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Schloßhauer JL, Tholen L, Körner A, Kubick S, Chatzopoulou S, Hönow A, Zemella A. Promoting the production of challenging proteins via induced expression in CHO cells and modified cell-free lysates harboring T7 RNA polymerase and mutant eIF2α. Synth Syst Biotechnol 2024; 9:416-424. [PMID: 38601208 PMCID: PMC11004649 DOI: 10.1016/j.synbio.2024.03.011] [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: 12/08/2023] [Revised: 02/12/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024] Open
Abstract
Chinese hamster ovary (CHO) cells are crucial in biopharmaceutical production due to their scalability and capacity for human-like post-translational modifications. However, toxic proteins and membrane proteins are often difficult-to-express in living cells. Alternatively, cell-free protein synthesis can be employed. This study explores innovative strategies for enhancing the production of challenging proteins through the modification of CHO cells by investigating both, cell-based and cell-free approaches. A major result in our study involves the integration of a mutant eIF2 translation initiation factor and T7 RNA polymerase into CHO cell lysates for cell-free protein synthesis. This resulted in elevated yields, while eliminating the necessity for exogenous additions during cell-free production, thereby substantially enhancing efficiency. Additionally, we explore the potential of the Rosa26 genomic site for the integration of T7 RNA polymerase and cell-based tetracycline-controlled protein expression. These findings provide promising advancements in bioproduction technologies, offering flexibility to switch between cell-free and cell-based protein production as needed.
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Affiliation(s)
- Jeffrey L. Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Lena Tholen
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
| | - Alexander Körner
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus –Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Sofia Chatzopoulou
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
| | - Anja Hönow
- New/era/mabs GmbH, August-Bebel-Str. 89, 14482, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
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2
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Allen-Coyle TJ, Roca BC, Costello A, Barron N, Keenan J, Clynes M, O’Neill F, O’Sullivan F. miRNA- and Cell Line-Specific Constraints on Precursor miRNA Processing of Stably Transfected Pancreatic Cancer and Other Mammalian Cells. Int J Mol Sci 2024; 25:5666. [PMID: 38891854 PMCID: PMC11172344 DOI: 10.3390/ijms25115666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
MicroRNAs (miRNAs) regulate approximately one-third of all human genes. The dysregulation of miRNAs has been implicated in the development of numerous human diseases, including cancers. In our investigation focusing on altering specific miRNA expression in human pancreatic cancer cells, we encountered an interesting finding. While two expression vector designs effectively enhanced miR-708 levels, they were unable to elevate mature forms of miR-29b, -1290, -2467, and -6831 in pancreatic cancer cell lines. This finding was also observed in a panel of other non-pancreatic cancer cell lines, suggesting that miRNA processing efficiency was cell line specific. Using a step-by-step approach in each step of miRNA processing, we ruled out alternative strand selection by the RISC complex and transcriptional interference at the primary miRNA (pri-miRNA) level. DROSHA processing and pri-miRNA export from the nucleus also appeared to be occurring normally. We observed precursor (pre-miRNA) accumulation only in cell lines where mature miRNA expression was not achieved, suggesting that the block was occurring at the pre-miRNA stage. To further confirm this, synthetic pre-miRNA mimics that bypass DICER processing were processed into mature miRNAs in all cases. This study has demonstrated the distinct behaviours of different miRNAs with the same vector in the same cell line, the same miRNA between the two vector designs, and with the same miRNA across different cell lines. We identified a stable vector pre-miRNA processing block. Our findings on the structural and sequence differences between successful and non-successful vector designs could help to inform future chimeric miRNA design strategies and act as a guide to other researchers on the intricate processing dynamics that can impact vector efficiency. Our research confirms the potential of miRNA mimics to surmount some of these complexities.
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Affiliation(s)
- Taylor J. Allen-Coyle
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Berta Capella Roca
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Alan Costello
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Niall Barron
- Cell Engineering Group, National Institute for Bioprocessing Research and Training (NIBRT), A94 X099 Dublin, Ireland
| | - Joanne Keenan
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Martin Clynes
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Fiona O’Neill
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Finbarr O’Sullivan
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
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3
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Nathans JF, Ayers JL, Shendure J, Simpson CL. Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin. J Invest Dermatol 2024; 144:936-949. [PMID: 38643988 PMCID: PMC11034889 DOI: 10.1016/j.jid.2024.02.006] [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: 12/19/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 04/23/2024]
Abstract
The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.
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Affiliation(s)
- Jenny F Nathans
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jessica L Ayers
- Molecular Medicine and Mechanisms of Disease PhD Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Dermatology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Cory L Simpson
- Department of Dermatology, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA.
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4
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De Carluccio G, Fusco V, di Bernardo D. Engineering a synthetic gene circuit for high-performance inducible expression in mammalian systems. Nat Commun 2024; 15:3311. [PMID: 38632224 PMCID: PMC11024104 DOI: 10.1038/s41467-024-47592-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: 09/28/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Inducible gene expression systems can be used to control the expression of a gene of interest by means of a small-molecule. One of the most common designs involves engineering a small-molecule responsive transcription factor (TF) and its cognate promoter, which often results in a compromise between minimal uninduced background expression (leakiness) and maximal induced expression. Here, we focus on an alternative strategy using quantitative synthetic biology to mitigate leakiness while maintaining high expression, without modifying neither the TF nor the promoter. Through mathematical modelling and experimental validations, we design the CASwitch, a mammalian synthetic gene circuit based on combining two well-known network motifs: the Coherent Feed-Forward Loop (CFFL) and the Mutual Inhibition (MI). The CASwitch combines the CRISPR-Cas endoribonuclease CasRx with the state-of-the-art Tet-On3G inducible gene system to achieve high performances. To demonstrate the potentialities of the CASwitch, we apply it to three different scenarios: enhancing a whole-cell biosensor, controlling expression of a toxic gene and inducible production of Adeno-Associated Virus (AAV) vectors.
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Affiliation(s)
- Giuliano De Carluccio
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
| | - Virginia Fusco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, Naples, Italy.
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy.
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5
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Henriques C, Lopes MM, Silva AC, Lobo DD, Badin RA, Hantraye P, Pereira de Almeida L, Nobre RJ. Viral-based animal models in polyglutamine disorders. Brain 2024; 147:1166-1189. [PMID: 38284949 DOI: 10.1093/brain/awae012] [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: 07/09/2023] [Revised: 11/26/2023] [Accepted: 12/30/2023] [Indexed: 01/30/2024] Open
Abstract
Polyglutamine disorders are a complex group of incurable neurodegenerative disorders caused by an abnormal expansion in the trinucleotide cytosine-adenine-guanine tract of the affected gene. To better understand these disorders, our dependence on animal models persists, primarily relying on transgenic models. In an effort to complement and deepen our knowledge, researchers have also developed animal models of polyglutamine disorders employing viral vectors. Viral vectors have been extensively used to deliver genes to the brain, not only for therapeutic purposes but also for the development of animal models, given their remarkable flexibility. In a time- and cost-effective manner, it is possible to use different transgenes, at varying doses, in diverse targeted tissues, at different ages, and in different species, to recreate polyglutamine pathology. This paper aims to showcase the utility of viral vectors in disease modelling, share essential considerations for developing animal models with viral vectors, and provide a comprehensive review of existing viral-based animal models for polyglutamine disorders.
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Affiliation(s)
- Carina Henriques
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Miguel M Lopes
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Ana C Silva
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Diana D Lobo
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Romina Aron Badin
- CEA, DRF, Institute of Biology François Jacob, Molecular Imaging Research Center (MIRCen), 92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, Université Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), 92265 Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institute of Biology François Jacob, Molecular Imaging Research Center (MIRCen), 92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, Université Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), 92265 Fontenay-aux-Roses, France
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Rui Jorge Nobre
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
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Hong J, Sohn KC, Park HW, Jeon H, Ju E, Lee JG, Lee JS, Rho J, Hur GM, Ro H. All-in-one IQ toggle switches with high versatilities for fine-tuning of transgene expression in mammalian cells and tissues. Mol Ther Methods Clin Dev 2024; 32:101202. [PMID: 38374964 PMCID: PMC10875299 DOI: 10.1016/j.omtm.2024.101202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
The transgene toggling device is recognized as a powerful tool for gene- and cell-based biological research and precision medicine. However, many of these devices often operate in binary mode, exhibit unacceptable leakiness, suffer from transgene silencing, show cytotoxicity, and have low potency. Here, we present a novel transgene switch, SIQ, wherein all the elements for gene toggling are packed into a single vector. SIQ has superior potency in inducing transgene expression in response to tebufenozide compared with the Gal4/UAS system, while completely avoiding transgene leakiness. Additionally, the ease and versatility of SIQ make it possible with a single construct to perform transient transfection, establish stable cell lines by targeting a predetermined genomic locus, and simultaneously produce adenovirus for transduction into cells and mammalian tissues. Furthermore, we integrated a cumate switch into SIQ, called SIQmate, to operate a Boolean AND logic gate, enabling swift toggling-off of the transgene after the removal of chemical inducers, tebufenozide and cumate. Both SIQ and SIQmate offer precise transgene toggling, making them adjustable for various researches, including synthetic biology, genome engineering, and therapeutics.
