1
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Opsomer L, Jana S, Mertens I, Cui X, Hoogenboom R, Sanders NN. Efficient in vitro and in vivo transfection of self-amplifying mRNA with linear poly(propylenimine) and poly(ethylenimine-propylenimine) random copolymers as non-viral carriers. J Mater Chem B 2024; 12:3927-3946. [PMID: 38563779 DOI: 10.1039/d3tb03003b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Messenger RNA (mRNA) based vaccines have been introduced worldwide to combat the Covid-19 pandemic. These vaccines consist of non-amplifying mRNA formulated in lipid nanoparticles (LNPs). Consequently, LNPs are considered benchmark non-viral carriers for nucleic acid delivery. However, the formulation and manufacturing of these mRNA-LNP nanoparticles are expensive and time-consuming. Therefore, we used self-amplifying mRNA (saRNA) and synthesized novel polymers as alternative non-viral carrier platform to LNPs, which enable a simple, rapid, one-pot formulation of saRNA-polyplexes. Our novel polymer-based carrier platform consists of randomly concatenated ethylenimine and propylenimine comonomers, resulting in linear, poly(ethylenimine-ran-propylenimine) (L-PEIx-ran-PPIy) copolymers with controllable degrees of polymerization. Here we demonstrate in multiple cell lines, that our saRNA-polyplexes show comparable to higher in vitro saRNA transfection efficiencies and higher cell viabilities compared to formulations with Lipofectamine MessengerMAX™ (LFMM), a commercial, lipid-based carrier considered to be the in vitro gold standard carrier. This is especially true for our in vitro best performing saRNA-polyplexes with N/P 5, which are characterised with a size below 100 nm, a positive zeta potential, a near 100% encapsulation efficiency, a high retention capacity and the ability to protect the saRNA from degradation mediated by RNase A. Furthermore, an ex vivo hemolysis assay with pig red blood cells demonstrated that the saRNA-polyplexes exhibit negligible hemolytic activity. Finally, a bioluminescence-based in vivo study was performed over a 35-day period, and showed that the polymers result in a higher and prolonged bioluminescent signal compared to naked saRNA and L-PEI based polyplexes. Moreover, the polymers show different expression profiles compared to those of LNPs, with one of our new polymers (L-PPI250) demonstrating a higher sustained expression for at least 35 days after injection.
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Affiliation(s)
- Lisa Opsomer
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium.
| | - Somdeb Jana
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium.
| | - Ine Mertens
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium.
| | - Xiaole Cui
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium.
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium.
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium.
- Cancer Research Institute (CRIG), Ghent University, B-9000 Ghent, Belgium
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2
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Ding Y, Tous C, Choi J, Chen J, Wong WW. Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells. Nat Commun 2024; 15:1572. [PMID: 38383558 PMCID: PMC10881482 DOI: 10.1038/s41467-024-45795-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
RNA plays an indispensable role in mammalian cell functions. Cas13, a class of RNA-guided ribonuclease, is a flexible tool for modifying and regulating coding and non-coding RNAs, with enormous potential for creating new cell functions. However, the lack of control over Cas13 activity has limited its cell engineering capability. Here, we present the CRISTAL (Control of RNA with Inducible SpliT CAs13 Orthologs and Exogenous Ligands) platform. CRISTAL is powered by a collection (10 total) of orthogonal split inducible Cas13 effectors that can be turned ON or OFF via small molecules in multiple cell types, providing precise temporal control. Also, we engineer Cas13 logic circuits that can respond to endogenous signaling and exogenous small molecule inputs. Furthermore, the orthogonality, low leakiness, and high dynamic range of our inducible Cas13d and Cas13b enable the design and construction of a robust incoherent feedforward loop, leading to near-perfect and tunable adaptation response. Finally, using our inducible Cas13 effectors, we achieve simultaneous multiplexed control of multiple genes in vitro and in mice. Together, our CRISTAL design represents a powerful platform for precisely regulating RNA dynamics to advance cell engineering and elucidate RNA biology.
