1
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Blahetek G, Mayer C, Zuber J, Lenter M, Strobel B. Suppression of toxic transgene expression by optimized artificial miRNAs increases AAV vector yields in HEK-293 cells. Mol Ther Methods Clin Dev 2024; 32:101280. [PMID: 39015407 PMCID: PMC11250862 DOI: 10.1016/j.omtm.2024.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/07/2024] [Indexed: 07/18/2024]
Abstract
Adeno-associated virus (AAV) vectors have become the leading platform for gene delivery in both preclinical research and therapeutic applications, making the production of high-titer AAV preparations essential. To date, most AAV-based studies use constitutive promoters (e.g., CMV, CAG), which are also active in human embryonic kidney (HEK)-293 producer cells, thus leading to the expression of the transgene already during production. Depending on the transgene's function, this might negatively impact producer cell performance and result in decreased AAV vector yields. Here, we evaluated a panel of diverse microRNA (miRNA)-based shRNA designs to identify a highly potent artificial miRNA for the transient suppression of transgenes during AAV production. Our results demonstrate that insertion of miRNA target sites into the 3' UTR of the transgene and simultaneous expression of the corresponding miRNA from the 3' UTR of conventional AAV production plasmids (rep/cap, pHelper) enabled efficient silencing of toxic transgene expression, thereby increasing AAV vector yields up to 240-fold. This strategy not only allows to maintain the traditional triple-transfection protocol, but also represents a universally applicable approach to suppress toxic transgenes, thereby boosting vector yields with so far unprecedented efficiency.
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Affiliation(s)
- Gina Blahetek
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Christine Mayer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Martin Lenter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Benjamin Strobel
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
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2
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Hughes AC, Pittman BG, Xu B, Gammons JW, Webb CM, Nolen HG, Chapman P, Bikoff JB, Schwarz LA. A single-vector intersectional AAV strategy for interrogating cellular diversity and brain function. Nat Neurosci 2024; 27:1400-1410. [PMID: 38802592 DOI: 10.1038/s41593-024-01659-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
As discovery of cellular diversity in the brain accelerates, so does the need for tools that target cells based on multiple features. Here we developed Conditional Viral Expression by Ribozyme Guided Degradation (ConVERGD), an adeno-associated virus-based, single-construct, intersectional targeting strategy that combines a self-cleaving ribozyme with traditional FLEx switches to deliver molecular cargo to specific neuronal subtypes. ConVERGD offers benefits over existing intersectional expression platforms, such as expanded intersectional targeting with up to five recombinase-based features, accommodation of larger and more complex payloads and a vector that is easy to modify for rapid toolkit expansion. In the present report we employed ConVERGD to characterize an unexplored subpopulation of norepinephrine (NE)-producing neurons within the rodent locus coeruleus that co-express the endogenous opioid gene prodynorphin (Pdyn). These studies showcase ConVERGD as a versatile tool for targeting diverse cell types and reveal Pdyn-expressing NE+ locus coeruleus neurons as a small neuronal subpopulation capable of driving anxiogenic behavioral responses in rodents.
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Affiliation(s)
- Alex C Hughes
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Human Cell Types, Allen Institute for Brain Science, Seattle, WA, USA
| | - Brittany G Pittman
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jesse W Gammons
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charis M Webb
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hunter G Nolen
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Phillip Chapman
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jay B Bikoff
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lindsay A Schwarz
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Mukherjee S, Barash D. Designing RNA switches for synthetic biology using inverse-RNA-folding. Trends Biotechnol 2024; 42:517-521. [PMID: 38040620 DOI: 10.1016/j.tibtech.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023]
Abstract
RNA switches respond to specific ligands to control gene expression. They are widely used in synthetic biology applications and hold potential for future RNA-based therapeutic breakthroughs. However, the crux is their precise design. Here, we will discuss how inverse-RNA-folding could be utilized for the accurate design of RNA switches.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA; Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel.