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Affiliation(s)
- Jeongkwan Hong
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Kyung-Cheol Sohn
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon 301 747, Korea (ROK)
| | - Hye-Won Park
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Hyoeun Jeon
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Eunjin Ju
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon 301 747, Korea (ROK)
| | - Jae-Geun Lee
- Microbiome Convergence Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jeong-Soo Lee
- Microbiome Convergence Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KRIBB School, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jaerang Rho
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Gang Min Hur
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon 301 747, Korea (ROK)
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
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Nassauer L, Staecker H, Huang P, Renslo B, Goblet M, Harre J, Warnecke A, Schott JW, Morgan M, Galla M, Schambach A. Protection from cisplatin-induced hearing loss with lentiviral vector-mediated ectopic expression of the anti-apoptotic protein BCL-XL. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102157. [PMID: 38450280 PMCID: PMC10915631 DOI: 10.1016/j.omtn.2024.102157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/15/2024] [Indexed: 03/08/2024]
Abstract
Cisplatin is a highly effective chemotherapeutic agent, but it can cause sensorineural hearing loss (SNHL) in patients. Cisplatin-induced ototoxicity is closely related to the accumulation of reactive oxygen species (ROS) and subsequent death of hair cells (HCs) and spiral ganglion neurons (SGNs). Despite various strategies to combat ototoxicity, only one therapeutic agent has thus far been clinically approved. Therefore, we have developed a gene therapy concept to protect cochlear cells from cisplatin-induced toxicity. Self-inactivating lentiviral (LV) vectors were used to ectopically express various antioxidant enzymes or anti-apoptotic proteins to enhance the cellular ROS scavenging or prevent apoptosis in affected cell types. In direct comparison, anti-apoptotic proteins mediated a stronger reduction in cytotoxicity than antioxidant enzymes. Importantly, overexpression of the most promising candidate, Bcl-xl, achieved an up to 2.5-fold reduction in cisplatin-induced cytotoxicity in HEI-OC1 cells, phoenix auditory neurons, and primary SGN cultures. BCL-XL protected against cisplatin-mediated tissue destruction in cochlear explants. Strikingly, in vivo application of the LV BCL-XL vector improved hearing and increased HC survival in cisplatin-treated mice. In conclusion, we have established a preclinical gene therapy approach to protect mice from cisplatin-induced ototoxicity that has the potential to be translated to clinical use in cancer patients.
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Affiliation(s)
- Larissa Nassauer
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Hinrich Staecker
- Department of Otolaryngology-Head and Neck Surgery, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Peixin Huang
- Department of Otolaryngology-Head and Neck Surgery, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Bryan Renslo
- Department of Otolaryngology-Head and Neck Surgery, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Madeleine Goblet
- Department of Otorhinolaryngology, Head and Neck Surgery, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence “Hearing4all”, Hannover Medical School, 30625 Hannover, Germany
| | - Jennifer Harre
- Department of Otorhinolaryngology, Head and Neck Surgery, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence “Hearing4all”, Hannover Medical School, 30625 Hannover, Germany
| | - Athanasia Warnecke
- Department of Otorhinolaryngology, Head and Neck Surgery, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence “Hearing4all”, Hannover Medical School, 30625 Hannover, Germany
| | - Juliane W. Schott
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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8
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Rabinowitch I, Colón-Ramos DA, Krieg M. Understanding neural circuit function through synaptic engineering. Nat Rev Neurosci 2024; 25:131-139. [PMID: 38172626 DOI: 10.1038/s41583-023-00777-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Synapses are a key component of neural circuits, facilitating rapid and specific signalling between neurons. Synaptic engineering - the synthetic insertion of new synaptic connections into in vivo neural circuits - is an emerging approach for neural circuit interrogation. This approach is especially powerful for establishing causality in neural circuit structure-function relationships, for emulating synaptic plasticity and for exploring novel patterns of circuit connectivity. Contrary to other approaches for neural circuit manipulation, synaptic engineering targets specific connections between neurons and functions autonomously with no user-controlled external activation. Synaptic engineering has been successfully implemented in several systems and in different forms, including electrical synapses constructed from ectopically expressed connexin gap junction proteins, synthetic optical synapses composed of presynaptic photon-emitting luciferase coupled with postsynaptic light-gated channels, and artificial neuropeptide signalling pathways. This Perspective describes these different methods and how they have been applied, and examines how the field may advance.
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Affiliation(s)
- Ithai Rabinowitch
- Department of Medical Neurobiology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Daniel A Colón-Ramos
- Wu Tsai Institute, Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Michael Krieg
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
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9
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Bello AJ, Popoola A, Okpuzor J, Ihekwaba-Ndibe AE, Olorunniji FJ. A Genetic Circuit Design for Targeted Viral RNA Degradation. Bioengineering (Basel) 2023; 11:22. [PMID: 38247899 PMCID: PMC10813695 DOI: 10.3390/bioengineering11010022] [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: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Advances in synthetic biology have led to the design of biological parts that can be assembled in different ways to perform specific functions. For example, genetic circuits can be designed to execute specific therapeutic functions, including gene therapy or targeted detection and the destruction of invading viruses. Viral infections are difficult to manage through drug treatment. Due to their high mutation rates and their ability to hijack the host's ribosomes to make viral proteins, very few therapeutic options are available. One approach to addressing this problem is to disrupt the process of converting viral RNA into proteins, thereby disrupting the mechanism for assembling new viral particles that could infect other cells. This can be done by ensuring precise control over the abundance of viral RNA (vRNA) inside host cells by designing biological circuits to target vRNA for degradation. RNA-binding proteins (RBPs) have become important biological devices in regulating RNA processing. Incorporating naturally upregulated RBPs into a gene circuit could be advantageous because such a circuit could mimic the natural pathway for RNA degradation. This review highlights the process of viral RNA degradation and different approaches to designing genetic circuits. We also provide a customizable template for designing genetic circuits that utilize RBPs as transcription activators for viral RNA degradation, with the overall goal of taking advantage of the natural functions of RBPs in host cells to activate targeted viral RNA degradation.
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Affiliation(s)
- Adebayo J. Bello
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Biological Sciences, Redeemer’s University, Ede 232101, Osun State, Nigeria
| | - Abdulgafar Popoola
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Medical Laboratory Science, Kwara State University, Malete, Ilorin 241102, Kwara State, Nigeria
| | - Joy Okpuzor
- Department of Cell Biology & Genetics, University of Lagos, Akoka, Lagos 101017, Lagos State, Nigeria;
| | | | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
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10
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Stepanov AI, Zhurlova PA, Shuvaeva AA, Sokolinskaya EL, Gurskaya NG, Lukyanov KA, Putlyaeva LV. Optogenetics for sensors: On-demand fluorescent labeling of histone epigenetics. Biochem Biophys Res Commun 2023; 687:149174. [PMID: 37939505 DOI: 10.1016/j.bbrc.2023.149174] [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: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Post-translational modifications of histones to a large extent determine the functional state of chromatin loci. Dynamic visualization of histone modifications with genetically encoded fluorescent sensors makes it possible to monitor changes in the epigenetic state of a single living cell. At the same time, the sensors can potentially compete with endogenous factors recognizing these modifications. Thus, prolonged binding of the sensors to chromatin can affect normal epigenetic regulation. Here, we report an optogenetic sensor for live-cell visualization of histone H3 methylated at lysine-9 (H3K9me3) named MPP8-LAMS (MPP8-based light-activated modification sensor). MPP8-LAMS consists of several fusion protein parts (from N- to C-terminus): i) nuclear export signal (NES), ii) far-red fluorescent protein Katushka, iii) H3K9me3-binding reader domain of the human M phase phosphoprotein 8 (MPP8), iv) the light-responsive AsLOV2 domain, which exposes a nuclear localization signal (NLS) upon blue light stimulation. In the dark, due to the NES, MPP8-LAMS is localized in the cytosol. Under blue light illumination, MPP8-LAMS underwent an efficient translocation from cytosol to nucleus, enabling visualization of H3K9me3-enriched loci. Such an on-demand visualization minimizes potential impact on cell physiology as most of the time the sensor is separated from its target. In general, the present work extends the application of optogenetics to the area of advanced use of genetically encoded sensors.
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Affiliation(s)
- Afanasii I Stepanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Polina A Zhurlova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Alexandra A Shuvaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, 141701 Dolgoprudny, Russia
| | - Elena L Sokolinskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Nadya G Gurskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Lidia V Putlyaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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11
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Rovira E, Moreno B, Razquin N, Blázquez L, Hernández-Alcoceba R, Fortes P, Pastor F. Engineering U1-Based Tetracycline-Inducible Riboswitches to Control Gene Expression in Mammals. ACS NANO 2023; 17:23331-23346. [PMID: 37971502 DOI: 10.1021/acsnano.3c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Synthetic riboswitches are promising regulatory devices due to their small size, lack of immunogenicity, and ability to fine-tune gene expression in the absence of exogenous trans-acting factors. Based on a gene inhibitory system developed at our lab, termed U1snRNP interference (U1i), we developed tetracycline (TC)-inducible riboswitches that modulate mRNA polyadenylation through selective U1 snRNP recruitment. First, we engineered different TC-U1i riboswitches, which repress gene expression unless TC is added, leading to inductions of gene expression of 3-to-4-fold. Second, we developed a technique called Systematic Evolution of Riboswitches by Exponential Enrichment (SEREX), to isolate riboswitches with enhanced U1 snRNP binding capacity and activity, achieving inducibilities of up to 8-fold. Interestingly, by multiplexing riboswitches we increased inductions up to 37-fold. Finally, we demonstrated that U1i-based riboswitches are dose-dependent and reversible and can regulate the expression of reporter and endogenous genes in culture cells and mouse models, resulting in attractive systems for gene therapy applications. Our work probes SEREX as a much-needed technology for the in vitro identification of riboswitches capable of regulating gene expression in vivo.