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Affiliation(s)
- Yage Ding
- Department of Biomedical Engineering, Biological Design Center, Boston University, Boston, MA, 2215, USA
| | - Cristina Tous
- Department of Biomedical Engineering, Biological Design Center, Boston University, Boston, MA, 2215, USA
| | - Jaehoon Choi
- Department of Biomedical Engineering, Biological Design Center, Boston University, Boston, MA, 2215, USA
| | - Jingyao Chen
- Department of Biomedical Engineering, Biological Design Center, Boston University, Boston, MA, 2215, USA
| | - Wilson W Wong
- Department of Biomedical Engineering, Biological Design Center, Boston University, Boston, MA, 2215, USA.
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3
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Pfeifer BA, Beitelshees M, Hill A, Bassett J, Jones CH. Harnessing synthetic biology for advancing RNA therapeutics and vaccine design. NPJ Syst Biol Appl 2023; 9:60. [PMID: 38036580 PMCID: PMC10689799 DOI: 10.1038/s41540-023-00323-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Recent global events have drawn into focus the diversity of options for combatting disease across a spectrum of prophylactic and therapeutic approaches. The recent success of the mRNA-based COVID-19 vaccines has paved the way for RNA-based treatments to revolutionize the pharmaceutical industry. However, historical treatment options are continuously updated and reimagined in the context of novel technical developments, such as those facilitated through the application of synthetic biology. When it comes to the development of genetic forms of therapies and vaccines, synthetic biology offers diverse tools and approaches to influence the content, dosage, and breadth of treatment with the prospect of economic advantage provided in time and cost benefits. This can be achieved by utilizing the broad tools within this discipline to enhance the functionality and efficacy of pharmaceutical agent sequences. This review will describe how synthetic biology principles can augment RNA-based treatments through optimizing not only the vaccine antigen, therapeutic construct, therapeutic activity, and delivery vector. The enhancement of RNA vaccine technology through implementing synthetic biology has the potential to shape the next generation of vaccines and therapeutics.
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Affiliation(s)
- Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | | | - Andrew Hill
- Pfizer, 66 Hudson Boulevard, New York, NY, 10001, USA
| | - Justin Bassett
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
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4
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Zhao Z, Sun Y, Li M, Yu Q. Construction of Candida albicans Adhesin-Exposed Synthetic Cells for Preventing Systemic Fungal Infection. Vaccines (Basel) 2023; 11:1521. [PMID: 37896925 PMCID: PMC10611093 DOI: 10.3390/vaccines11101521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The development of efficient fungal vaccines is urgent for preventing life-threatening systemic fungal infections. In this study, we prepared a synthetic, cell-based fungal vaccine for preventing systemic fungal infections using synthetic biology techniques. The synthetic cell EmEAP1 was constructed by transforming the Escherichia coli chassis using a de novo synthetic fragment encoding the protein mChEap1 that was composed of the E. coli OmpA peptide, the fluorescence protein mCherry, the Candida albicans adhesin Eap1, and the C-terminally transmembrane region. The EmEAP1 cells highly exposed the mChEap1 on the cell surface under IPTG induction. The fungal vaccine was then prepared by mixing the EmEAP1 cells with aluminum hydroxide gel and CpG. Fluorescence quantification revealed that the fungal vaccine was stable even after 112 days of storage. After immunization in mice, the vaccine resided in the lymph nodes, inducing the recruitment of CD11c+ dendritic cells. Moreover, the vaccine strongly activated the CD4+ T splenocytes and elicited high levels of anti-Eap1 IgG. By the prime-boost immunization, the vaccine prolonged the survival time of the mice infected by the C. albicans cells and attenuated fungal colonization together with inflammation in the kidneys. This study sheds light on the development of synthetic biology-based fungal vaccines for the prevention of life-threatening fungal infections.
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Affiliation(s)
- Zirun Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Z.Z.); (Y.S.); (M.L.)
| | - Ying Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Z.Z.); (Y.S.); (M.L.)
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Z.Z.); (Y.S.); (M.L.)
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Z.Z.); (Y.S.); (M.L.)
