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Tomita T, Nakajima Y, Ohmiya Y, Miyazaki K. Novel three-dimensional live skin-like in vitro composite for bioluminescence reporter gene assay. FEBS J 2024. [PMID: 39148322 DOI: 10.1111/febs.17246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/20/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
We genetically manipulated HaCaT cells, a spontaneously immortalised normal keratinocyte cell line, to stably express two different coloured luciferase reporter genes, driven by interleukin 8 (IL-8) and ubiquitin-C (UBC) promoters, respectively. Subsequently, we generated a three-dimensional (3D) skin-like in vitro composite (SLIC) utilising these cells, with the objective of monitoring bioluminescence emitted from the SLIC. This SLIC was generated on non-woven silica fibre membranes in differentiation medium. Immunohistochemical analyses of skin differentiation markers in the SLIC revealed the expression of keratins 2 and 10, filaggrin, and involucrin, indicating mature skin characteristics. This engineered SLIC was employed for real-time bioluminescence monitoring, allowing the assessment of time- and dose-dependent responses to UV stress, as well as to hydrophilic and hydrophobic chemical loads. Notably, evaluation of responses to hydrophobic substances has been challenging with conventional 2D cell culture methods, suggesting the need for a new approach, which this technology could address. Our observations suggest that engineered SLIC with constitutively expressing reporters driven by selected promoters which are tailored to specific objectives, significantly facilitates assays exploring the physiological functions of skin cells based on genetic response mechanisms. It also highlights new avenues for evaluating the physiological impacts of various compounds designed for topical application to human skin.
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Affiliation(s)
- Tatsunosuke Tomita
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoshihiro Nakajima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Japan
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
- Osaka Institute of Technology (OIT), Omiya, Japan
| | - Koyomi Miyazaki
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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2
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Milito A, Aschern M, McQuillan JL, Yang JS. Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3833-3850. [PMID: 37025006 DOI: 10.1093/jxb/erad100] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Microalgae hold enormous potential to provide a safe and sustainable source of high-value compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly progressing climate change. Bioengineering microalgal strains will be key to optimizing and modifying their metabolic outputs, and to render them competitive with established industrial biotechnology hosts, such as bacteria or yeast. To achieve this, precise and tuneable control over transgene expression will be essential, which would require the development and rational design of synthetic promoters as a key strategy. Among green microalgae, Chlamydomonas reinhardtii represents the reference species for bioengineering and synthetic biology; however, the repertoire of functional synthetic promoters for this species, and for microalgae generally, is limited in comparison to other commercial chassis, emphasizing the need to expand the current microalgal gene expression toolbox. Here, we discuss state-of-the-art promoter analyses, and highlight areas of research required to advance synthetic promoter development in C. reinhardtii. In particular, we exemplify high-throughput studies performed in other model systems that could be applicable to microalgae, and propose novel approaches to interrogating algal promoters. We lastly outline the major limitations hindering microalgal promoter development, while providing novel suggestions and perspectives for how to overcome them.
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Affiliation(s)
- Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Moritz Aschern
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Josie L McQuillan
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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3
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Kawasaki S, Ono H, Hirosawa M, Kuwabara T, Sumi S, Lee S, Woltjen K, Saito H. Programmable mammalian translational modulators by CRISPR-associated proteins. Nat Commun 2023; 14:2243. [PMID: 37076490 PMCID: PMC10115826 DOI: 10.1038/s41467-023-37540-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Translational modulation based on RNA-binding proteins can be used to construct artificial gene circuits, but RNA-binding proteins capable of regulating translation efficiently and orthogonally remain scarce. Here we report CARTRIDGE (Cas-Responsive Translational Regulation Integratable into Diverse Gene control) to repurpose Cas proteins as translational modulators in mammalian cells. We demonstrate that a set of Cas proteins efficiently and orthogonally repress or activate the translation of designed mRNAs that contain a Cas-binding RNA motif in the 5'-UTR. By linking multiple Cas-mediated translational modulators, we designed and built artificial circuits like logic gates, cascades, and half-subtractor circuits. Moreover, we show that various CRISPR-related technologies like anti-CRISPR and split-Cas9 platforms could be similarly repurposed to control translation. Coupling Cas-mediated translational and transcriptional regulation enhanced the complexity of synthetic circuits built by only introducing a few additional elements. Collectively, CARTRIDGE has enormous potential as a versatile molecular toolkit for mammalian synthetic biology.