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Affiliation(s)
- Eric Rovira
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
| | - Beatriz Moreno
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
| | - Nerea Razquin
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
| | - Lorea Blázquez
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031 Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ruben Hernández-Alcoceba
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid 28029, Spain
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid 28029, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid 28029, Spain
| | - Fernando Pastor
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid 28029, Spain
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12
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Meinzinger A, Zsigmond Á, Horváth P, Kellenberger A, Paréj K, Tallone T, Flachner B, Cserhalmi M, Lőrincz Z, Cseh S, Shmerling D. RuX: A Novel, Flexible, and Sensitive Mifepristone-Induced Transcriptional Regulation System. Int J Cell Biol 2023; 2023:7121512. [PMID: 37941807 PMCID: PMC10630016 DOI: 10.1155/2023/7121512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023] Open
Abstract
Inducible gene regulation methods are indispensable in diverse biological applications, yet many of them have severe limitations in their applicability. These include inducer toxicity, a limited variety of organisms the given system can be used in, and side effects of the induction method. In this study, a novel inducible system, the RuX system, was created using a mutant ligand-binding domain of the glucocorticoid receptor (CS1/CD), used together with various genetic elements such as the Gal4 DNA-binding domain or Cre recombinase. The RuX system is shown to be capable of over 1000-fold inducibility, has flexible applications, and is offered for use in cell cultures.
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Affiliation(s)
| | | | | | | | | | - Tiziano Tallone
- Department of Endocrinology, Metabolism and Cardiovascular Research, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Sándor Cseh
- TargetEx Biosciences Ltd., Dunakeszi, Hungary
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13
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Appelbaum J, Wei J, Mukherjee R, Ishida T, Rosser J, Saxby C, Chase J, Carlson M, Sather C, Rahfeldt W, Meechan M, Baldwin M, Flint L, Spurrell C, Gustafson J, Johnson A, Jensen M. Context-specific synthetic T cell promoters from assembled transcriptional elements. RESEARCH SQUARE 2023:rs.3.rs-3339290. [PMID: 37886484 PMCID: PMC10602160 DOI: 10.21203/rs.3.rs-3339290/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Genetic engineering of human lymphocytes for therapeutic applications is constrained by a lack of transgene transcriptional control, resulting in a compromised therapeutic index. Incomplete understanding of transcriptional logic limits the rational design of contextually responsive genetic modules1. Here, we juxtaposed rationally curated transcriptional response element (TRE) oligonucleotides by random concatemerization to generate a library from which we selected context-specific inducible synthetic promoters (iSynPros). Through functional selection, we screened an iSynPro library for "IF-THEN" logic-gated transcriptional responses in human CD8+ T cells expressing a 4-1BB second generation chimeric antigen receptor (CAR). iSynPros exhibiting stringent off-states in quiescent T cells and CAR activation-dependent transcriptional responsiveness were cloned and subjected to TRE composition and pattern analysis, as well as performance in regulating candidate antitumor potency enhancement modules. These data reveal synthetic TRE grammar can mediate logic-gated transgene transcription in human T cells that, when applied to CAR T cell engineering, enhance potency and improve therapeutic indices.
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Affiliation(s)
| | - Jia Wei
- Seattle Children's Research Institute
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14
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Kook YH, Lee H, Lee J, Jeong Y, Rho J, Heo WD, Lee S. AAV-compatible optogenetic tools for activating endogenous calcium channels in vivo. Mol Brain 2023; 16:73. [PMID: 37848907 PMCID: PMC10583393 DOI: 10.1186/s13041-023-01061-7] [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: 08/30/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Calcium ions (Ca2+) play pivotal roles in regulating diverse brain functions, including cognition, emotion, locomotion, and learning and memory. These functions are intricately regulated by a variety of Ca2+-dependent cellular processes, encompassing synaptic plasticity, neuro/gliotransmitter release, and gene expression. In our previous work, we developed 'monster OptoSTIM1' (monSTIM1), an improved OptoSTIM1 that selectively activates Ca2+-release-activated Ca2+ (CRAC) channels in the plasma membrane through blue light, allowing precise control over intracellular Ca2+ signaling and specific brain functions. However, the large size of the coding sequence of monSTIM1 poses a limitation for its widespread use, as it exceeds the packaging capacity of adeno-associated virus (AAV). To address this constraint, we have introduced monSTIM1 variants with reduced coding sequence sizes and established AAV-based systems for expressing them in neurons and glial cells in the mouse brain. Upon expression by AAVs, these monSTIM1 variants significantly increased the expression levels of cFos in neurons and astrocytes in the hippocampal CA1 region following non-invasive light illumination. The use of monSTIM1 variants offers a promising avenue for investigating the spatiotemporal roles of Ca2+-mediated cellular activities in various brain functions. Furthermore, this toolkit holds potential as a therapeutic strategy for addressing brain disorders associated with aberrant Ca2+ signaling.
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Affiliation(s)
- Yeon Hee Kook
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
- Department of Bioscience and Biotechnology, Graduate School, Chungnam National University, Daejeon, 34134, Korea
| | - Hyoin Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Jinsu Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yeonji Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jaerang Rho
- Department of Bioscience and Biotechnology, Graduate School, Chungnam National University, Daejeon, 34134, Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
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15
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Jara TC, Park K, Vahmani P, Van Eenennaam AL, Smith LR, Denicol AC. Stem cell-based strategies and challenges for production of cultivated meat. NATURE FOOD 2023; 4:841-853. [PMID: 37845547 DOI: 10.1038/s43016-023-00857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023]
Abstract
Cultivated meat scale-up and industrial production will require multiple stable cell lines from different species to recreate the organoleptic and nutritional properties of meat from livestock. In this Review, we explore the potential of stem cells to create the major cellular components of cultivated meat. By using developments in the fields of tissue engineering and biomedicine, we explore the advantages and disadvantages of strategies involving primary adult and pluripotent stem cells for generating cell sources that can be grown at scale. These myogenic, adipogenic or extracellular matrix-producing adult stem cells as well as embryonic or inducible pluripotent stem cells are discussed for their proliferative and differentiation capacity, necessary for cultivated meat. We examine the challenges for industrial scale-up, including differentiation and culture protocols, as well as genetic modification options for stem cell immortalization and controlled differentiation. Finally, we discuss stem cell-related safety and regulatory challenges for bringing cultivated meat to the marketplace.
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Affiliation(s)
- T C Jara
- Department of Animal Science, University of California Davis, Davis, CA, USA
| | - K Park
- Department of Animal Science, University of California Davis, Davis, CA, USA
| | - P Vahmani
- Department of Animal Science, University of California Davis, Davis, CA, USA
| | - A L Van Eenennaam
- Department of Animal Science, University of California Davis, Davis, CA, USA
| | - L R Smith
- Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, CA, USA.
| | - A C Denicol
- Department of Animal Science, University of California Davis, Davis, CA, USA
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16
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Bachhav B, de Rossi J, Llanos CD, Segatori L. Cell factory engineering: Challenges and opportunities for synthetic biology applications. Biotechnol Bioeng 2023; 120:2441-2459. [PMID: 36859509 PMCID: PMC10440303 DOI: 10.1002/bit.28365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/14/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
The production of high-quality recombinant proteins is critical to maintaining a continuous supply of biopharmaceuticals, such as therapeutic antibodies. Engineering mammalian cell factories presents a number of limitations typically associated with the proteotoxic stress induced upon aberrant accumulation of off-pathway protein folding intermediates, which eventually culminate in the induction of apoptosis. In this review, we will discuss advances in cell engineering and their applications at different hierarchical levels of control of the expression of recombinant proteins, from transcription and translational to posttranslational modifications and subcellular trafficking. We also highlight challenges and unique opportunities to apply modern synthetic biology tools to the design of programmable cell factories for improved biomanufacturing of therapeutic proteins.
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Affiliation(s)
- Bhagyashree Bachhav
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
| | - Jacopo de Rossi
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Carlos D. Llanos
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Laura Segatori
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
- Department of Bioengineering, Rice University, Houston, United States
- Department of Biosciences, Rice University, Houston, United States
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17
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Capece M, Tessari A, Mills J, Vinciguerra GLR, Louke D, Lin C, McElwain BK, Miles WO, Coppola V, Davies AE, Palmieri D, Croce CM. A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis. Cell Death Differ 2023; 30:2078-2091. [PMID: 37537305 PMCID: PMC10482871 DOI: 10.1038/s41418-023-01191-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/02/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
The discrimination of protein biological functions in different phases of the cell cycle is limited by the lack of experimental approaches that do not require pre-treatment with compounds affecting the cell cycle progression. Therefore, potential cycle-specific biological functions of a protein of interest could be biased by the effects of cell treatments. The OsTIR1/auxin-inducible degron (AID) system allows "on demand" selective and reversible protein degradation upon exposure to the phytohormone auxin. In the current format, this technology does not allow to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespectively of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population, as with previously available approaches. Here, we introduce a new AID system to Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS system), which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. We validated the ROLECCS technology by down regulating the protein levels of TP53, one of the most studied tumor suppressor genes, with a widely known role in cell cycle progression. By using our novel tool, we observed that TP53 degradation is associated with increased number of micronuclei, and this phenotype is specifically achieved when TP53 is lost in S/G2/M phases of the cell cycle, but not in G1. Therefore, we propose the use of the ROLECCS system as a new improved way of studying the differential roles that target proteins may have in specific phases of the cell cycle.