- Research Center for Infectious Diseases, Nankai University, Tianjin 300350, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Tianjin 300350, China
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5
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Ding Y, Tous C, Choi J, Chen J, Wong WW. Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533499. [PMID: 36993327 PMCID: PMC10055290 DOI: 10.1101/2023.03.20.533499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
RNA plays an indispensable role in mammalian cell functions. Cas13, a class of RNA-guided ribonuclease, is a flexible tool for modifying and regulating coding and non-coding RNAs, with enormous potential for creating new cell functions. However, the lack of control over Cas13 activity has limited its cell engineering capability. Here, we present the CRISTAL ( C ontrol of R NA with Inducible S pli T C A s13 Orthologs and Exogenous L igands) platform. CRISTAL is powered by a collection (10 total) of orthogonal split inducible Cas13s that can be turned ON or OFF via small molecules in multiple cell types, providing precise temporal control. Also, we engineered Cas13 logic circuits that can respond to endogenous signaling and exogenous small molecule inputs. Furthermore, the orthogonality, low leakiness, and high dynamic range of our inducible Cas13d and Cas13b enable the design and construction of a robust incoherent feedforward loop, leading to near-perfect and tunable adaptation response. Finally, using our inducible Cas13s, we achieve simultaneous multiplexed control of multiple genes in vitro and in mice. Together, our CRISTAL design represents a powerful platform for precisely regulating RNA dynamics to advance cell engineering and elucidate RNA biology.
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6
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Kameda S, Ohno H, Saito H. Synthetic circular RNA switches and circuits that control protein expression in mammalian cells. Nucleic Acids Res 2023; 51:e24. [PMID: 36642090 PMCID: PMC9976894 DOI: 10.1093/nar/gkac1252] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
Synthetic messenger RNA (mRNA) has been focused on as an emerging application for mRNA-based therapies and vaccinations. Recently, synthetic circular RNAs (circRNAs) have shown promise as a new class of synthetic mRNA that enables superior stability and persistent gene expression in cells. However, translational control of circRNA remained challenging. Here, we develop 'circRNA switches' capable of controlling protein expression from circRNA by sensing intracellular RNA or proteins. We designed microRNA (miRNA) and protein-responsive circRNA switches by inserting miRNA-binding or protein-binding sequences into untranslated regions (UTRs), or Coxsackievirus B3 Internal Ribosome Entry Site (CVB3 IRES), respectively. Engineered circRNAs efficiently expressed reporter proteins without inducing severe cell cytotoxicity and immunogenicity, and responded to target miRNAs or proteins, controlling translation levels from circRNA in a cell type-specific manner. Moreover, we constructed circRNA-based gene circuits that selectively activated translation by detecting endogenous miRNA, by connecting miRNA and protein-responsive circRNAs. The designed circRNA circuits performed better than the linear mRNA-based circuits in terms of persistent expression levels. Synthetic circRNA devices provide new insights into RNA engineering and have a potential for RNA synthetic biology and therapies.
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Affiliation(s)
- Shigetoshi Kameda
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan.,Graduate School of Medicine, Kyoto University,Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirohisa Ohno
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan
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7
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Correa S, Grosskopf AK, Lopez Hernandez H, Chan D, Yu AC, Stapleton LM, Appel EA. Translational Applications of Hydrogels. Chem Rev 2021; 121:11385-11457. [PMID: 33938724 PMCID: PMC8461619 DOI: 10.1021/acs.chemrev.0c01177] [Citation(s) in RCA: 332] [Impact Index Per Article: 110.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 12/17/2022]
Abstract
Advances in hydrogel technology have unlocked unique and valuable capabilities that are being applied to a diverse set of translational applications. Hydrogels perform functions relevant to a range of biomedical purposes-they can deliver drugs or cells, regenerate hard and soft tissues, adhere to wet tissues, prevent bleeding, provide contrast during imaging, protect tissues or organs during radiotherapy, and improve the biocompatibility of medical implants. These capabilities make hydrogels useful for many distinct and pressing diseases and medical conditions and even for less conventional areas such as environmental engineering. In this review, we cover the major capabilities of hydrogels, with a focus on the novel benefits of injectable hydrogels, and how they relate to translational applications in medicine and the environment. We pay close attention to how the development of contemporary hydrogels requires extensive interdisciplinary collaboration to accomplish highly specific and complex biological tasks that range from cancer immunotherapy to tissue engineering to vaccination. We complement our discussion of preclinical and clinical development of hydrogels with mechanical design considerations needed for scaling injectable hydrogel technologies for clinical application. We anticipate that readers will gain a more complete picture of the expansive possibilities for hydrogels to make practical and impactful differences across numerous fields and biomedical applications.