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
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4
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Düchs MJ, Kratzer RF, Vieyra-Garcia P, Strobel B, Schönberger T, Groß P, Aljayyoussi G, Gupta A, Lang I, Klein H, Morilla SM, Hopf S, Park J, Kreuz S, Klugmann M, Igney FH. Riboswitch-controlled IL-12 gene therapy reduces hepatocellular cancer in mice. Front Immunol 2024; 15:1360063. [PMID: 38558809 PMCID: PMC10979303 DOI: 10.3389/fimmu.2024.1360063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/14/2024] [Indexed: 04/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) and solid cancers with liver metastases are indications with high unmet medical need. Interleukin-12 (IL-12) is a proinflammatory cytokine with substantial anti-tumor properties, but its therapeutic potential has not been realized due to severe toxicity. Here, we show that orthotopic liver tumors in mice can be treated by targeting hepatocytes via systemic delivery of adeno-associated virus (AAV) vectors carrying the murine IL-12 gene. Controlled cytokine production was achieved in vivo by using the tetracycline-inducible K19 riboswitch. AAV-mediated expression of IL-12 led to STAT4 phosphorylation, interferon-γ (IFNγ) production, infiltration of T cells and, ultimately, tumor regression. By detailed analyses of efficacy and tolerability in healthy and tumor-bearing animals, we could define a safe and efficacious vector dose. As a potential clinical candidate, we characterized vectors carrying the human IL-12 (huIL-12) gene. In mice, bioactive human IL-12 was expressed in a vector dose-dependent manner and could be induced by tetracycline, suggesting tissue-specific AAV vectors with riboswitch-controlled expression of highly potent proinflammatory cytokines as an attractive approach for vector-based cancer immunotherapy.
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Affiliation(s)
- Matthias J. Düchs
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ramona F. Kratzer
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Pablo Vieyra-Garcia
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim RCV GmbH & Co. KG, Vienna, Austria
| | - Benjamin Strobel
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Tanja Schönberger
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Peter Groß
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ghaith Aljayyoussi
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Aradhana Gupta
- Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Isabel Lang
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Holger Klein
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sandra Martinez Morilla
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim RCV GmbH & Co. KG, Ridgefield, CT, United States
| | - Stefan Hopf
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim RCV GmbH & Co. KG, Vienna, Austria
| | - John Park
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sebastian Kreuz
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Matthias Klugmann
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Frederik H. Igney
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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5
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Mansouri M, Fussenegger M. Small-Molecule Regulators for Gene Switches to Program Mammalian Cell Behaviour. Chembiochem 2024; 25:e202300717. [PMID: 38081780 DOI: 10.1002/cbic.202300717] [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: 10/18/2023] [Revised: 12/11/2023] [Indexed: 01/13/2024]
Abstract
Synthetic or natural small molecules have been extensively employed as trigger signals or inducers to regulate engineered gene circuits introduced into living cells in order to obtain desired outputs in a controlled and predictable manner. Here, we provide an overview of small molecules used to drive synthetic-biology-based gene circuits in mammalian cells, together with examples of applications at different levels of control, including regulation of DNA manipulation, RNA synthesis and editing, and protein synthesis, maturation, and trafficking. We also discuss the therapeutic potential of these small-molecule-responsive gene circuits, focusing on the advantages and disadvantages of using small molecules as triggers, the mechanisms involved, and the requirements for selecting suitable molecules, including efficiency, specificity, orthogonality, and safety. Finally, we explore potential future directions for translation of these devices to clinical medicine.
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Affiliation(s)
- Maysam Mansouri
- ETH Zurich, Department of Biosystems Science and Engineering, Klingelbergstrasse 48, CH-4056, Basel, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Klingelbergstrasse 48, CH-4056, Basel, Switzerland
- University of Basel, Faculty of Science, Klingelbergstrasse 48, CH-4056, Basel, Switzerland
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6
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Teixeira AP, Fussenegger M. Synthetic Gene Circuits for Regulation of Next-Generation Cell-Based Therapeutics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309088. [PMID: 38126677 PMCID: PMC10885662 DOI: 10.1002/advs.202309088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Arming human cells with synthetic gene circuits enables to expand their capacity to execute superior sensing and response actions, offering tremendous potential for innovative cellular therapeutics. This can be achieved by assembling components from an ever-expanding molecular toolkit, incorporating switches based on transcriptional, translational, or post-translational control mechanisms. This review provides examples from the three classes of switches, and discusses their advantages and limitations to regulate the activity of therapeutic cells in vivo. Genetic switches designed to recognize internal disease-associated signals often encode intricate actuation programs that orchestrate a reduction in the sensed signal, establishing a closed-loop architecture. Conversely, switches engineered to detect external molecular or physical cues operate in an open-loop fashion, switching on or off upon signal exposure. The integration of such synthetic gene circuits into the next generation of chimeric antigen receptor T-cells is already enabling precise calibration of immune responses in terms of magnitude and timing, thereby improving the potency and safety of therapeutic cells. Furthermore, pre-clinical engineered cells targeting other chronic diseases are gathering increasing attention, and this review discusses the path forward for achieving clinical success. With synthetic biology at the forefront, cellular therapeutics holds great promise for groundbreaking treatments.
