1
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Nazneen F, Thompson EA, Blackwell C, Bai JS, Huang F, Bai F. An effective live-attenuated Zika vaccine candidate with a modified 5' untranslated region. NPJ Vaccines 2023; 8:50. [PMID: 37005424 PMCID: PMC10066991 DOI: 10.1038/s41541-023-00650-w] [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: 08/15/2022] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Zika virus (ZIKV) is a mosquito-transmitted flavivirus that has caused devastating congenital Zika syndrome (CZS), including microcephaly, congenital malformation, and fetal demise in human newborns in recent epidemics. ZIKV infection can also cause Guillain-Barré syndrome (GBS) and meningoencephalitis in adults. Despite intensive research in recent years, there are no approved vaccines or antiviral therapeutics against CZS and adult Zika diseases. In this report, we developed a novel live-attenuated ZIKV strain (named Z7) by inserting 50 RNA nucleotides (nt) into the 5' untranslated region (UTR) of a pre-epidemic ZIKV Cambodian strain, FSS13025. We used this particular ZIKV strain as it is attenuated in neurovirulence, immune antagonism, and mosquito infectivity compared with the American epidemic isolates. Our data demonstrate that Z7 replicates efficiently and produces high titers without causing apparent cytopathic effects (CPE) in Vero cells or losing the insert sequence, even after ten passages. Significantly, Z7 induces robust humoral and cellular immune responses that completely prevent viremia after a challenge with a high dose of an American epidemic ZIKV strain PRVABC59 infection in type I interferon (IFN) receptor A deficient (Ifnar1-/-) mice. Moreover, adoptive transfer of plasma collected from Z7 immunized mice protects Ifnar1-/- mice from ZIKV (strain PRVABC59) infection. These results suggest that modifying the ZIKV 5' UTR is a novel strategy to develop live-attenuated vaccine candidates for ZIKV and potentially for other flaviviruses.
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Affiliation(s)
- Farzana Nazneen
- Cell and Molecular Biology Program, Center for Molecular and Cellular Biosciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - E Ashley Thompson
- Cell and Molecular Biology Program, Center for Molecular and Cellular Biosciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Claire Blackwell
- Cell and Molecular Biology Program, Center for Molecular and Cellular Biosciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Jonathan S Bai
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Faqing Huang
- Chemistry and Biochemistry Program, Center for Molecular and Cellular Biosciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Fengwei Bai
- Cell and Molecular Biology Program, Center for Molecular and Cellular Biosciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA.
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2
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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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3
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Ono H, Saito H. Sensing intracellular signatures with synthetic mRNAs. RNA Biol 2023; 20:588-602. [PMID: 37582192 PMCID: PMC10431736 DOI: 10.1080/15476286.2023.2244791] [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] [Revised: 06/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
The bottom-up assembly of biological components in synthetic biology has contributed to a better understanding of natural phenomena and the development of new technologies for practical applications. Over the past few decades, basic RNA research has unveiled the regulatory roles of RNAs underlying gene regulatory networks; while advances in RNA biology, in turn, have highlighted the potential of a wide variety of RNA elements as building blocks to construct artificial systems. In particular, synthetic mRNA-based translational regulators, which respond to signals in cells and regulate the production of encoded output proteins, are gaining attention with the recent rise of mRNA therapeutics. In this Review, we discuss recent progress in RNA synthetic biology, mainly focusing on emerging technologies for sensing intracellular protein and RNA molecules and controlling translation.
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Affiliation(s)
- Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
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4
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Synthetic RNA-based post-transcriptional expression control methods and genetic circuits. Adv Drug Deliv Rev 2022; 184:114196. [PMID: 35288218 DOI: 10.1016/j.addr.2022.114196] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/08/2022] [Indexed: 12/19/2022]
Abstract
RNA-based synthetic genetic circuits provide an alternative for traditional transcription-based circuits in applications where genomic integration is to be avoided. Incorporating various post-transcriptional control methods into such circuits allows for controlling the behaviour of the circuit through the detection of certain biomolecular inputs or reconstituting defined circuit behaviours, thus manipulating cellular functions. In this review, recent developments of various types of post-transcriptional control methods in mammalian cells are discussed as well as auxiliary components that allow for the creation and development of mRNA-based switches. How such post-transcriptional switches are combined into synthetic circuits as well as their applications in biomedical and preclinical settings are also described. Finally, we examine the challenges that need to be surmounted before RNA-based synthetic circuits can be reliably deployed into clinical settings.