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Affiliation(s)
- Marina Capece
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Anna Tessari
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Joseph Mills
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Darian Louke
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Bryan K McElwain
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Alexander E Davies
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
- Gene Editing Shared Resource, The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
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18
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Fu Q, Polanco A, Lee YS, Yoon S. Critical challenges and advances in recombinant adeno-associated virus (rAAV) biomanufacturing. Biotechnol Bioeng 2023; 120:2601-2621. [PMID: 37126355 DOI: 10.1002/bit.28412] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/27/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
Gene therapy is a promising therapeutic approach for genetic and acquired diseases nowadays. Among DNA delivery vectors, recombinant adeno-associated virus (rAAV) is one of the most effective and safest vectors used in commercial drugs and clinical trials. However, the current yield of rAAV biomanufacturing lags behind the necessary dosages for clinical and commercial use, which embodies a concentrated reflection of low productivity of rAAV from host cells, difficult scalability of the rAAV-producing bioprocess, and high levels of impurities materialized during production. Those issues directly impact the price of gene therapy medicine in the market, limiting most patients' access to gene therapy. In this context, the current practices and several critical challenges associated with rAAV gene therapy bioprocesses are reviewed, followed by a discussion of recent advances in rAAV-mediated gene therapy and other therapeutic biological fields that could improve biomanufacturing if these advances are integrated effectively into the current systems. This review aims to provide the current state-of-the-art technology and perspectives to enhance the productivity of rAAV while reducing impurities during production of rAAV.
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Affiliation(s)
- Qiang Fu
- Department of Biomedical Engineering and Biotechnology, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Ashli Polanco
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
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19
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Blutt SE, Coarfa C, Neu J, Pammi M. Multiomic Investigations into Lung Health and Disease. Microorganisms 2023; 11:2116. [PMID: 37630676 PMCID: PMC10459661 DOI: 10.3390/microorganisms11082116] [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: 07/12/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Diseases of the lung account for more than 5 million deaths worldwide and are a healthcare burden. Improving clinical outcomes, including mortality and quality of life, involves a holistic understanding of the disease, which can be provided by the integration of lung multi-omics data. An enhanced understanding of comprehensive multiomic datasets provides opportunities to leverage those datasets to inform the treatment and prevention of lung diseases by classifying severity, prognostication, and discovery of biomarkers. The main objective of this review is to summarize the use of multiomics investigations in lung disease, including multiomics integration and the use of machine learning computational methods. This review also discusses lung disease models, including animal models, organoids, and single-cell lines, to study multiomics in lung health and disease. We provide examples of lung diseases where multi-omics investigations have provided deeper insight into etiopathogenesis and have resulted in improved preventative and therapeutic interventions.
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Affiliation(s)
- Sarah E. Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Josef Neu
- Department of Pediatrics, Section of Neonatology, University of Florida, Gainesville, FL 32611, USA;
| | - Mohan Pammi
- Department of Pediatrics, Section of Neonatology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX 77030, USA
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20
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Rados T, Andre K, Cerletti M, Bisson A. A sweet new set of inducible and constitutive promoters in Haloferax volcanii. Front Microbiol 2023; 14:1204876. [PMID: 37637112 PMCID: PMC10448506 DOI: 10.3389/fmicb.2023.1204876] [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: 04/12/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Inducible promoters are one of cellular and molecular biology's most important technical tools. The ability to deplete, replete, and overexpress genes on demand is the foundation of most functional studies. Here, we developed and characterized a new xylose-responsive promoter (Pxyl), the second inducible promoter system for the model haloarcheon Haloferax volcanii. Generating RNA-seq datasets from cultures in the presence of four historically used inducers (arabinose, xylose, maltose, and IPTG), we mapped upregulated genomic regions primarily repressed in the absence of the above inducers. We found a highly upregulated promoter that controls the expression of the xacEA (HVO_B0027-28) operon in the pHV3 chromosome. To characterize this promoter region, we cloned msfGFP (monomeric superfold green fluorescent protein) under the control of two upstream regions into a modified pTA962 vector: the first 250 bp (P250) and the whole 750 bp intergenic fragments (P750). The P250 sequence drove the expression of msfGFP constitutively, and its expression did not respond to the presence or absence of xylose. However, the P750 promoter showed not only to be repressed in the absence of xylose but also expressed higher levels of msfGFP than the previously described inducible promoter PtnaA in the presence of the inducer. Finally, we validated the inducible Pxyl promoter by reproducing morphological phenotypes already described in the literature. By overexpressing the tubulin-like FtsZ1 and FtsZ2, we observed similar but slightly more pronounced morphological defects than the tryptophan-inducible promoter PtnaA. FtsZ1 overexpression created larger, deformed cells, whereas cells overexpressing FtsZ2 were smaller but mostly retained their shape. In summary, this work contributes a new xylose-inducible promoter that could be used simultaneously with the well-established PtnaA in functional studies in H. volcanii in the future.
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Affiliation(s)
- Theopi Rados
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Katherine Andre
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Micaela Cerletti
- Department of Biology, Brandeis University, Waltham, MA, United States
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Alex Bisson
- Department of Biology, Brandeis University, Waltham, MA, United States
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21
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Arancibia D, Pol I, Vargas-Fernández M, Zárate RV, Signorelli JR, Zamorano P. OPTO-BLUE: An Integrated Bidirectional Optogenetic Lentiviral Platform for Controlled Light-Induced Gene Expression. Int J Mol Sci 2023; 24:ijms24119537. [PMID: 37298488 DOI: 10.3390/ijms24119537] [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: 05/01/2023] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Regulated systems for transgene expression are useful tools in basic research and a promising platform in biomedicine due to their regulated transgene expression by an inducer. The emergence of optogenetics expression systems enabled the construction of light-switchable systems, enhancing the spatial and temporal resolution of a transgene. The LightOn system is an optogenetic tool that regulates the expression of a gene of interest using blue light as an inducer. This system is based on a photosensitive protein (GAVPO), which dimerizes and binds to the UASG sequence in response to blue light, triggering the expression of a downstream transgene. Previously, we adapted the LightOn system to a dual lentiviral vector system for neurons. Here, we continue the optimization and assemble all components of the LightOn system into a single lentiviral plasmid, the OPTO-BLUE system. For functional validation, we used enhanced green fluorescent protein (EGFP) as an expression reporter (OPTO-BLUE-EGFP) and evaluated the efficiency of EGFP expression by transfection and transduction in HEK293-T cells exposed to continuous blue-light illumination. Altogether, these results prove that the optimized OPTO-BLUE system allows the light-controlled expression of a reporter protein according to a specific time and light intensity. Likewise, this system should provide an important molecular tool to modulate gene expression of any protein by blue light.
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Affiliation(s)
- Duxan Arancibia
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Iracy Pol
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Martín Vargas-Fernández
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Rafaella V Zárate
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
- Instituto Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Janetti R Signorelli
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Pedro Zamorano
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta 1240000, Chile
- Instituto Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile
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22
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Azad T, Rezaei R, Singaravelu R, Pelin A, Boulton S, Petryk J, Onsu KA, Martin NT, Hoskin V, Ghahremani M, Marotel M, Marius R, He X, Crupi MJF, Hoang HD, Nik-Akhtar A, Ahmadi M, Zamani NK, Golshani A, Alain T, Greer P, Ardolino M, Dickinson BC, Tai LH, Ilkow CS, Bell JC. Synthetic virology approaches to improve the safety and efficacy of oncolytic virus therapies. Nat Commun 2023; 14:3035. [PMID: 37236967 PMCID: PMC10213590 DOI: 10.1038/s41467-023-38651-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The large coding potential of vaccinia virus (VV) vectors is a defining feature. However, limited regulatory switches are available to control viral replication as well as timing and dosing of transgene expression in order to facilitate safe and efficacious payload delivery. Herein, we adapt drug-controlled gene switches to enable control of virally encoded transgene expression, including systems controlled by the FDA-approved rapamycin and doxycycline. Using ribosome profiling to characterize viral promoter strength, we rationally design fusions of the operator element of different drug-inducible systems with VV promoters to produce synthetic promoters yielding robust inducible expression with undetectable baseline levels. We also generate chimeric synthetic promoters facilitating additional regulatory layers for VV-encoded synthetic transgene networks. The switches are applied to enable inducible expression of fusogenic proteins, dose-controlled delivery of toxic cytokines, and chemical regulation of VV replication. This toolbox enables the precise modulation of transgene circuitry in VV-vectored oncolytic virus design.
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Affiliation(s)
- Taha Azad
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
- Centre de Recherche du CHUS, Sherbrooke, QC, J1H 5N4, Canada
| | - Reza Rezaei
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Ragunath Singaravelu
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, CA 94158, USA
| | - Stephen Boulton
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Julia Petryk
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | | | | | - Victoria Hoskin
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Mina Ghahremani
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Marie Marotel
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, K1H, Canada
| | - Ricardo Marius
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Xiaohong He
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Mathieu J F Crupi
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Huy-Dung Hoang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Abolfazl Nik-Akhtar
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Mahsa Ahmadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Nika Kooshki Zamani
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Tommy Alain
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Peter Greer
- Department of Pathology and Molecular Medicine, Queens University, Kingston, ON, K7L 3N6, Canada
| | - Michele Ardolino
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, K1H, Canada
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Lee-Hwa Tai
- Centre de Recherche du CHUS, Sherbrooke, QC, J1H 5N4, Canada
- Department of Immunology & Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Carolina S Ilkow
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - John C Bell
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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23
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Stout AJ, Zhang X, Letcher SM, Rittenberg ML, Shub M, Chai KM, Kaul M, Kaplan DL. Engineered autocrine signaling eliminates muscle cell FGF2 requirements for cultured meat production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537163. [PMID: 37131805 PMCID: PMC10153192 DOI: 10.1101/2023.04.17.537163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cultured meat is a promising technology that faces substantial cost barriers which are currently driven largely by the price of media components. Growth factors such as fibroblast growth factor 2 (FGF2) drive the cost of serum-free media for relevant cells including muscle satellite cells. Here, we engineered immortalized bovine satellite cells (iBSCs) for inducible expression of FGF2 and/or mutated RasG12V in order to overcome media growth factor requirements through autocrine signaling. Engineered cells were able to proliferate over multiple passages in FGF2-free medium, thereby eliminating the need for this costly component. Additionally, cells maintained their myogenicity, albeit with reduced differentiation capacity. Ultimately, this offers a proof-of-principle for lower-cost cultured meat production through cell line engineering.
