 China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; Beijing 100191 China
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15
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Zhang Z, Xu H, Si L, Chen Y, Zhang B, Wang Y, Wu Y, Zhou X, Zhang L, Zhou D. Construction of an inducible stable cell line for efficient incorporation of unnatural amino acids in mammalian cells. Biochem Biophys Res Commun 2017; 489:490-496. [DOI: 10.1016/j.bbrc.2017.05.178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
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16
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Sakin V, Hanne J, Dunder J, Anders-Össwein M, Laketa V, Nikić I, Kräusslich HG, Lemke EA, Müller B. A Versatile Tool for Live-Cell Imaging and Super-Resolution Nanoscopy Studies of HIV-1 Env Distribution and Mobility. Cell Chem Biol 2017; 24:635-645.e5. [PMID: 28457706 DOI: 10.1016/j.chembiol.2017.04.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/12/2017] [Accepted: 04/06/2017] [Indexed: 12/27/2022]
Abstract
The envelope glycoproteins (Env) of HIV-1 mediate cell entry through fusion of the viral envelope with a target cell membrane. Intramembrane mobility and clustering of Env trimers at the viral budding site are essential for its function. Previous live-cell and super-resolution microscopy studies were limited by lack of a functional fluorescent Env derivative, requiring antibody labeling for detection. Introduction of a bio-orthogonal amino acid by genetic code expansion, combined with click chemistry, offers novel possibilities for site-specific, minimally invasive labeling. Using this approach, we established efficient incorporation of non-canonical amino acids within HIV-1 Env in mammalian cells. The engineered protein retained plasma membrane localization, glycosylation, virion incorporation, and fusogenic activity, and could be rapidly and specifically labeled with synthetic dyes. This strategy allowed us to revisit Env dynamics and nanoscale distribution at the plasma membrane close to its native state, applying fluorescence recovery after photo bleaching and STED nanoscopy, respectively.
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Affiliation(s)
- Volkan Sakin
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Janina Hanne
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; Optical Nanoscopy Division, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Jessica Dunder
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Maria Anders-Össwein
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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17
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Fatty acid synthase cooperates with protrudin to facilitate membrane outgrowth of cellular protrusions. Sci Rep 2017; 7:46569. [PMID: 28429738 PMCID: PMC5399442 DOI: 10.1038/srep46569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/17/2017] [Indexed: 01/02/2023] Open
Abstract
Cellular protrusion formation capacity is a key feature of developing neurons and many eukaryotic cells. However, the mechanisms underlying membrane growth in protrusion formation are largely unclear. In this study, photo-reactive unnatural amino acid 3-(3-methyl-3H-diazirin-3-yl)-propamino-carbonyl-Nε-l-lysine was incorporated by a genetic code expansion strategy into protrudin, a protein localized in acidic endosomes and in the endoplasmic reticulum, that induces cellular protrusion and neurite formation. The modified protrudin was used for covalent trapping of protrudin-interacting proteins in living cells. Fatty acid synthase (FASN), which synthesizes free fatty acids, was identified to transiently interact with protrudin. Further characterization revealed a unique cooperation mechanism in which protrudin cooperates with FASN to facilitate cellular protrusion formation. This work reveals a novel mechanism involved in protrusion formation that is dependent on transient interaction between FASN and protrudin, and establishes a creative strategy to investigate transient protein-protein interactions in mammalian cells.