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5
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Nakanishi H. Protein-Based Systems for Translational Regulation of Synthetic mRNAs in Mammalian Cells. Life (Basel) 2021; 11:life11111192. [PMID: 34833067 PMCID: PMC8621430 DOI: 10.3390/life11111192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 11/16/2022] Open
Abstract
Synthetic mRNAs, which are produced by in vitro transcription, have been recently attracting attention because they can express any transgenes without the risk of insertional mutagenesis. Although current synthetic mRNA medicine is not designed for spatiotemporal or cell-selective regulation, many preclinical studies have developed the systems for the translational regulation of synthetic mRNAs. Such translational regulation systems will cope with high efficacy and low adverse effects by producing the appropriate amount of therapeutic proteins, depending on the context. Protein-based regulation is one of the most promising approaches for the translational regulation of synthetic mRNAs. As synthetic mRNAs can encode not only output proteins but also regulator proteins, all components of protein-based regulation systems can be delivered as synthetic mRNAs. In addition, in the protein-based regulation systems, the output protein can be utilized as the input for the subsequent regulation to construct multi-layered gene circuits, which enable complex and sophisticated regulation. In this review, I introduce what types of proteins have been used for translational regulation, how to combine them, and how to design effective gene circuits.
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Affiliation(s)
- Hideyuki Nakanishi
- Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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6
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Fukunaga K, Yokobayashi Y. Directed evolution of orthogonal RNA-RBP pairs through library-vs-library in vitro selection. Nucleic Acids Res 2021; 50:601-616. [PMID: 34219162 PMCID: PMC8789040 DOI: 10.1093/nar/gkab527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022] Open
Abstract
RNA-binding proteins (RBPs) and their RNA ligands play many critical roles in gene regulation and RNA processing in cells. They are also useful for various applications in cell biology and synthetic biology. However, re-engineering novel and orthogonal RNA-RBP pairs from natural components remains challenging while such synthetic RNA-RBP pairs could significantly expand the RNA-RBP toolbox for various applications. Here, we report a novel library-vs-library in vitro selection strategy based on Phage Display coupled with Systematic Evolution of Ligands by EXponential enrichment (PD-SELEX). Starting with pools of 1.1 × 1012 unique RNA sequences and 4.0 × 108 unique phage-displayed L7Ae-scaffold (LS) proteins, we selected RNA-RBP complexes through a two-step affinity purification process. After six rounds of library-vs-library selection, the selected RNAs and LS proteins were analyzed by next-generation sequencing (NGS). Further deconvolution of the enriched RNA and LS protein sequences revealed two synthetic and orthogonal RNA-RBP pairs that exhibit picomolar affinity and >4000-fold selectivity.
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Affiliation(s)
- Keisuke Fukunaga
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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7
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Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes. Nat Commun 2021; 12:1576. [PMID: 33707432 PMCID: PMC7952577 DOI: 10.1038/s41467-021-21578-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 01/20/2021] [Indexed: 01/03/2023] Open
Abstract
We apply an oligo-library and machine learning-approach to characterize the sequence and structural determinants of binding of the phage coat proteins (CPs) of bacteriophages MS2 (MCP), PP7 (PCP), and Qβ (QCP) to RNA. Using the oligo library, we generate thousands of candidate binding sites for each CP, and screen for binding using a high-throughput dose-response Sort-seq assay (iSort-seq). We then apply a neural network to expand this space of binding sites, which allowed us to identify the critical structural and sequence features for binding of each CP. To verify our model and experimental findings, we design several non-repetitive binding site cassettes and validate their functionality in mammalian cells. We find that the binding of each CP to RNA is characterized by a unique space of sequence and structural determinants, thus providing a more complete description of CP-RNA interaction as compared with previous low-throughput findings. Finally, based on the binding spaces we demonstrate a computational tool for the successful design and rapid synthesis of functional non-repetitive binding-site cassettes. Phage-coat proteins can be used to build synthetic biology parts. Here the authors use an oligo library and machine learning to predict and verify sequences based on binding scores.