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Affiliation(s)
- Andrew J. Stout
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Xiaoli Zhang
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Sophia M. Letcher
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Miriam L. Rittenberg
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michelle Shub
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Kristin M. Chai
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Maya Kaul
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - David L. Kaplan
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
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24
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Single-Cell Labeling Strategies to Dissect Neuronal Structures and Local Functions. BIOLOGY 2023; 12:biology12020321. [PMID: 36829594 PMCID: PMC9953318 DOI: 10.3390/biology12020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
The brain network consists of ten billion neurons and is the most complex structure in the universe. Understanding the structure of complex brain networks and neuronal functions is one of the main goals of modern neuroscience. Since the seminal invention of Golgi staining, single-cell labeling methods have been among the most potent approaches for dissecting neuronal structures and neural circuits. Furthermore, the development of sparse single-cell transgenic methods has enabled single-cell gene knockout studies to examine the local functions of various genes in neural circuits and synapses. Here, we review non-transgenic single-cell labeling methods and recent advances in transgenic strategies for sparse single neuronal labeling. These methods and strategies will fundamentally contribute to the understanding of brain structure and function.
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25
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Chen LY, Wang WW, Wozniak JM, Parker CG. A heterobifunctional molecule system for targeted protein acetylation in cells. Methods Enzymol 2023; 681:287-323. [PMID: 36764762 DOI: 10.1016/bs.mie.2022.08.014] [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: 10/14/2022]
Abstract
Protein acetylation is a vital biological process that regulates myriad cellular events. Despite its profound effects on protein function, there are limited research tools to dynamically and selectively regulate protein acetylation. To address this, we developed an acetylation tagging system, called AceTAG, to target proteins for chemically induced acetylation directly in live cells. AceTAG uses heterobifunctional molecules composed of a ligand for the lysine acetyltransferase p300/CBP and a FKBP12F36V ligand. Target proteins are genetically tagged with FKBP12F36V and brought in proximity with p300/CBP by AceTAG molecules to subsequently undergo protein-specific acetylation. Targeted acetylation of proteins in cells using AceTAG is selective, rapid, and can be modulated in a dose-dependent fashion, enabling controlled investigations of acetylated protein targets directly in cells. In this protocol, we focus on (1) generation of AceTAG constructs and cell lines, (2) in vitro characterization of AceTAG mediated ternary complex formation and cellular target engagement studies; and (3) in situ characterization of AceTAG induced acetylation of targeted proteins by immunoblotting and quantitative proteomics. The robust procedures described herein should enable the use of AceTAG to explore the roles of acetylation for a variety of protein targets.
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Affiliation(s)
- Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Wesley Wei Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States.
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26
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Zhong V, Archibald BN, Brophy JAN. Transcriptional and post-transcriptional controls for tuning gene expression in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102315. [PMID: 36462457 DOI: 10.1016/j.pbi.2022.102315] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Plant biotechnologists seek to modify plants through genetic reprogramming, but our ability to precisely control gene expression in plants is still limited. Here, we review transcription and translation in the model plants Arabidopsis thaliana and Nicotiana benthamiana with an eye toward control points that may be used to predictably modify gene expression. We highlight differences in gene expression requirements between these plants and other species, and discuss the ways in which our understanding of gene expression has been used to engineer plants. This review is intended to serve as a resource for plant scientists looking to achieve precise control over gene expression.
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Affiliation(s)
- Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Bella N Archibald
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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27
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Navigating the Multiverse of Antisense RNAs: The Transcription- and RNA-Dependent Dimension. Noncoding RNA 2022; 8:ncrna8060074. [PMID: 36412909 PMCID: PMC9680235 DOI: 10.3390/ncrna8060074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
Evidence accumulated over the past decades shows that the number of identified antisense transcripts is continuously increasing, promoting them from transcriptional noise to real genes with specific functions. Indeed, recent studies have begun to unravel the complexity of the antisense RNA (asRNA) world, starting from the multidimensional mechanisms that they can exert in physiological and pathological conditions. In this review, we discuss the multiverse of the molecular functions of asRNAs, describing their action through transcription-dependent and RNA-dependent mechanisms. Then, we report the workflow and methodologies to study and functionally characterize single asRNA candidates.
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28
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Bravo-Pérez C, Toderici M, Chambers JE, Martínez-Menárguez JA, Garrido-Rodriguez P, Pérez-Sanchez H, de la Morena-Barrio B, Padilla J, Miñano A, Cifuentes-Riquelme R, Vicente V, Lozano ML, Marciniak SJ, de la Morena-Barrio ME, Corral J. Full-length antithrombin frameshift variant with aberrant C-terminus causes endoplasmic reticulum retention with a dominant-negative effect. JCI Insight 2022; 7:161430. [PMID: 36214221 PMCID: PMC9675572 DOI: 10.1172/jci.insight.161430] [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: 04/28/2022] [Accepted: 08/24/2022] [Indexed: 02/02/2023] Open
Abstract
Antithrombin, a major endogenous anticoagulant, is a serine protease inhibitor (serpin). We characterized the biological and clinical impact of variants involving C-terminal antithrombin. We performed comprehensive molecular, cellular, and clinical characterization of patients with C-terminal antithrombin variants from a cohort of 444 unrelated individuals with confirmed antithrombin deficiency. We identified 17 patients carrying 12 C-terminal variants, 5 of whom had the p.Arg445Serfs*17 deletion. Five missense variants caused qualitative deficiency, and 7, including 4 insertion-deletion variants, induced severe quantitative deficiency, particularly p.Arg445Serfs*17 (antithrombin <40%). This +1 frameshift variant had a molecular size similar to that of WT antithrombin but possessed a different C-terminus. Morphologic and cotransfection experiments showed that recombinant p.Arg445Serfs*17 was retained at the endoplasmic reticulum and had a dominant-negative effect on WT antithrombin. Characterization of different 1+ frameshift, aberrant C-terminal variants revealed that protein secretion was determined by frameshift site. The introduction of Pro441 in the aberrant C-terminus, shared by 5 efficiently secreted variants, partially rescued p.Arg445Serfs*17 secretion. C-terminal antithrombin mutants have notable heterogeneity, related to variant type and localization. Aberrant C-terminal variants caused by 1+ frameshift, with similar size as WT antithrombin, may be secreted or not, depending on frameshift site. The severe clinical phenotypes of these genetic changes are consistent with their dominant-negative effects.
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Affiliation(s)
- Carlos Bravo-Pérez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Mara Toderici
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Joseph E. Chambers
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - José A. Martínez-Menárguez
- Department of Cell Biology and Histology, Medical School, Biomedical Research Institute of Murcia, University of Murcia, Campus Mare Nostrum, Murcia, Spain
| | - Pedro Garrido-Rodriguez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Horacio Pérez-Sanchez
- Structural Bioinformatics and High Performance Computing Research Group, Universidad Católica de Murcia, Murcia, Spain
| | - Belén de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - José Padilla
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Antonia Miñano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Rosa Cifuentes-Riquelme
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Vicente Vicente
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Maria L. Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Stefan J. Marciniak
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Maria Eugenia de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
| | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, University of Murcia, Biomedical Research Institute of Murcia, CB15/00055-CIBERER, Murcia, Spain
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29
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Hu ZG, Dong ZQ, Miao JH, Li KJ, Wang J, Chen P, Lu C, Pan MH. Identification of the Key Functional Domains of Bombyx mori Nucleopolyhedrovirus IE1 Protein. Int J Mol Sci 2022; 23:ijms231810276. [PMID: 36142194 PMCID: PMC9499007 DOI: 10.3390/ijms231810276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Abstract
The immediate early protein 1 (IE1) acts as a transcriptional activator and is essential for viral gene transcription and viral DNA replication. However, the key regulatory domains of IE1 remain poorly understood. Here, we analyzed the sequence characteristics of Bombyx mori nucleopolyhedrovirus (BmNPV) IE1 and identified the key functional domains of BmNPV IE1 by stepwise truncation. Our results showed that BmNPV IE1 was highly similar to Autographa californica nucleopolyhedrovirus (AcMNPV) IE1, but was less conserved with IE1 of other baculoviruses, the C-terminus of IE1 was more conserved than the N-terminus, and BmNPV IE1 was also necessary for BmNPV proliferation. Moreover, we found that IE1158–208 was a major nuclear localization element, and IE11–157 and IE1539–559 were minor nuclear localization elements, but the combination of these two minor elements was equally sufficient to fully mediate the nuclear entry of IE1. Meanwhile, IE11–258, IE1560–584, and the association of amino acids 258 and 259 were indispensable for the transactivation activity of BmNPV IE1. These results systematically resolve the functional domains of BmNPV IE1, which contribute to the understanding of the mechanism of baculovirus infection and provide a possibility to synthesize a small molecule IE1-truncated mutant as an agonist or antagonist.
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Affiliation(s)
- Zhi-Gang Hu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Zhan-Qi Dong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
- Key Laboratory for Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400716, China
| | - Jiang-Hao Miao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Ke-Jie Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Jie Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
- Key Laboratory for Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400716, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
- Key Laboratory for Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400716, China
- Correspondence: (C.L.); (M.-H.P.); Tel.: +86-023-68250076 (M.-H.P.)
| | - Min-Hui Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
- Key Laboratory for Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400716, China
- Correspondence: (C.L.); (M.-H.P.); Tel.: +86-023-68250076 (M.-H.P.)