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Affiliation(s)
- Shunsuke Kawasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Moe Hirosawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takeru Kuwabara
- Faculty of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shunsuke Sumi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Suji Lee
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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4
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Duan Y, Tan Y, Wei X, Pei X, Li M. Versatile Strategy for the Construction of a Transcription Factor-Based Orthogonal Gene Expression Toolbox in Monascus spp. ACS Synth Biol 2023; 12:213-223. [PMID: 36625512 DOI: 10.1021/acssynbio.2c00500] [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: 01/11/2023]
Abstract
Gene expression is needed to be conducted in an orthogonal manner and controllable independently from the host's native regulatory system. However, there is a shortage of gene expression regulatory toolboxes that function orthogonally from each other and toward the host. Herein, we developed a strategy based on the mutant library to generate orthogonal gene expression toolboxes. A transcription factor, MaR, located in the Monascus azaphilone biosynthetic gene cluster, was taken as a typical example. Nine DNA-binding residues of MaR were identified by molecular simulation and site-directed mutagenesis. We created five MaR multi-site saturation mutagenesis libraries consisting of 10743 MaR variants on the basis of five cognate promoters. A functional analysis revealed that all five tested promoters were orthogonally regulated by five different MaR variants, respectively. Furthermore, fine gene expression tunability and high signal sensitivity of this toolbox are demonstrated by introducing chemically inducible expression modules, designing synthetic promoter elements, and creating protein-protein interaction between MaRs. This study paves the way for a bottom-up approach to build orthogonal gene expression toolboxes.
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Affiliation(s)
- Yali Duan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province430070, China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
| | - Yingao Tan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province430070, China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
| | - Xuetuan Wei
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou310012, China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province430070, China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
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5
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Berling E, Nicolle R, Laforêt P, Ronzitti G. Gene therapy review: Duchenne muscular dystrophy case study. Rev Neurol (Paris) 2023; 179:90-105. [PMID: 36517287 DOI: 10.1016/j.neurol.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Gene therapy, i.e., any therapeutic approach involving the use of genetic material as a drug and more largely altering the transcription or translation of one or more genes, covers a wide range of innovative methods for treating diseases, including neurological disorders. Although they share common principles, the numerous gene therapy approaches differ greatly in their mechanisms of action. They also differ in their maturity for some are already used in clinical practice while others have never been used in humans. The aim of this review is to present the whole range of gene therapy techniques through the example of Duchenne muscular dystrophy (DMD). DMD is a severe myopathy caused by mutations in the dystrophin gene leading to the lack of functional dystrophin protein. It is a disease known to all neurologists and in which almost all gene therapy methods were applied. Here we discuss the mechanisms of gene transfer techniques with or without viral vectors, DNA editing with or without matrix repair and those acting at the RNA level (RNA editing, exon skipping and STOP-codon readthrough). For each method, we present the results obtained in DMD with a particular focus on clinical data. This review aims also to outline the advantages, limitations and risks of gene therapy related to the approach used.