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8
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Eisenhut P, Mebrahtu A, Moradi Barzadd M, Thalén N, Klanert G, Weinguny M, Sandegren A, Su C, Hatton D, Borth N, Rockberg J. Systematic use of synthetic 5'-UTR RNA structures to tune protein translation improves yield and quality of complex proteins in mammalian cell factories. Nucleic Acids Res 2020; 48:e119. [PMID: 33051690 PMCID: PMC7672427 DOI: 10.1093/nar/gkaa847] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/28/2020] [Accepted: 09/22/2020] [Indexed: 12/30/2022] Open
Abstract
Predictably regulating protein expression levels to improve recombinant protein production has become an important tool, but is still rarely applied to engineer mammalian cells. We therefore sought to set-up an easy-to-implement toolbox to facilitate fast and reliable regulation of protein expression in mammalian cells by introducing defined RNA hairpins, termed 'regulation elements (RgE)', in the 5'-untranslated region (UTR) to impact translation efficiency. RgEs varying in thermodynamic stability, GC-content and position were added to the 5'-UTR of a fluorescent reporter gene. Predictable translation dosage over two orders of magnitude in mammalian cell lines of hamster and human origin was confirmed by flow cytometry. Tuning heavy chain expression of an IgG with the RgEs to various levels eventually resulted in up to 3.5-fold increased titers and fewer IgG aggregates and fragments in CHO cells. Co-expression of a therapeutic Arylsulfatase-A with RgE-tuned levels of the required helper factor SUMF1 demonstrated that the maximum specific sulfatase activity was already attained at lower SUMF1 expression levels, while specific production rates steadily decreased with increasing helper expression. In summary, we show that defined 5'-UTR RNA-structures represent a valid tool to systematically tune protein expression levels in mammalian cells and eventually help to optimize recombinant protein expression.
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Affiliation(s)
- Peter Eisenhut
- ACIB Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
- BOKU University of Natural Resources and Life Sciences, Department of Biotechnology, Vienna 1190, Austria
| | - Aman Mebrahtu
- KTH Royal Institute of Technology, Department of Protein Science, 10691 Stockholm, Sweden
| | - Mona Moradi Barzadd
- KTH Royal Institute of Technology, Department of Protein Science, 10691 Stockholm, Sweden
| | - Niklas Thalén
- KTH Royal Institute of Technology, Department of Protein Science, 10691 Stockholm, Sweden
| | - Gerald Klanert
- ACIB Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Marcus Weinguny
- ACIB Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
- BOKU University of Natural Resources and Life Sciences, Department of Biotechnology, Vienna 1190, Austria
| | - Anna Sandegren
- Affibody Medical AB, Scheeles väg 2, SE-171 65 Solna, Sweden
| | - Chao Su
- SOBI AB, Tomtebodavägen 23A, Stockholm, Sweden
| | - Diane Hatton
- AstraZeneca, Biopharmaceutical Development, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Nicole Borth
- ACIB Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
- BOKU University of Natural Resources and Life Sciences, Department of Biotechnology, Vienna 1190, Austria
| | - Johan Rockberg
- KTH Royal Institute of Technology, Department of Protein Science, 10691 Stockholm, Sweden
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9
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Horie F, Endo K, Ito K. Artificial Protein-Responsive Riboswitches Upregulate Non-AUG Translation Initiation in Yeast. ACS Synth Biol 2020; 9:1623-1631. [PMID: 32531157 DOI: 10.1021/acssynbio.0c00206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Artificial control of gene expression is one of the core technologies for engineering biological systems. Riboswitches are cis-acting elements on mRNA that regulate gene expression in a ligand-dependent manner often seen in prokaryotes, but rarely in eukaryotes. Because of the poor variety of such elements available in eukaryotic systems, the number of artificially engineered eukaryotic riboswitches, especially of the upregulation type, is still limited. Here, we developed a design principle for upregulation-type riboswitches that utilize non-AUG initiation induced by ribosomal stalling in a ligand-dependent manner in Saccharomyces cerevisiae. Our design principle simply required the proper positioning of a near-cognate start codon relative to the RNA aptamer. Intriguingly, the CUG codon was the most preferable for non-AUG ON switches in terms of output level and switch performance. This work establishes novel choices for artificial genetic control in eukaryotes with versatile potential for industrial and biomedical applications as well as basic research.