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30
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Shupe J, Zhang A, Odenwelder DC, Dobrowsky T. Gene therapy: challenges in cell culture scale-up. Curr Opin Biotechnol 2022; 75:102721. [DOI: 10.1016/j.copbio.2022.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/04/2022] [Accepted: 03/02/2022] [Indexed: 11/03/2022]
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31
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Morris G, Schorge S. Gene Therapy for Neurological Disease: State of the Art and Opportunities for Next-generation Approaches. Neuroscience 2022; 490:309-314. [PMID: 35304290 DOI: 10.1016/j.neuroscience.2022.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/22/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022]
Abstract
Gene therapy for rare monogenetic neurological disorders is reaching clinics and offering hope to families affected by these diseases. There is also potential for gene therapy to offer new and effective treatments for common, non-genetic disorders. Treatments for Parkinson's Disease are in clinical trials, and treatments for refractory epilepsies are due to enter first-in-human clinical trials in 2022. Gene therapies for these disorders are based on delivering genes that address the mechanism of the disease, not repairing a mutated gene. Similar 'mechanistic' gene therapies could offer treatments to a wide range of neurological and neuropsychiatric diseases where there is a known mechanism that could be restored using gene therapy. However, the permanent nature of most gene therapies is a serious drawback for translation of gene therapies to a wide-range of diseases because it could present risk of irreversible adverse effects. Several lines of research are aimed at developing gene therapy approaches that allow for the treatment to be turned on and off, including: using proteins activated by exogenous ligands, and promoters turned on by activators. We review these approaches and propose an overall de-risking strategy for gene therapy for common neurological and psychiatric diseases. This approach is based on using a temporary mRNA-based treatment to initially assess efficacy and safety of the planned manipulation, and only following with permanent, virally-delivered treatment if the approach appears safe and effective.
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Affiliation(s)
- Gareth Morris
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Stephanie Schorge
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom.
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32
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Bazarek S, Johnston BR, Sten M, Mandeville R, Eggan K, Wainger BJ, Brown JM. Spinal motor neuron transplantation to enhance nerve reconstruction strategies: Towards a cell therapy. Exp Neurol 2022; 353:114054. [PMID: 35341748 DOI: 10.1016/j.expneurol.2022.114054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/19/2022]
Abstract
Nerve transfers have become a powerful intervention to restore function following devastating paralyzing injuries. A major limitation to peripheral nerve repair and reconstructive strategies is the progressive, fibrotic degeneration of the distal nerve and denervated muscle, eventually precluding recovery of these targets and thus defining a time window within which reinnervation must occur. One proven strategy in the clinic has been the sacrifice and transfer of an adjacent distal motor nerve to provide axons to occupy, and thus preserve (or "babysit"), the target muscle. However, available nearby nerves are limited in severe brachial plexus or spinal cord injury. An alternative and novel proposition is the transplantation of spinal motor neurons (SMNs) derived from human induced pluripotent stem cells (iPSCs) into the target nerve to extend their axons to occupy and preserve the targets. These cells could potentially be delivered through minimally invasive or percutaneous techniques. Several reports have demonstrated survival, functional innervation, and muscular preservation following transplantation of SMNs into rodent nerves. Advances in the generation, culture, and differentiation of human iPSCs now offer the possibility for an unlimited supply of clinical grade SMNs. This review will discuss the previous reports of peripheral SMN transplantation, outline key considerations, and propose next steps towards advancing this approach to clinic. Stem cells have garnered great enthusiasm for their potential to revolutionize medicine. However, this excitement has often led to premature clinical studies with ill-defined cell products and mechanisms of action, particularly in spinal cord injury. We believe the peripheral transplantation of a defined SMN population to address neuromuscular degeneration will be transformative in augmenting current reconstructive strategies. By thus removing the current barriers of time and distance, this strategy would dramatically enhance the potential for reconstruction and functional recovery in otherwise hopeless paralyzing injuries. Furthermore, this strategy may be used as a permanent axon replacement following destruction of lower motor neurons and would enable exogenous stimulation options, such as pacing of transplanted SMN axons in the phrenic nerve to avoid mechanical ventilation in high cervical cord injury or amyotrophic lateral sclerosis.
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Affiliation(s)
- Stanley Bazarek
- Department of Neurosurgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, United States of America; Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Benjamin R Johnston
- Department of Neurosurgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, United States of America; Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Margaret Sten
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Ross Mandeville
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
| | - Kevin Eggan
- BioMarin Pharmaceutical Inc., San Rafael, CA, United States of America
| | - Brian J Wainger
- Departments of Neurology and Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America.
| | - Justin M Brown
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America.
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33
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Identification of Genomic Safe Harbors in the Anhydrobiotic Cell Line, Pv11. Genes (Basel) 2022; 13:genes13030406. [PMID: 35327960 PMCID: PMC8949610 DOI: 10.3390/genes13030406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/22/2022] Open
Abstract
Genomic safe harbors (GSHs) provide ideal integration sites for generating transgenic organisms and cells and can be of great benefit in advancing the basic and applied biology of a particular species. Here we report the identification of GSHs in a dry-preservable insect cell line, Pv11, which derives from the sleeping chironomid, Polypedilum vanderplanki, and similar to the larvae of its progenitor species exhibits extreme desiccation tolerance. To identify GSHs, we carried out genome analysis of transgenic cell lines established by random integration of exogenous genes and found four candidate loci. Targeted knock-in was performed into these sites and the phenotypes of the resulting transgenic cell lines were examined. Precise integration was achieved for three candidate GSHs, and in all three cases integration did not alter the anhydrobiotic ability or the proliferation rate of the cell lines. We therefore suggest these genomic loci represent GSHs in Pv11 cells. Indeed, we successfully constructed a knock-in system and introduced an expression unit into one of these GSHs. We therefore identified several GSHs in Pv11 cells and developed a new technique for producing transgenic Pv11 cells without affecting the phenotype.
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34
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Doshi A, Bandey I, Nevozhay D, Varadarajan N, Cirino PC. Design and characterization of a salicylic acid-inducible gene expression system for Jurkat cells. J Biotechnol 2022; 346:11-14. [PMID: 35051448 PMCID: PMC9618363 DOI: 10.1016/j.jbiotec.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 12/11/2021] [Accepted: 01/13/2022] [Indexed: 11/29/2022]
Abstract
With continued progress in cell and gene therapies, there is an immediate need for exogenously tunable gene expression systems with safe and predictable behavior in specific human cell types. Here, we demonstrate the ability of the salicylic acid (SA)-inducible MarR repressor protein from Escherichia coli to regulate target gene expression in a human T lymphocyte cell line. Two lentiviral vectors, one encoding an enhanced green fluorescent protein (EGFP) reporter cassette and the other a repressor cassette, were sequentially transduced into Jurkat cells, using fluorescence-activated cell sorting (FACS) to isolate stable Jurkat progeny. As a result, EGFP expression was repressed by MarR and was inducible upon the addition of SA (~1.3 fold). This represents the first example of functional expression of bacterial MarR in mammalian cells, and opens the possibility for further development of regulated, SA-tunable gene expression system for T-cells.
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Affiliation(s)
- Aarti Doshi
- Dept. of Biology and Biochemistry, University of Houston, Houston, TX, USA.
| | - Irfan Bandey
- Dept. of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
| | - Dmitry Nevozhay
- Dept. of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia.
| | - Navin Varadarajan
- Dept. of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
| | - Patrick C. Cirino
- Dept. of Biology and Biochemistry, University of Houston, Houston, TX,Dept. of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
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35
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Becirovic E. Maybe you can turn me on: CRISPRa-based strategies for therapeutic applications. Cell Mol Life Sci 2022; 79:130. [PMID: 35152318 PMCID: PMC8840918 DOI: 10.1007/s00018-022-04175-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/17/2022]
Abstract
AbstractSince the revolutionary discovery of the CRISPR-Cas technology for programmable genome editing, its range of applications has been extended by multiple biotechnological tools that go far beyond its original function as “genetic scissors”. One of these further developments of the CRISPR-Cas system allows genes to be activated in a targeted and efficient manner. These gene-activating CRISPR-Cas modules (CRISPRa) are based on a programmable recruitment of transcription factors to specific loci and offer several key advantages that make them particularly attractive for therapeutic applications. These advantages include inter alia low off-target effects, independence of the target gene size as well as the potential to develop gene- and mutation-independent therapeutic strategies. Herein, I will give an overview on the currently available CRISPRa modules and discuss recent developments, future potentials and limitations of this approach with a focus on therapeutic applications and in vivo delivery.
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Affiliation(s)
- Elvir Becirovic
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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36
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Chee WKD, Yeoh JW, Dao VL, Poh CL. Thermogenetics: Applications come of age. Biotechnol Adv 2022; 55:107907. [PMID: 35041863 DOI: 10.1016/j.biotechadv.2022.107907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.
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Affiliation(s)
- Wai Kit David Chee
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Viet Linh Dao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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37
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Aimaier R, Chung M, Zhu H, Yu Q. The spatiotemporal expression of NRAS and occurrence of giant congenital melanocytic nevi. Exp Dermatol 2022; 31:582-585. [PMID: 35020224 DOI: 10.1111/exd.14527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/30/2021] [Accepted: 01/08/2022] [Indexed: 11/28/2022]
Abstract
The mechanism underlying giant congenital melanocytic nevus (GCMN) formation is not fully understood. According to recent research, NRAS gene mutation is the main driving factor in GCMN. Melanocytic precursor cells proliferate during the embryonic stage after acquiring NRAS mutations. However, why GCMN undergoes intense proliferation in the embryonic stage and then stops postnatally remains unknown. The current theory for this phenomenon is that the GCMN undergoes oncogene-induced senescence. However, there is not enough evidence to indicate that senescence induces growth arrest in GCMN. In this study, we hypothesized that the expression level of the NRAS gene changes dynamically during the development and differentiation of neural crest cells into melanocytes and that the NRAS expression level determines whether the cell proliferates or becomes quiescent.