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Affiliation(s)
- E Berling
- Neurology department, Raymond Poincaré university hospital, AP-HP, Garches, France; Nord-Est-Île-de-France neuromuscular reference center, FHU PHENIX, Garches, France; U 1179 Inserm, université Paris-Saclay, Montigny-Le-Bretonneux, France.
| | - R Nicolle
- Université Paris Cité, Inserm UMR1163, Imagine Institute, Clinical Bioinformatics laboratory, 75015 Paris, France
| | - P Laforêt
- Neurology department, Raymond Poincaré university hospital, AP-HP, Garches, France; Nord-Est-Île-de-France neuromuscular reference center, FHU PHENIX, Garches, France; U 1179 Inserm, université Paris-Saclay, Montigny-Le-Bretonneux, France
| | - G Ronzitti
- Université Paris Cité, Inserm UMR1163, Imagine Institute, Clinical Bioinformatics laboratory, 75015 Paris, France; Genethon, Evry, France
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6
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Lu Y, Happi Mbakam C, Song B, Bendavid E, Tremblay JP. Improvements of nuclease and nickase gene modification techniques for the treatment of genetic diseases. Front Genome Ed 2022; 4:892769. [PMID: 35958050 PMCID: PMC9360573 DOI: 10.3389/fgeed.2022.892769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/08/2022] [Indexed: 12/20/2022] Open
Abstract
Advancements in genome editing make possible to exploit the functions of enzymes for efficient DNA modifications with tremendous potential to treat human genetic diseases. Several nuclease genome editing strategies including Meganucleases (MNs), Zinc Finger Nucleases (ZFNs), Transcription Activator-like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated proteins (CRISPR-Cas) have been developed for the correction of genetic mutations. CRISPR-Cas has further been engineered to create nickase genome editing tools including Base editors and Prime editors with much precision and efficacy. In this review, we summarized recent improvements in nuclease and nickase genome editing approaches for the treatment of genetic diseases. We also highlighted some limitations for the translation of these approaches into clinical applications.
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Affiliation(s)
- Yaoyao Lu
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Cedric Happi Mbakam
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Bo Song
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Eli Bendavid
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Jacques-P. Tremblay
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
- *Correspondence: Jacques-P. Tremblay,
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7
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Genome Editing: A Promising Approach for Achieving Abiotic Stress Tolerance in Plants. Int J Genomics 2022; 2022:5547231. [PMID: 35465040 PMCID: PMC9033345 DOI: 10.1155/2022/5547231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/24/2022] [Indexed: 12/26/2022] Open
Abstract
The susceptibility of crop plants towards abiotic stresses is highly threatening to assure global food security as it results in almost 50% annual yield loss. To address this issue, several strategies like plant breeding and genetic engineering have been used by researchers from time to time. However, these approaches are not sufficient to ensure stress resilience due to the complexity associated with the inheritance of abiotic stress adaptive traits. Thus, researchers were prompted to develop novel techniques with high precision that can address the challenges connected to the previous strategies. Genome editing is the latest approach that is in the limelight for improving the stress tolerance of plants. It has revolutionized crop research due to its versatility and precision. The present review is an update on the different genome editing tools used for crop improvement so far and the various challenges associated with them. It also highlights the emerging potential of genome editing for developing abiotic stress-resilient crops.
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8
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Khakimzhan A, Garenne D, Tickman B, Fontana J, Carothers J, Noireaux V. Complex dependence of CRISPR-Cas9 binding strength on guide RNA spacer lengths. Phys Biol 2021; 18:056003. [PMID: 34102625 DOI: 10.1088/1478-3975/ac091e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022]
Abstract
It is established that for CRISPR-Cas9 applications guide RNAs with 17-20 bp long spacer sequences are optimal for accurate target binding and cleavage. In this work we perform cell-free CRISPRa (CRISPR activation) and CRISPRi (CRISPR inhibition) experiments to demonstrate the existence of a complex dependence of CRISPR-Cas9 binding as a function of the spacer length and complementarity. Our results show that significantly truncated or mismatched spacer sequences can form stronger guide-target bonds than the conventional 17-20 bp long spacers. To explain this phenomenon, we take into consideration previous structural and single-molecule CRISPR-Cas9 experiments and develop a novel thermodynamic model of CRISPR-Cas9 target recognition.
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Affiliation(s)
- Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN 55455, United States of America
| | - David Garenne
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN 55455, United States of America
| | - Benjamin Tickman
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States of America
| | - Jason Fontana
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States of America
| | - James Carothers
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States of America
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States of America
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN 55455, United States of America
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