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Affiliation(s)
- Fumihiro Horie
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Kei Endo
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Koichi Ito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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10
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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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11
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Parr CJC, Wada S, Kotake K, Kameda S, Matsuura S, Sakashita S, Park S, Sugiyama H, Kuang Y, Saito H. N 1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells. Nucleic Acids Res 2020; 48:e35. [PMID: 32090264 PMCID: PMC7102939 DOI: 10.1093/nar/gkaa070] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 12/26/2019] [Accepted: 02/12/2020] [Indexed: 01/04/2023] Open
Abstract
Synthetic messenger RNA (mRNA) tools often use pseudouridine and 5-methyl cytidine as substitutions for uridine and cytidine to avoid the immune response and cytotoxicity induced by introducing mRNA into cells. However, the influence of base modifications on the functionality of the RNA tools is poorly understood. Here we show that synthetic mRNA switches containing N1-methylpseudouridine (m1Ψ) as a substitution of uridine substantially out-performed all other modified bases studied, exhibiting enhanced microRNA and protein sensitivity, better cell-type separation ability, and comparably low immune stimulation. We found that the observed phenomena stem from the high protein expression from m1Ψ containing mRNA and efficient translational repression in the presence of target microRNAs or proteins. In addition, synthetic gene circuits with m1Ψ significantly improve performance in cells. These findings indicate that synthetic mRNAs with m1Ψ modification have enormous potentials in the research and application of biofunctional RNA tools.
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Affiliation(s)
- Callum J C Parr
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53, Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shunsuke Wada
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53, Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kenjiro Kotake
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53, Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shigetoshi Kameda
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53, Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Satoshi Matsuura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53, Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Souhei Sakashita
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Yi Kuang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53, Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
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12
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Caliciviral protein-based artificial translational activator for mammalian gene circuits with RNA-only delivery. Nat Commun 2020; 11:1297. [PMID: 32157083 PMCID: PMC7064597 DOI: 10.1038/s41467-020-15061-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
Synthetic RNA-based gene circuits enable sophisticated gene regulation without the risk of insertional mutagenesis. While various RNA binding proteins have been used for translational repression in gene circuits, the direct translational activation of synthetic mRNAs has not been achieved. Here we develop Caliciviral VPg-based Translational activator (CaVT), which activates the translation of synthetic mRNAs without the canonical 5'-cap. The level of translation can be modulated by changing the locations, sequences, and modified nucleosides of CaVT-binding motifs in the target mRNAs, enabling the simultaneous translational activation and repression of different mRNAs with RNA-only delivery. We demonstrate the efficient regulation of apoptosis and genome editing by tuning translation levels with CaVT. In addition, we design programmable CaVT that responds to endogenous microRNAs or small molecules, achieving both cell-state-specific and conditional translational activation from synthetic mRNAs. CaVT will become an important tool in synthetic biology for both biological studies and future therapeutic applications.
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13
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Ohno H, Akamine S, Saito H. Synthetic mRNA-Based Systems in Mammalian Cells. ACTA ACUST UNITED AC 2020; 4:e1900247. [PMID: 32402126 DOI: 10.1002/adbi.201900247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 02/02/2023]
Abstract
Living organisms are programmed to perform multiple functions by sensing intra- and extra-cellular environments and by controlling gene expressions. Synthetic biologists aim to program cells by mimicking, designing, and constructing genetic circuits. Synthetic mRNA-based genetic switches and circuits have attracted attention for future therapeutic applications because of their safety and functional diversity. Here, the mRNA-based switches and circuits that detect specific microRNAs or proteins expressed in a target cell to control transgene expression and cell fate are reviewed. Future perspectives of artificial RNA systems for cell engineering will also be addressed.