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Affiliation(s)
- Rehanguli Aimaier
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China
| | - Manhon Chung
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China
| | - Hainan Zhu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China
| | - Qingxiong Yu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China
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38
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Renna P, Ripoli C, Dagliyan O, Pastore F, Rinaudo M, Re A, Paciello F, Grassi C. Engineering a switchable single‐chain
TEV
protease to control protein maturation in living neurons. Bioeng Transl Med 2022; 7:e10292. [PMID: 35600650 PMCID: PMC9115699 DOI: 10.1002/btm2.10292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/13/2021] [Accepted: 12/30/2021] [Indexed: 11/18/2022] Open
Abstract
Engineered proteases are promising tools to address physiological and pathophysiological questions as well as to develop new therapeutic approaches. Here we introduce a new genetically encoded engineered single‐chain tobacco etch virus protease, allowing to control proprotein cleavage in different compartments of living mammalian cells. We demonstrated a set of controllable proteolytic effects, including cytosolic protein cleavage, inducible gene expression, and maturation of brain‐derived neurotrophic factor (BDNF) in the secretory pathway thus showing the versatility of this technique. Of note, the secretory pathway exhibits different characteristics from the cytosol and it is difficult to target because inaccessible to some small molecules. We were able to induce ligand‐mediated BDNF maturation and monitor its effects on dendritic spines in hippocampal pyramidal cells and in the mouse brain. This strategy paves the way to dissect proteolytic cleavage product signaling in various processes as well as for future therapeutic applications.
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Affiliation(s)
- Pietro Renna
- Department of Neuroscience Università Cattolica del Sacro Cuore, 00168 Rome Italy
| | - Cristian Ripoli
- Department of Neuroscience Università Cattolica del Sacro Cuore, 00168 Rome Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome Italy
| | - Onur Dagliyan
- Department of Neurobiology Harvard Medical School Boston MA USA
| | - Francesco Pastore
- Department of Neuroscience Università Cattolica del Sacro Cuore, 00168 Rome Italy
| | - Marco Rinaudo
- Department of Neuroscience Università Cattolica del Sacro Cuore, 00168 Rome Italy
| | - Agnese Re
- Department of Neuroscience Università Cattolica del Sacro Cuore, 00168 Rome Italy
| | - Fabiola Paciello
- Department of Neuroscience Università Cattolica del Sacro Cuore, 00168 Rome Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome Italy
| | - Claudio Grassi
- Department of Neuroscience Università Cattolica del Sacro Cuore, 00168 Rome Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome Italy
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39
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Yuen JSK, Stout AJ, Kawecki NS, Letcher SM, Theodossiou SK, Cohen JM, Barrick BM, Saad MK, Rubio NR, Pietropinto JA, DiCindio H, Zhang SW, Rowat AC, Kaplan DL. Perspectives on scaling production of adipose tissue for food applications. Biomaterials 2022; 280:121273. [PMID: 34933254 PMCID: PMC8725203 DOI: 10.1016/j.biomaterials.2021.121273] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023]
Abstract
With rising global demand for food proteins and significant environmental impact associated with conventional animal agriculture, it is important to develop sustainable alternatives to supplement existing meat production. Since fat is an important contributor to meat flavor, recapitulating this component in meat alternatives such as plant based and cell cultured meats is important. Here, we discuss the topic of cell cultured or tissue engineered fat, growing adipocytes in vitro that could imbue meat alternatives with the complex flavor and aromas of animal meat. We outline potential paths for the large scale production of in vitro cultured fat, including adipogenic precursors during cell proliferation, methods to adipogenically differentiate cells at scale, as well as strategies for converting differentiated adipocytes into 3D cultured fat tissues. We showcase the maturation of knowledge and technology behind cell sourcing and scaled proliferation, while also highlighting that adipogenic differentiation and 3D adipose tissue formation at scale need further research. We also provide some potential solutions for achieving adipose cell differentiation and tissue formation at scale based on contemporary research and the state of the field.
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Affiliation(s)
- John S K Yuen
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Andrew J Stout
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - N Stephanie Kawecki
- Department of Bioengineering, University of California Los Angeles, 410 Westwood Plaza, Los Angeles, CA, 90095, USA; Department of Integrative Biology & Physiology, University of California Los Angeles, Terasaki Life Sciences Building, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Sophia M Letcher
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Sophia K Theodossiou
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Julian M Cohen
- W. M. Keck Science Department, Pitzer College, 925 N Mills Ave, Claremont, CA, 91711, USA
| | - Brigid M Barrick
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Michael K Saad
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Natalie R Rubio
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Jaymie A Pietropinto
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Hailey DiCindio
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Sabrina W Zhang
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Amy C Rowat
- Department of Bioengineering, University of California Los Angeles, 410 Westwood Plaza, Los Angeles, CA, 90095, USA; Department of Integrative Biology & Physiology, University of California Los Angeles, Terasaki Life Sciences Building, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - David L Kaplan
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, 4 Colby St, Medford, MA, 02155, USA.
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40
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Huang L, Zheng Z, Bai D, Han X. Stem Cells from Human Exfoliated Deciduous Teeth and their Promise as Preventive and Therapeutic Strategies for Neurological Diseases and Injuries. Curr Stem Cell Res Ther 2021; 17:527-536. [PMID: 34967291 DOI: 10.2174/1574888x17666211229155533] [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: 08/11/2021] [Revised: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022]
Abstract
Stem cells from human exfoliated deciduous teeth (SHEDs) are relatively easy to isolate from exfoliated deciduous teeth, which are obtained via dental therapy as biological waste. SHEDs originate from the embryonic neural crest and therefore have considerable potential for neurogenic differentiation. Currently, an increasing amount of research attention is focused on the therapeutic applications of SHEDs in neurological diseases and injuries. In this article, we summarize the biological characteristics of SHEDs and the potential role of SHEDs and their derivatives, including conditioned medium from SHEDs and the exosomes they secrete, in the prevention and treatment of neurological diseases and injuries.
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Affiliation(s)
- Lingyi Huang
- West China College of Stomatology/ State Key Laboratory of Oral Diseases, Sichuan University, Chengdu 610041, China
| | - Zizhuo Zheng
- West China College of Stomatology/ State Key Laboratory of Oral Diseases, Sichuan University, Chengdu 610041, China
| | - Ding Bai
- West China College of Stomatology/ State Key Laboratory of Oral Diseases, Sichuan University, Chengdu 610041, China
| | - Xianglong Han
- West China College of Stomatology/ State Key Laboratory of Oral Diseases, Sichuan University, Chengdu 610041, China
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41
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IQ-Switch is a QF-based innocuous, silencing-free, and inducible gene switch system in zebrafish. Commun Biol 2021; 4:1405. [PMID: 34916605 PMCID: PMC8677817 DOI: 10.1038/s42003-021-02923-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/24/2021] [Indexed: 11/08/2022] Open
Abstract
Though various transgene expression switches have been adopted in a wide variety of organisms for basic and biomedical research, intrinsic obstacles of those existing systems, including toxicity and silencing, have been limiting their use in vertebrate transgenesis. Here we demonstrate a novel QF-based binary transgene switch (IQ-Switch) that is relatively free of driver toxicity and transgene silencing, and exhibits potent and highly tunable transgene activation by the chemical inducer tebufenozide, a non-toxic lipophilic molecule to developing zebrafish with negligible background. The interchangeable IQ-Switch makes it possible to elicit ubiquitous and tissue specific transgene expression in a spatiotemporal manner. We generated a RASopathy disease model using IQ-Switch and demonstrated that the RASopathy symptoms were ameliorated by the specific BRAF(V600E) inhibitor vemurafenib, validating the therapeutic use of the gene switch. The orthogonal IQ-Switch provides a state-of-the-art platform for flexible regulation of transgene expression in zebrafish, potentially applicable in cell-based systems and other model organisms.
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42
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Bolshakov AP. Problems with Technologies of Genomic Editing and Transgenesis. NEUROCHEM J+ 2021. [DOI: 10.1134/s1819712421040036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Lam CKC, Truong K. Design of a synthesis-friendly hypoxia-responsive promoter for cell-based therapeutics. Eng Life Sci 2021; 21:848-856. [PMID: 34899121 PMCID: PMC8638314 DOI: 10.1002/elsc.202100045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/11/2021] [Accepted: 10/16/2021] [Indexed: 11/24/2022] Open
Abstract
Towards the goal of making 'smart' cell therapies, one that recognizes disease conditions (e.g. hypoxia) and then produces mitigating biologics, it is important to develop suitable promoters. Currently, hypoxia responsive promoters are composed of strongly repeated sequences containing hypoxia response elements upstream of a minimal core promoter. Unfortunately, such repeated sequences have inherent genomic instability that may compromise the long-term consistency of cell-based therapeutics. Thus, we designed a synthesis-friendly hypoxia-inducible promoter (named SFHp) that has GC content between 25% and 75% and no repeats greater than 9 base pairs. In HEK293 cells stably integrated with genes regulated by synthetic SFHp, we demonstrated inducible reporter expression with fluorescent proteins, cell morphology rewiring with our previously engineered RhoA protein and intercellular cell signalling with secreted cytokines. These experiments exemplify the potential usage of SFHp in cell-based therapeutics with integrated genetic circuits that inducibly respond to the disease microenvironment.