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Affiliation(s)
- Santiago Correa
- Materials
Science & Engineering, Stanford University, Stanford, California 94305, United States
| | - Abigail K. Grosskopf
- Chemical
Engineering, Stanford University, Stanford, California 94305, United States
| | - Hector Lopez Hernandez
- Materials
Science & Engineering, Stanford University, Stanford, California 94305, United States
| | - Doreen Chan
- Chemistry, Stanford University, Stanford, California 94305, United States
| | - Anthony C. Yu
- Materials
Science & Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Eric A. Appel
- Materials
Science & Engineering, Stanford University, Stanford, California 94305, United States
- Bioengineering, Stanford University, Stanford, California 94305, United States
- Pediatric
Endocrinology, Stanford University School
of Medicine, Stanford, California 94305, United States
- ChEM-H Institute, Stanford
University, Stanford, California 94305, United States
- Woods
Institute for the Environment, Stanford
University, Stanford, California 94305, United States
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8
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Irvine DJ, Aung A, Silva M. Controlling timing and location in vaccines. Adv Drug Deliv Rev 2020; 158:91-115. [PMID: 32598970 PMCID: PMC7318960 DOI: 10.1016/j.addr.2020.06.019] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
Vaccines are one of the most powerful technologies supporting public health. The adaptive immune response induced by immunization arises following appropriate activation and differentiation of T and B cells in lymph nodes. Among many parameters impacting the resulting immune response, the presence of antigen and inflammatory cues for an appropriate temporal duration within the lymph nodes, and further within appropriate subcompartments of the lymph nodes– the right timing and location– play a critical role in shaping cellular and humoral immunity. Here we review recent advances in our understanding of how vaccine kinetics and biodistribution impact adaptive immunity, and the underlying immunological mechanisms that govern these responses. We discuss emerging approaches to engineer these properties for future vaccines, with a focus on subunit vaccines.
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Affiliation(s)
- Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Aereas Aung
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Murillo Silva
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
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9
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Kawasaki S, Ono H, Hirosawa M, Saito H. RNA and protein-based nanodevices for mammalian post-transcriptional circuits. Curr Opin Biotechnol 2020; 63:99-110. [DOI: 10.1016/j.copbio.2019.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022]
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10
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Ono H, Kawasaki S, Saito H. Orthogonal Protein-Responsive mRNA Switches for Mammalian Synthetic Biology. ACS Synth Biol 2020; 9:169-174. [PMID: 31765565 DOI: 10.1021/acssynbio.9b00343] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The lack of available genetic modules is a fundamental issue in mammalian synthetic biology. Especially, the variety of genetic parts for translational control are limited. Here we report a new set of synthetic mRNA-based translational switches by engineering RNA-binding proteins (RBPs) and RBP-binding RNA motifs (aptamers) that perform strong translational repression. We redesigned the RNA motifs with RNA scaffolds and improved the efficiency of the repression to target RBPs. Using new and previously reported mRNA switches, we demonstrated that the orthogonality of translational regulation was ensured among five different RBP-responsive switches. Moreover, the new switches functioned not only with plasmid introduction, but also with RNA-only delivery, which provides a transient and safer regulation of expression. The translational regulators using RNA-protein interactions provide an alternative strategy to construct complex genetic circuits for future cell engineering and therapeutics.
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Affiliation(s)
- 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, Kyoto 606-8507, Japan
| | - 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
| | - 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
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11
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Synthetic RNA-based logic computation in mammalian cells. Nat Commun 2018; 9:4847. [PMID: 30451868 PMCID: PMC6242901 DOI: 10.1038/s41467-018-07181-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
Synthetic biological circuits are designed to regulate gene expressions to control cell function. To date, these circuits often use DNA-delivery methods, which may lead to random genomic integration. To lower this risk, an all RNA system, in which the circuit and delivery method are constituted of RNA components, is preferred. However, the construction of complexed circuits using RNA-delivered devices in living cells has remained a challenge. Here we show synthetic mRNA-delivered circuits with RNA-binding proteins for logic computation in mammalian cells. We create a set of logic circuits (AND, OR, NAND, NOR, and XOR gates) using microRNA (miRNA)- and protein-responsive mRNAs as decision-making controllers that are used to express transgenes in response to intracellular inputs. Importantly, we demonstrate that an apoptosis-regulatory AND gate that senses two miRNAs can selectively eliminate target cells. Thus, our synthetic RNA circuits with logic operation could provide a powerful tool for future therapeutic applications.