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18
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Si L, Xu H, Zhou X, Zhang Z, Tian Z, Wang Y, Wu Y, Zhang B, Niu Z, Zhang C, Fu G, Xiao S, Xia Q, Zhang L, Zhou D. Generation of influenza A viruses as live but replication-incompetent virus vaccines. Science 2016; 354:1170-1173. [DOI: 10.1126/science.aah5869] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/08/2016] [Indexed: 01/16/2023]
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Abstract
Transcription activator-like effector nucleases (TALENs) are one of several types of programmable, engineered nucleases that bind and cleave specific DNA sequences. Cellular machinery repairs the cleaved DNA by introducing indels. In this review, we emphasize the potential, explore progress, and identify challenges in using TALENs as a therapeutic tool to treat HIV infection. TALENs have less off-target editing and can be more effective at tolerating HIV escape mutations than CRISPR/Cas-9. Scientists have explored TALEN-mediated editing of host genes such as viral entry receptors (CCR5 and CXCR4) and a protein involved in proviral integration (LEDGF/p75). Viral targets include the proviral DNA, particularly focused on the long terminal repeats. Major challenges with translating gene therapy from bench to bedside are improving cleavage efficiency and delivery, while minimizing off-target editing, cytotoxicity, and immunogenicity. However, rapid improvements in TALEN technology are enhancing cleavage efficiency and specificity. Therapeutic testing in animal models of HIV infection will help determine whether TALENs are a viable HIV treatment therapy. TALENs or other engineered nucleases could shift the therapeutic paradigm from life-long antiretroviral therapy toward eradication of HIV infection.
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20
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Xu H, Wang Y, Lu J, Zhang B, Zhang Z, Si L, Wu L, Yao T, Zhang C, Xiao S, Zhang L, Xia Q, Zhou D. Re-exploration of the Codon Context Effect on Amber Codon-Guided Incorporation of Noncanonical Amino Acids in Escherichia coli by the Blue-White Screening Assay. Chembiochem 2016; 17:1250-6. [PMID: 27028123 DOI: 10.1002/cbic.201600117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022]
Abstract
The effect of codon context on amber codon-guided incorporation of noncanonical amino acids (NAAs) has been previously examined by antibiotic selection. Here, we re-explored this effect by screening a library in which three nucleotides upstream and downstream of the amber codon were randomised, and inserted within the lacZ-α gene. Thousands of clones were obtained and distinguished by the depth of blue colour upon exposure to X-gal. Large-scale sequencing revealed remarkable preferences in nucleotides downstream of the amber codon, and moderate preferences for upstream nucleotides. Nucleotide preference was quantified by a dual-luciferase assay, which verified that the optimum context for NAA incorporation, AATTAGACT, was applicable to different proteins. Our work provides a general guide for engineering amber codons into genes of interest in bacteria.
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Affiliation(s)
- Huan Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Yan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Jiaqi Lu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Ziwei Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Longlong Si
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Ling Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Tianzhuo Yao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Chuanling Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Sulong Xiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China.
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China.
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21
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Zhang B, Yang Q, Chen J, Wu L, Yao T, Wu Y, Xu H, Zhang L, Xia Q, Zhou D. CRISPRi-Manipulation of Genetic Code Expansion via RF1 for Reassignment of Amber Codon in Bacteria. Sci Rep 2016; 6:20000. [PMID: 26818534 PMCID: PMC4730227 DOI: 10.1038/srep20000] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/22/2015] [Indexed: 11/09/2022] Open
Abstract
The precise engineering of proteins in bacteria via the amber codon has been hampered by the poor incorporation of unnatural amino acid (UAA). Here we explored the amber assignment as a sense codon for UAA by CRISPRi targeting release factor 1 (RF1). Scanning of RF1 gene with sgRNAs identified target loci that differentiate RF1 repressions. Quantitation of RF1 repressions versus UAA incorporation indicated an increasing interrelation with the amber reassignment maximized upon RF1 knockdown to ~30%, disclosing the beneficial role of RF1 in amber assignment. However, further RF1 repression reversed this trend resulting from the detrimental effects on host cell growth, disclosing the harmful aspect of RF1 in reassignment of the amber codon. Our data indicate RF1 as a switch manipulating genetic code expansion and pave a direction via CRISPRi for precise engineering and efficient production of proteins in bacteria.
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Affiliation(s)
- Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
| | - Qi Yang
- Department of Chemical Biology, Peking University, Beijing 100191, China
| | - Jingxian Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
| | - Ling Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
| | - Tianzhuo Yao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
| | - Yiming Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
| | - Huan Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
| | - Qing Xia
- Department of Chemical Biology, Peking University, Beijing 100191, China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences
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