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Affiliation(s)
- Hirohisa Ohno
- 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Sae Akamine
- 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
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14
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Kopniczky MB, Canavan C, McClymont DW, Crone MA, Suckling L, Goetzmann B, Siciliano V, MacDonald JT, Jensen K, Freemont PS. Cell-Free Protein Synthesis as a Prototyping Platform for Mammalian Synthetic Biology. ACS Synth Biol 2020; 9:144-156. [PMID: 31899623 DOI: 10.1021/acssynbio.9b00437] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The field of mammalian synthetic biology is expanding quickly, and technologies for engineering large synthetic gene circuits are increasingly accessible. However, for mammalian cell engineering, traditional tissue culture methods are slow and cumbersome, and are not suited for high-throughput characterization measurements. Here we have utilized mammalian cell-free protein synthesis (CFPS) assays using HeLa cell extracts and liquid handling automation as an alternative to tissue culture and flow cytometry-based measurements. Our CFPS assays take a few hours, and we have established optimized protocols for small-volume reactions using automated acoustic liquid handling technology. As a proof-of-concept, we characterized diverse types of genetic regulation in CFPS, including T7 constitutive promoter variants, internal ribosomal entry sites (IRES) constitutive translation-initiation sequence variants, CRISPR/dCas9-mediated transcription repression, and L7Ae-mediated translation repression. Our data shows simple regulatory elements for use in mammalian cells can be quickly prototyped in a CFPS model system.
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Affiliation(s)
- Margarita B. Kopniczky
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Caoimhe Canavan
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - David W. McClymont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Michael A. Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, U.K
| | - Lorna Suckling
- London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Bruno Goetzmann
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Velia Siciliano
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - James T. MacDonald
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Kirsten Jensen
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, U.K
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, U.K
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15
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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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16
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Nakanishi H, Saito H. Mammalian gene circuits with biomolecule-responsive RNA devices. Curr Opin Chem Biol 2019; 52:16-22. [DOI: 10.1016/j.cbpa.2019.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/05/2019] [Accepted: 04/15/2019] [Indexed: 02/06/2023]
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17
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Shen CC, Hsu MN, Chang CW, Lin MW, Hwu JR, Tu Y, Hu YC. Synthetic switch to minimize CRISPR off-target effects by self-restricting Cas9 transcription and translation. Nucleic Acids Res 2019; 47:e13. [PMID: 30462300 PMCID: PMC6379646 DOI: 10.1093/nar/gky1165] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/17/2018] [Accepted: 11/02/2018] [Indexed: 12/27/2022] Open
Abstract
CRISPR/Cas9 is a powerful genome editing system but uncontrolled Cas9 nuclease expression triggers off-target effects and even in vivo immune responses. Inspired by synthetic biology, here we built a synthetic switch that self-regulates Cas9 expression not only in the transcription step by guide RNA-aided self-cleavage of cas9 gene, but also in the translation step by L7Ae:K-turn repression system. We showed that the synthetic switch enabled simultaneous transcriptional and translational repression, hence stringently attenuating the Cas9 expression. The restricted Cas9 expression induced high efficiency on-target indel mutation while minimizing the off-target effects. Furthermore, we unveiled the correlation between Cas9 expression kinetics and on-target/off-target mutagenesis. The synthetic switch conferred detectable Cas9 expression and concomitant high frequency on-target mutagenesis at as early as 6 h, and restricted the Cas9 expression and off-target effects to minimal levels through 72 h. The synthetic switch is compact enough to be incorporated into viral vectors for self-regulation of Cas9 expression, thereby providing a novel 'hit and run' strategy for in vivo genome editing.
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Affiliation(s)
- 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
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - 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
| | - 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
| | - Yi Tu
- Department of Life Science, National Taiwan 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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18
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Endo K, Hayashi K, Saito H. Numerical operations in living cells by programmable RNA devices. SCIENCE ADVANCES 2019; 5:eaax0835. [PMID: 31457099 PMCID: PMC6703868 DOI: 10.1126/sciadv.aax0835] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/12/2019] [Indexed: 05/04/2023]
Abstract
Integrated bioengineering systems can make executable decisions according to the cell state. To sense the state, multiple biomarkers are detected and processed via logic gates with synthetic biological devices. However, numerical operations have not been achieved. Here, we show a design principle for messenger RNA (mRNA) devices that recapitulates intracellular information by multivariate calculations in single living cells. On the basis of this principle and the collected profiles of multiple microRNA activities, we demonstrate that rationally programmed mRNA sets classify living human cells and track their change during differentiation. Our mRNA devices automatically perform multivariate calculation and function as a decision-maker in response to dynamic intracellular changes in living cells.