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12
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Small-molecule-based regulation of RNA-delivered circuits in mammalian cells. Nat Chem Biol 2018; 14:1043-1050. [DOI: 10.1038/s41589-018-0146-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 09/11/2018] [Indexed: 12/24/2022]
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13
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Lin MW, Tseng YW, Shen CC, Hsu MN, Hwu JR, Chang CW, Yeh CJ, Chou MY, Wu JC, Hu YC. Synthetic switch-based baculovirus for transgene expression control and selective killing of hepatocellular carcinoma cells. Nucleic Acids Res 2018; 46:e93. [PMID: 29905834 PMCID: PMC6125686 DOI: 10.1093/nar/gky447] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/04/2018] [Accepted: 05/31/2018] [Indexed: 12/13/2022] Open
Abstract
Baculovirus (BV) holds promise as a vector for anticancer gene delivery to combat the most common liver cancer-hepatocellular carcinoma (HCC). However, in vivo BV administration inevitably results in BV entry into non-HCC normal cells, leaky anticancer gene expression and possible toxicity. To improve the safety, we employed synthetic biology to engineer BV for transgene expression regulation. We first uncovered that miR-196a and miR-126 are exclusively expressed in HCC and normal cells, respectively, which allowed us to engineer a sensor based on distinct miRNA expression signature. We next assembled a synthetic switch by coupling the miRNA sensor and RNA binding protein L7Ae for translational repression, and incorporated the entire device into a single BV. The recombinant BV efficiently entered HCC and normal cells and enabled cis-acting transgene expression control, by turning OFF transgene expression in normal cells while switching ON transgene expression in HCC cells. Using pro-apoptotic hBax as the transgene, the switch-based BV selectively killed HCC cells in separate culture and mixed culture of HCC and normal cells. These data demonstrate the potential of synthetic switch-based BV to distinguish HCC and non-HCC normal cells for selective transgene expression control and killing of HCC cells.
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Affiliation(s)
- Mei-Wei Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Yen-Wen Tseng
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Che Shen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Mu-Nung Hsu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Jih-Ru Hwu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chung-Ju Yeh
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Min-Yuan Chou
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Jaw-Ching Wu
- Medical Research Department, Taipei Veterans General Hospital, Taipei Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
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14
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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15
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Self-Amplifying Replicon RNA Delivery to Dendritic Cells by Cationic Lipids. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:118-134. [PMID: 30195751 PMCID: PMC6023837 DOI: 10.1016/j.omtn.2018.04.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 04/29/2018] [Accepted: 04/29/2018] [Indexed: 01/09/2023]
Abstract
Advances in RNA technology during the past two decades have led to the construction of replication-competent RNA, termed replicons, RepRNA, or self-amplifying mRNA, with high potential for vaccine applications. Cytosolic delivery is essential for their translation and self-replication, without infectious progeny generation, providing high levels of antigen expression for inducing humoral and cellular immunity. Synthetic nanoparticle-based delivery vehicles can both protect the RNA molecules and facilitate targeting of dendritic cells—critical for immune defense development. Several cationic lipids were assessed, with RepRNA generated from classical swine fever virus encoding nucleoprotein genes of influenza A virus. The non-cytopathogenic nature of the RNA allowed targeting to dendritic cells without destroying the cells—important for prolonged antigen production and presentation. Certain lipids were more effective at delivery and at promoting translation of RepRNA than others. Selection of particular lipids provided delivery to dendritic cells that resulted in translation, demonstrating that delivery efficiency could not guarantee translation. The observed translation in vitro was reproduced in vivo by inducing immune responses against the encoded influenza virus antigens. Cationic lipid-mediated delivery shows potential for promoting RepRNA vaccine delivery to dendritic cells, particularly when combined with additional delivery elements.