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Affiliation(s)
| | - Kevin Truong
- Institute of Biomedical EngineeringUniversity of TorontoTorontoONCanada
- Edward S. RogersSr. Department of Electrical and Computer EngineeringUniversity of TorontoTorontoONCanada
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44
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Chao CC, Shen PW, Tzeng TY, Kung HJ, Tsai TF, Wong YH. Human iPSC-Derived Neurons as A Platform for Deciphering the Mechanisms behind Brain Aging. Biomedicines 2021; 9:1635. [PMID: 34829864 PMCID: PMC8615703 DOI: 10.3390/biomedicines9111635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
With an increased life expectancy among humans, aging has recently emerged as a major focus in biomedical research. The lack of in vitro aging models-especially for neurological disorders, where access to human brain tissues is limited-has hampered the progress in studies on human brain aging and various age-associated neurodegenerative diseases at the cellular and molecular level. In this review, we provide an overview of age-related changes in the transcriptome, in signaling pathways, and in relation to epigenetic factors that occur in senescent neurons. Moreover, we explore the current cell models used to study neuronal aging in vitro, including immortalized cell lines, primary neuronal culture, neurons directly converted from fibroblasts (Fib-iNs), and iPSC-derived neurons (iPSC-iNs); we also discuss the advantages and limitations of these models. In addition, the key phenotypes associated with cellular senescence that have been observed by these models are compared. Finally, we focus on the potential of combining human iPSC-iNs with genome editing technology in order to further our understanding of brain aging and neurodegenerative diseases, and discuss the future directions and challenges in the field.
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Affiliation(s)
- Chuan-Chuan Chao
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Department of Neurology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Po-Wen Shen
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan;
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tsai-Yu Tzeng
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Biochemistry and Molecular Medicine, Comprehensive Cancer Center, University of California at Davis, Sacramento, CA 95817, USA
| | - Ting-Fen Tsai
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Hui Wong
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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45
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Rombaut M, Boeckmans J, Rodrigues RM, van Grunsven LA, Vanhaecke T, De Kock J. Direct reprogramming of somatic cells into induced hepatocytes: Cracking the Enigma code. J Hepatol 2021; 75:690-705. [PMID: 33989701 DOI: 10.1016/j.jhep.2021.04.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/10/2023]
Abstract
There is an unmet need for functional primary human hepatocytes to support the pharmaceutical and (bio)medical demand. The unique discovery, a decade ago, that somatic cells can be drawn out of their apparent biological lockdown to reacquire a pluripotent state has revealed a completely new avenue of possibilities for generating surrogate human hepatocytes. Since then, the number of papers reporting the direct conversion of somatic cells into induced hepatocytes (iHeps) has burgeoned. A hepatic cell fate can be established via the ectopic expression of native liver-enriched transcription factors in somatic cells, thereby bypassing the need for an intermediate (pluripotent) stem cell state. That said, understanding and eventually controlling the processes that give rise to functional iHeps remains challenging. In this review, we provide an overview of the state-of-the-art reprogramming cocktails and techniques, as well as their corresponding conversion efficiencies. Special attention is paid to the role of liver-enriched transcription factors as hepatogenic reprogramming tools and small molecules as facilitators of hepatic transdifferentiation. To conclude, we formulate recommendations to optimise, standardise and enrich the in vitro production of iHeps to reach clinical standards, and propose minimal criteria for their characterisation.
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Affiliation(s)
- Matthias Rombaut
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
| | - Joost Boeckmans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Robim M Rodrigues
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Leo A van Grunsven
- Liver Cell Biology Research Group, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Joery De Kock
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
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Sahillioglu AC, Schumacher TN. Safety switches for adoptive cell therapy. Curr Opin Immunol 2021; 74:190-198. [PMID: 34389174 DOI: 10.1016/j.coi.2021.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022]
Abstract
Adoptive transfer of allogeneic and genetically modified T cells, such as CAR-T and TCR-T cells, can induce profound immune reactivity against cancer tissue. At the same time, these therapies are associated with severe off-target and on-target toxicities. For this reason, the development of genetic safety switches that can be used to control the activity of T cells in vivo has become an active field of research. With the spectrum of technologies developed, reversible control of cell products either by supply or removal of small molecules, by supply of protein-based regulators, or by physical stimuli such as light, ultrasound or heat, has become feasible. In this review, we describe the mechanistic classes of genetic safety switches, such as transcription-based or protein-based control of antigen receptors, split receptors, small molecule responsive antibodies, as well as universal remote controls, and discuss their advantages and limitations.
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Affiliation(s)
- Ali Can Sahillioglu
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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Cazier AP, Blazeck J. Advances in promoter engineering: novel applications and predefined transcriptional control. Biotechnol J 2021; 16:e2100239. [PMID: 34351706 DOI: 10.1002/biot.202100239] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Synthetic biology continues to progress by relying on more robust tools for transcriptional control, of which promoters are the most fundamental component. Numerous studies have sought to characterize promoter function, determine principles to guide their engineering, and create promoters with stronger expression or tailored inducible control. In this review, we will summarize promoter architecture and highlight recent advances in the field, focusing on the novel applications of inducible promoter design and engineering towards metabolic engineering and cellular therapeutic development. Additionally, we will highlight how the expansion of new, machine learning techniques for modeling and engineering promoter sequences are enabling more accurate prediction of promoter characteristics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew P Cazier
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
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The Cutting Edge of Disease Modeling: Synergy of Induced Pluripotent Stem Cell Technology and Genetically Encoded Biosensors. Biomedicines 2021; 9:biomedicines9080960. [PMID: 34440164 PMCID: PMC8392144 DOI: 10.3390/biomedicines9080960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/02/2021] [Indexed: 11/17/2022] Open
Abstract
The development of cell models of human diseases based on induced pluripotent stem cells (iPSCs) and a cell therapy approach based on differentiated iPSC derivatives has provided a powerful stimulus in modern biomedical research development. Moreover, it led to the creation of personalized regenerative medicine. Due to this, in the last decade, the pathological mechanisms of many monogenic diseases at the cell level have been revealed, and clinical trials of various cell products derived from iPSCs have begun. However, it is necessary to reach a qualitatively new level of research with cell models of diseases based on iPSCs for more efficient searching and testing of drugs. Biosensor technology has a great application prospect together with iPSCs. Biosensors enable researchers to monitor ions, molecules, enzyme activities, and channel conformation in live cells and use them in live imaging and drug screening. These probes facilitate the measurement of steady-state concentrations or activity levels and the observation and quantification of in vivo flux and kinetics. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of the false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the benefits of using biosensors in drug screening. Here, we discuss the possibilities of using biosensor technology in combination with cell models based on human iPSCs and gene editing systems. Furthermore, we focus on the current achievements and problems of using these methods.
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Sun WS, Yang H, No JG, Lee H, Lee N, Lee M, Kang MJ, Oh KB. Select Porcine Elongation Factor 1α Sequences Mediate Stable High-Level and Upregulated Expression of Heterologous Genes in Porcine Cells in Response to Primate Serum. Genes (Basel) 2021; 12:genes12071046. [PMID: 34356062 PMCID: PMC8304002 DOI: 10.3390/genes12071046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
Genetically engineered (GE) pigs with various combinations of genetic profiles have been developed using heterologous promoters. This study aimed to identify autologous promoters for high and ubiquitous expression of xenotransplantation relevant genes in GE pigs. A 1.4 kb upstream regulatory sequence of porcine elongation factor 1α (pEF1α) gene was selected and isolated for use as a promoter. Activity of the pEF1α promoter was subsequently compared with that of the cytomegalovirus (CMV) promoter, CMV enhancer/chicken β-actin (CAG) promoter, and human EF1α (hEF1α) promoter in different types of pig-derived cells. Comparative analysis of luciferase and mutant human leukocyte antigen class E-F2A-β-2 microglobulin (HLA-E) expression driven by pEF1α, CMV, CAG, and hEF1α promoters revealed the pEF1α promoter mediated comparable expression levels with those of the CAG promoter in porcine ear skin fibroblasts (PEFs) and porcine kidney-15 (PK-15) cells, but lower than those of the CAG promoter in porcine aortic endothelial cells (PAECs). The pEF1α promoter provided long-term stable HLA-E expression in PEFs, but the CAG promoter failed to sustain those levels of expression. For xenogeneic serum-induced cytotoxicity assays, the cells were cultured for several hours in growth medium supplemented with primate serum. Notably, the pEF1α promoter induced significant increases in luciferase and HLA-E expression in response to primate serum in PAECs compared with those driven by the CAG promoter, suggesting the pEF1α promoter could regulate temporal expression of heterologous genes under xenogeneic-cytotoxic conditions. These results suggest the pEF1α promoter may be valuable for development of GE pigs spatiotemporally and stably expressing immunomodulatory genes for xenotransplantation.
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Affiliation(s)
- Wu-Sheng Sun
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea; (W.-S.S.); (H.Y.); (J.G.N.); (H.L.); (N.L.); (M.L.)
| | - Hyeon Yang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea; (W.-S.S.); (H.Y.); (J.G.N.); (H.L.); (N.L.); (M.L.)
| | - Jin Gu No
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea; (W.-S.S.); (H.Y.); (J.G.N.); (H.L.); (N.L.); (M.L.)
| | - Haesun Lee
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea; (W.-S.S.); (H.Y.); (J.G.N.); (H.L.); (N.L.); (M.L.)
| | - Nahyun Lee
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea; (W.-S.S.); (H.Y.); (J.G.N.); (H.L.); (N.L.); (M.L.)
| | - Minguk Lee
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea; (W.-S.S.); (H.Y.); (J.G.N.); (H.L.); (N.L.); (M.L.)
| | - Man-Jong Kang
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea;
| | - Keon Bong Oh
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea; (W.-S.S.); (H.Y.); (J.G.N.); (H.L.); (N.L.); (M.L.)
- Correspondence: ; Tel.: +82-63-238-7254
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