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Affiliation(s)
- Kei Endo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Karin Hayashi
- 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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19
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Andres J, Blomeier T, Zurbriggen MD. Synthetic Switches and Regulatory Circuits in Plants. PLANT PHYSIOLOGY 2019; 179:862-884. [PMID: 30692218 PMCID: PMC6393786 DOI: 10.1104/pp.18.01362] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 05/20/2023]
Abstract
Synthetic biology is an established but ever-growing interdisciplinary field of research currently revolutionizing biomedicine studies and the biotech industry. The engineering of synthetic circuitry in bacterial, yeast, and animal systems prompted considerable advances for the understanding and manipulation of genetic and metabolic networks; however, their implementation in the plant field lags behind. Here, we review theoretical-experimental approaches to the engineering of synthetic chemical- and light-regulated (optogenetic) switches for the targeted interrogation and control of cellular processes, including existing applications in the plant field. We highlight the strategies for the modular assembly of genetic parts into synthetic circuits of different complexity, ranging from Boolean logic gates and oscillatory devices up to semi- and fully synthetic open- and closed-loop molecular and cellular circuits. Finally, we explore potential applications of these approaches for the engineering of novel functionalities in plants, including understanding complex signaling networks, improving crop productivity, and the production of biopharmaceuticals.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
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20
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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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21
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Zhitnyuk Y, Gee P, Lung MS, Sasakawa N, Xu H, Saito H, Hotta A. Efficient mRNA delivery system utilizing chimeric VSVG-L7Ae virus-like particles. Biochem Biophys Res Commun 2018; 505:1097-1102. [DOI: 10.1016/j.bbrc.2018.09.113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/17/2018] [Indexed: 10/28/2022]
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22
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Weenink T, van der Hilst J, McKiernan RM, Ellis T. Design of RNA hairpin modules that predictably tune translation in yeast. Synth Biol (Oxf) 2018; 3:ysy019. [PMID: 32995525 PMCID: PMC7445769 DOI: 10.1093/synbio/ysy019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Modular parts for tuning translation are prevalent in prokaryotic synthetic biology but lacking for eukaryotic synthetic biology. Working in Saccharomyces cerevisiae yeast, we here describe how hairpin RNA structures inserted into the 5′ untranslated region (5′UTR) of mRNAs can be used to tune expression levels by 100-fold by inhibiting translation. We determine the relationship between the calculated free energy of folding in the 5′UTR and in vivo protein abundance, and show that this enables rational design of hairpin libraries that give predicted expression outputs. Our approach is modular, working with different promoters and protein coding sequences, and outperforms promoter mutation as a way to predictably generate a library where a protein is induced to express at a range of different levels. With this new tool, computational RNA sequence design can be used to predictably fine-tune protein production for genes expressed in yeast.
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Affiliation(s)
- Tim Weenink
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Jelle van der Hilst
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Robert M McKiernan
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Tom Ellis
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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23
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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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24
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Ausländer S, Fussenegger M. Synthetic RNA-based switches for mammalian gene expression control. Curr Opin Biotechnol 2017; 48:54-60. [DOI: 10.1016/j.copbio.2017.03.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/10/2017] [Indexed: 01/25/2023]
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25
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Kawasaki S, Fujita Y, Nagaike T, Tomita K, Saito H. Synthetic mRNA devices that detect endogenous proteins and distinguish mammalian cells. Nucleic Acids Res 2017; 45:e117. [PMID: 28525643 PMCID: PMC5499560 DOI: 10.1093/nar/gkx298] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 04/13/2017] [Indexed: 01/04/2023] Open
Abstract
Synthetic biology has great potential for future therapeutic applications including autonomous cell programming through the detection of protein signals and the production of desired outputs. Synthetic RNA devices are promising for this purpose. However, the number of available devices is limited due to the difficulty in the detection of endogenous proteins within a cell. Here, we show a strategy to construct synthetic mRNA devices that detect endogenous proteins in living cells, control translation and distinguish cell types. We engineered protein-binding aptamers that have increased stability in the secondary structures of their active conformation. The designed devices can efficiently respond to target proteins including human LIN28A and U1A proteins, while the original aptamers failed to do so. Moreover, mRNA delivery of an LIN28A-responsive device into human induced pluripotent stem cells (hiPSCs) revealed that we can distinguish living hiPSCs and differentiated cells by quantifying endogenous LIN28A protein expression level. Thus, our endogenous protein-driven RNA devices determine live-cell states and program mammalian cells based on intracellular protein information.