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Ogawa A, Masuoka H, Ota T. Artificial OFF-Riboswitches That Downregulate Internal Ribosome Entry without Hybridization Switches in a Eukaryotic Cell-Free Translation System. ACS Synth Biol 2017; 6:1656-1662. [PMID: 28613837 DOI: 10.1021/acssynbio.7b00124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We constructed novel artificial riboswitches that function in a eukaryotic translation system (wheat germ extract), by rationally implanting an in vitro-selected aptamer into the intergenic internal ribosome entry site (IRES) of Plautia stali intestine virus. These eukaryotic OFF-riboswitches (OFF-eRSs) ligand-dose-dependently downregulate IRES-mediated translation without hybridization switches, which typical riboswitches utilize for gene regulation. The hybridization-switch-free mechanism not only allows for easy design but also requires less energy for regulation, resulting in a higher switching efficiency than hybridization-switch-based OFF-eRSs provide. In addition, even a small ligand such as theophylline can induce satisfactory repression, in contrast to other types of OFF-eRSs that modulate the 5' cap-dependent canonical translation. Because our proposed hybridization-switch-free OFF-eRSs are based on a versatile IRES that functions well in many types of eukaryotic translation systems, they would be widely usable elements for synthetic gene circuits in both cell-free and cell-based synthetic biology.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroki Masuoka
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Tsubasa Ota
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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17
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Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate. Nat Commun 2017; 8:540. [PMID: 28912471 PMCID: PMC5599586 DOI: 10.1038/s41467-017-00459-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 06/29/2017] [Indexed: 11/22/2022] Open
Abstract
Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA–protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA–protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour. Nucleic acid nanotechnology has great potential for future therapeutic applications. Here the authors build protein-driven RNA nanostructures that can function within mammalian cells and regulate the cell fate.
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18
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Higashikuni Y, Chen WC, Lu TK. Advancing therapeutic applications of synthetic gene circuits. Curr Opin Biotechnol 2017; 47:133-141. [PMID: 28750201 DOI: 10.1016/j.copbio.2017.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023]
Abstract
Synthetic biology aims to introduce new sense-and-respond capabilities into living cells, which would enable novel therapeutic strategies. The development of regulatory elements, molecular computing devices, and effector screening technologies has enabled researchers to design synthetic gene circuits in many organisms, including mammalian cells. Engineered gene networks, such as closed-loop circuits or Boolean logic gate circuits, can be used to program cells to perform specific functions with spatiotemporal control and restoration of homeostasis in response to the extracellular environment and intracellular signaling. In addition, genetically modified microbes can be designed as local delivery of therapeutic molecules. In this review, we will discuss recent advances in therapeutic applications of synthetic gene circuits, as well as challenges and future opportunities for biomedicine.
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Affiliation(s)
- Yasutomi Higashikuni
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA
| | - William Cw Chen
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA.
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19
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Luo X, Li B, Zhang X, Zhao W, Bratasz A, Deng B, McComb DW, Dong Y. Dual-functional lipid-like nanoparticles for delivery of mRNA and MRI contrast agents. NANOSCALE 2017; 9:1575-1579. [PMID: 28067926 PMCID: PMC5316423 DOI: 10.1039/c6nr08496f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Multi-functional nanomaterials possess unique properties, facilitating both therapeutic and diagnostic applications among others. Herein, we developed dual-functional lipid-like nanoparticles for simultaneous delivery of mRNA and magnetic resonance imaging (MRI) contrast agents in order to express functional proteins and provide real-time visualization. TT3-Gd18 LLNs were identified as a lead formulation, which was able to encapsulate 91% of mRNA and 74% of Gd. This formulation showed a comparable or a slightly higher delivery efficiency of mRNA compared to the initial TT3 LLNs. Moreover, a strong MRI signal was observed in the cell pellets treated with TT3-Gd18 LLNs. More importantly, TT3-Gd18 LLNs demonstrated an efficient delivery of mRNA and Gd contrast agents in vivo.