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Affiliation(s)
- Shunsuke Kawasaki
- Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan.,Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshihiko Fujita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takashi Nagaike
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, 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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26
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Endo K, Hayashi K, Saito H. High-resolution Identification and Separation of Living Cell Types by Multiple microRNA-responsive Synthetic mRNAs. Sci Rep 2016; 6:21991. [PMID: 26902536 PMCID: PMC4763229 DOI: 10.1038/srep21991] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/04/2016] [Indexed: 12/21/2022] Open
Abstract
The precise identification and separation of living cell types is critical to both study cell function and prepare cells for medical applications. However, intracellular information to distinguish live cells remains largely inaccessible. Here, we develop a method for high-resolution identification and separation of cell types by quantifying multiple microRNA (miRNA) activities in live cell populations. We found that a set of miRNA-responsive, in vitro synthesized mRNAs identify a specific cell population as a sharp peak and clearly separate different cell types based on less than two-fold differences in miRNA activities. Increasing the number of miRNA-responsive mRNAs enhanced the capability for cell identification and separation, as we precisely and simultaneously distinguished different cell types with similar miRNA profiles. In addition, the set of synthetic mRNAs separated HeLa cells into subgroups, uncovering heterogeneity of the cells and the level of resolution achievable. Our method could identify target live cells and improve the efficiency of cell purification from heterogeneous populations.
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Affiliation(s)
- Kei Endo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Karin Hayashi
- 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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27
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KARAGIANNIS P, FUJITA Y, SAITO H. RNA-based gene circuits for cell regulation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2016; 92:412-422. [PMID: 27840389 PMCID: PMC5328788 DOI: 10.2183/pjab.92.412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/24/2016] [Indexed: 05/20/2023]
Abstract
A major goal of synthetic biology is to control cell behavior. RNA-mediated genetic switches (RNA switches) are devices that serve this purpose, as they can control gene expressions in response to input signals. In general, RNA switches consist of two domains: an aptamer domain, which binds to an input molecule, and an actuator domain, which controls the gene expression. An input binding to the aptamer can cause the actuator to alter the RNA structure, thus changing access to translation machinery. The assembly of multiple RNA switches has led to complex gene circuits for cell therapies, including the selective killing of pathological cells and purification of cell populations. The inclusion of RNA binding proteins, such as L7Ae, increases the repertoire and precision of the circuit. In this short review, we discuss synthetic RNA switches for gene regulation and their potential therapeutic applications.
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Affiliation(s)
- Peter KARAGIANNIS
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshihiko FUJITA
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hirohide SAITO
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
- Correspondence should be addressed: H. 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 (e-mail: )
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28
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Kopniczky MB, Moore SJ, Freemont PS. Multilevel Regulation and Translational Switches in Synthetic Biology. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2015; 9:485-496. [PMID: 26336145 DOI: 10.1109/tbcas.2015.2451707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In contrast to the versatility of regulatory mechanisms in natural systems, synthetic genetic circuits have been so far predominantly composed of transcriptionally regulated modules. This is about to change as the repertoire of foundational tools for post-transcriptional regulation is quickly expanding. We provide an overview of the different types of translational regulators: protein, small molecule and ribonucleic acid (RNA) responsive and we describe the new emerging circuit designs utilizing these tools. There are several advantages of achieving multilevel regulation via translational switches and it is likely that such designs will have the greatest and earliest impact in mammalian synthetic biology for regenerative medicine and gene therapy applications.
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29
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Miki K, Endo K, Takahashi S, Funakoshi S, Takei I, Katayama S, Toyoda T, Kotaka M, Takaki T, Umeda M, Okubo C, Nishikawa M, Oishi A, Narita M, Miyashita I, Asano K, Hayashi K, Osafune K, Yamanaka S, Saito H, Yoshida Y. Efficient Detection and Purification of Cell Populations Using Synthetic MicroRNA Switches. Cell Stem Cell 2015; 16:699-711. [PMID: 26004781 DOI: 10.1016/j.stem.2015.04.005] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/26/2015] [Accepted: 04/13/2015] [Indexed: 11/15/2022]
Abstract
Isolation of specific cell types, including pluripotent stem cell (PSC)-derived populations, is frequently accomplished using cell surface antigens expressed by the cells of interest. However, specific antigens for many cell types have not been identified, making their isolation difficult. Here, we describe an efficient method for purifying cells based on endogenous miRNA activity. We designed synthetic mRNAs encoding a fluorescent protein tagged with sequences targeted by miRNAs expressed by the cells of interest. These miRNA switches control their translation levels by sensing miRNA activities. Several miRNA switches (miR-1-, miR-208a-, and miR-499a-5p-switches) efficiently purified cardiomyocytes differentiated from human PSCs, and switches encoding the apoptosis inducer Bim enriched for cardiomyocytes without cell sorting. This approach is generally applicable, as miR-126-, miR-122-5p-, and miR-375-switches purified endothelial cells, hepatocytes, and insulin-producing cells differentiated from hPSCs, respectively. Thus, miRNA switches can purify cell populations for which other isolation strategies are unavailable.
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Affiliation(s)
- Kenji Miki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8507, Japan
| | - Kei Endo
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Seiya Takahashi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Shunsuke Funakoshi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan; Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Ikue Takei
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Shota Katayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Taro Toyoda
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Maki Kotaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Tadashi Takaki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Masayuki Umeda
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Chikako Okubo
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Akiko Oishi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Megumi Narita
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Ito Miyashita
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Kanako Asano
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Karin Hayashi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Hirohide Saito
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
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30
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Saito H. [Synthetic RNA technologies to control functions of mammalian cells]. YAKUGAKU ZASSHI 2015; 135:399-404. [PMID: 25759049 DOI: 10.1248/yakushi.14-00240-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We recently succeeded in producing nanostructures made of RNA-protein (RNP) complexes. We show that RNA and the ribosomal protein L7Ae can form a triangular-like nanostructure that consists of three L7Ae proteins, which form the apices of the triangle, bound to one RNA scaffold. This shape is created through a 60° kink introduced into the RNA structure on L7Ae binding. By varying the size of the RNA scaffold we could in turn alter the overall size of the triangular nanostructure. Several functions can be added to this nanostructure by the introduction of effector proteins fused to L7Ae. The design and construction of functional RNP nanostructures that detect specific cancer cells are discussed herein. In parallel, we developed synthetic RNP translational switches to control production levels of particular proteins depending on certain input(s) within the intracellular environment. The RNP-binding module was successfully incorporated into mRNA to generate functional RNP switches. The designed ON/OFF translational switches detect expression of the trigger factor and repress or activate expression of a desired protein (e.g., apoptosis regulator) in target mammalian cells. Taken together, RNP-binding module could be employed for constructing designer genetic switches and functional nanostructures to regulate cellular processes.
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Affiliation(s)
- Hirohide Saito
- Centér for IPS Cell Research and Application, Kyoto University; 53 Kawahara-cho, Shogoin, Sakyo-ku, Kioto 606-8507, Japan; The Hakubi Center for Advanced Research, Kyoto University; Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Andries O, Kitada T, Bodner K, Sanders NN, Weiss R. Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review. Expert Rev Vaccines 2015; 14:313-31. [DOI: 10.1586/14760584.2015.997714] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Engineering of translation provides an alternative regulatory layer for controlling transgene expression in addition to transcriptional regulation. Synthetic mRNA switches that modulate translation of a target gene of interest in response to an intracellular protein could be a key regulator to construct a genetic circuit. Insertion of a protein binding RNA sequence in the 5' UTR of mRNA would allow for the generation of a protein-responsive RNA switch. Here we describe the design principle of the switch and methods for tuning and analyzing its translational activity in mammalian cells.
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