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Affiliation(s)
- X Luo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
| | - B Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
| | - X Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
| | - W Zhao
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
| | - A Bratasz
- Small Animal Imaging Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - B Deng
- Center for Electron Microscopy and Analysis, Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - D W McComb
- Center for Electron Microscopy and Analysis, Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Y Dong
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
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20
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Schwarz KA, Leonard JN. Engineering cell-based therapies to interface robustly with host physiology. Adv Drug Deliv Rev 2016; 105:55-65. [PMID: 27266446 DOI: 10.1016/j.addr.2016.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 12/21/2022]
Abstract
Engineered cell-based therapies comprise a rapidly growing clinical technology for treating disease by leveraging the natural capabilities of cells, including migration, information transduction, and biosynthesis and secretion. There now exists a substantial portfolio of intracellular and extracellular sensors that enable bioengineers to program cells to execute defined responses to specific changes in state or environmental cues. As our capability to construct more sophisticated cellular programs increases, assessing and improving the degree to which cell-based therapies perform as desired in vivo will become an increasingly important consideration and opportunity for technological advancement. In this review, we seek to describe both current capabilities and potential needs for building cell-based therapies that interface with host physiology in a manner that is robust - a phrase we use in this context to describe the achievement of therapeutic efficacy across a range of patients and implementations. We first review the portfolio of sensors and outputs currently available for use in cell-based therapies by highlighting key advancements and current gaps. Then, we propose a conceptual framework for evaluating and pursuing robust clinical performance of engineered cell-based therapies.
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21
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Sawlekar R, Montefusco F, Kulkarni VV, Bates DG. Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions. IEEE Trans Nanobioscience 2016; 15:443-454. [PMID: 27164599 DOI: 10.1109/tnb.2016.2560764] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs.
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22
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Huang S, Lee AJ, Tsoi R, Wu F, Zhang Y, Leong KW, You L. Coupling spatial segregation with synthetic circuits to control bacterial survival. Mol Syst Biol 2016; 12:859. [PMID: 26925805 PMCID: PMC4770385 DOI: 10.15252/msb.20156567] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Engineered bacteria have great potential for medical and environmental applications. Fulfilling this potential requires controllability over engineered behaviors and scalability of the engineered systems. Here, we present a platform technology, microbial swarmbot, which employs spatial arrangement to control the growth dynamics of engineered bacteria. As a proof of principle, we demonstrated a safeguard strategy to prevent unintended bacterial proliferation. In particular, we adopted several synthetic gene circuits to program collective survival in Escherichia coli: the engineered bacteria could only survive when present at sufficiently high population densities. When encapsulated by permeable membranes, these bacteria can sense the local environment and respond accordingly. The cells inside the microbial swarmbot capsules will survive due to their high densities. Those escaping from a capsule, however, will be killed due to a decrease in their densities. We demonstrate that this design concept is modular and readily generalizable. Our work lays the foundation for engineering integrated and programmable control of hybrid biological–material systems for diverse applications.
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Affiliation(s)
- Shuqiang Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Anna Jisu Lee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ryan Tsoi
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ying Zhang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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23
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Li B, Luo X, Deng B, Wang J, McComb DW, Shi Y, Gaensler KML, Tan X, Dunn AL, Kerlin BA, Dong Y. An Orthogonal Array Optimization of Lipid-like Nanoparticles for mRNA Delivery in Vivo. NANO LETTERS 2015; 15:8099-107. [PMID: 26529392 PMCID: PMC4869688 DOI: 10.1021/acs.nanolett.5b03528] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Systemic delivery of mRNA-based therapeutics remains a challenging issue for preclinical and clinical studies. Here, we describe new lipid-like nanoparticles (TT-LLNs) developed through an orthogonal array design, which demonstrates improved delivery efficiency of mRNA encoding luciferase in vitro by over 350-fold with significantly reduced experimental workload. One optimized TT3 LLN, termed O-TT3 LLNs, was able to restore the human factor IX (hFIX) level to normal physiological values in FIX-knockout mice. Consequently, these mRNA based nanomaterials merit further development for therapeutic applications.
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Affiliation(s)
- Bin Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xiao Luo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Binbin Deng
- Center for Electron Microscopy and Analysis, Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43212, United States
| | - Junfeng Wang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - David W. McComb
- Center for Electron Microscopy and Analysis, Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43212, United States
| | - Yimin Shi
- Department of Medicine, University of California-San Francisco, San Francisco, California 94143, United States
| | - Karin M. L. Gaensler
- Department of Medicine, University of California-San Francisco, San Francisco, California 94143, United States
| | - Xu Tan
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Amy L. Dunn
- Division of Hematology/Oncology/BMT, Nationwide Children’s Hospital, Columbus, Ohio 43205, United States
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio 43205, United States
| | - Bryce A. Kerlin
- Division of Hematology/Oncology/BMT, Nationwide Children’s Hospital, Columbus, Ohio 43205, United States
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio 43205, United States
- Center for Clinical and Translational Research, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio 43205, United States
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Corresponding Author:
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24
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Andries O, Mc Cafferty S, De Smedt SC, Weiss R, Sanders NN, Kitada T. N(1)-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice. J Control Release 2015; 217:337-44. [PMID: 26342664 DOI: 10.1016/j.jconrel.2015.08.051] [Citation(s) in RCA: 328] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/17/2015] [Accepted: 08/26/2015] [Indexed: 12/26/2022]
Abstract
Messenger RNA as a therapeutic modality is becoming increasingly popular in the field of gene therapy. The realization that nucleobase modifications can greatly enhance the properties of mRNA by reducing the immunogenicity and increasing the stability of the RNA molecule (the Kariko paradigm) has been pivotal for this revolution. Here we find that mRNAs containing the N(1)-methylpseudouridine (m1Ψ) modification alone and/or in combination with 5-methylcytidine (m5C) outperformed the current state-of-the-art pseudouridine (Ψ) and/or m5C/Ψ-modified mRNA platform by providing up to ~44-fold (when comparing double modified mRNAs) or ~13-fold (when comparing single modified mRNAs) higher reporter gene expression upon transfection into cell lines or mice, respectively. We show that (m5C/)m1Ψ-modified mRNA resulted in reduced intracellular innate immunogenicity and improved cellular viability compared to (m5C/)Ψ-modified mRNA upon in vitro transfection. The enhanced capability of (m5C/)m1Ψ-modified mRNA to express proteins may at least partially be due to the increased ability of the mRNA to evade activation of endosomal Toll-like receptor 3 (TLR3) and downstream innate immune signaling. We believe that the (m5C/)m1Ψ-mRNA platform presented here may serve as a new standard in the field of modified mRNA-based therapeutics.
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Affiliation(s)
- Oliwia Andries
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - Séan Mc Cafferty
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium
| | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, USA
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
| | - Tasuku Kitada
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, USA.
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25
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Sawlekar R, Montefusco F, Kulkarni V, Bates DG. Biomolecular implementation of a quasi sliding mode feedback controller based on DNA strand displacement reactions. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2015:949-952. [PMID: 26736420 DOI: 10.1109/embc.2015.7318520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A fundamental aim of synthetic biology is to achieve the capability to design and implement robust embedded biomolecular feedback control circuits. An approach to realize this objective is to use abstract chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks. Here, we employ this approach to facilitate the implementation of a class of nonlinear feedback controllers based on sliding mode control theory. We show how a set of two-step irreversible reactions with ultrasensitive response dynamics can provide a biomolecular implementation of a nonlinear quasi sliding mode (QSM) controller. We implement our controller in closed-loop with a prototype of a biological pathway and demonstrate that the nonlinear QSM controller outperforms a traditional linear controller by facilitating faster tracking response dynamics without introducing overshoots in the transient response.
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26
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Mignon C, Sodoyer R, Werle B. Antibiotic-free selection in biotherapeutics: now and forever. Pathogens 2015; 4:157-81. [PMID: 25854922 PMCID: PMC4493468 DOI: 10.3390/pathogens4020157] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/09/2015] [Accepted: 03/23/2015] [Indexed: 11/16/2022] Open
Abstract
The continuously improving sophistication of molecular engineering techniques gives access to novel classes of bio-therapeutics and new challenges for their production in full respect of the strengthening regulations. Among these biologic agents are DNA based vaccines or gene therapy products and to a lesser extent genetically engineered live vaccines or delivery vehicles. The use of antibiotic-based selection, frequently associated with genetic manipulation of microorganism is currently undergoing a profound metamorphosis with the implementation and diversification of alternative selection means. This short review will present examples of alternatives to antibiotic selection and their context of application to highlight their ineluctable invasion of the bio-therapeutic world.
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Affiliation(s)
- Charlotte Mignon
- Technology Research Institute Bioaster, 317 avenue Jean-Jaurés, 69007 Lyon, France.
| | - Régis Sodoyer
- Technology Research Institute Bioaster, 317 avenue Jean-Jaurés, 69007 Lyon, France.
| | - Bettina Werle
- Technology Research Institute Bioaster, 317 avenue Jean-Jaurés, 69007 Lyon, France.
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