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Affiliation(s)
- Ana P. Teixeira
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 48BaselCH‐4056Switzerland
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7
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A step closer to safe and efficient mammalian gene regulation. Nat Biotechnol 2024:10.1038/s41587-023-02020-2. [PMID: 38168981 DOI: 10.1038/s41587-023-02020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
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8
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Luo L, Jea JDY, Wang Y, Chao PW, Yen L. Control of mammalian gene expression by modulation of polyA signal cleavage at 5' UTR. Nat Biotechnol 2024:10.1038/s41587-023-01989-0. [PMID: 38168982 DOI: 10.1038/s41587-023-01989-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/13/2023] [Indexed: 01/05/2024]
Abstract
The ability to control gene expression in mammalian cells is crucial for safe and efficacious gene therapies and for elucidating gene functions. Current gene regulation systems have limitations such as harmful immune responses or low efficiency. We describe the pA regulator, an RNA-based switch that controls mammalian gene expression through modulation of a synthetic polyA signal (PAS) cleavage introduced into the 5' UTR of a transgene. The cleavage is modulated by a 'dual-mechanism'-(1) aptamer clamping to inhibit PAS cleavage and (2) drug-induced alternative splicing that removes the PAS, both activated by drug binding. This RNA-based methodology circumvents the immune responses observed in other systems and achieves a 900-fold induction with an EC50 of 0.5 µg ml-1 tetracycline (Tc), which is well within the FDA-approved dose range. The pA regulator effectively controls the luciferase transgene in live mice and the endogenous CD133 gene in human cells, in a dose-dependent and reversible manner with long-term stability.
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Affiliation(s)
- Liming Luo
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jocelyn Duen-Ya Jea
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yan Wang
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Pei-Wen Chao
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Laising Yen
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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9
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Wu Y, Zhu L, Zhang Y, Xu W. Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304852. [PMID: 37658499 DOI: 10.1002/smll.202304852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Indexed: 09/03/2023]
Abstract
Riboswitches have received significant attention over the last two decades for their multiple functionalities and great potential for applications in various fields. This article highlights and reviews the recent advances in biosensing and biotherapy. These fields involve a wide range of applications, such as food safety detection, environmental monitoring, metabolic engineering, live cell imaging, wearable biosensors, antibacterial drug targets, and gene therapy. The discovery, origin, and optimization of riboswitches are summarized to help readers better understand their multidimensional applications. Finally, this review discusses the multidimensional challenges and development of riboswitches in order to further expand their potential for novel applications.
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Affiliation(s)
- Yifan Wu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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10
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Rovira E, Moreno B, Razquin N, Blázquez L, Hernández-Alcoceba R, Fortes P, Pastor F. Engineering U1-Based Tetracycline-Inducible Riboswitches to Control Gene Expression in Mammals. ACS NANO 2023; 17:23331-23346. [PMID: 37971502 DOI: 10.1021/acsnano.3c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Synthetic riboswitches are promising regulatory devices due to their small size, lack of immunogenicity, and ability to fine-tune gene expression in the absence of exogenous trans-acting factors. Based on a gene inhibitory system developed at our lab, termed U1snRNP interference (U1i), we developed tetracycline (TC)-inducible riboswitches that modulate mRNA polyadenylation through selective U1 snRNP recruitment. First, we engineered different TC-U1i riboswitches, which repress gene expression unless TC is added, leading to inductions of gene expression of 3-to-4-fold. Second, we developed a technique called Systematic Evolution of Riboswitches by Exponential Enrichment (SEREX), to isolate riboswitches with enhanced U1 snRNP binding capacity and activity, achieving inducibilities of up to 8-fold. Interestingly, by multiplexing riboswitches we increased inductions up to 37-fold. Finally, we demonstrated that U1i-based riboswitches are dose-dependent and reversible and can regulate the expression of reporter and endogenous genes in culture cells and mouse models, resulting in attractive systems for gene therapy applications. Our work probes SEREX as a much-needed technology for the in vitro identification of riboswitches capable of regulating gene expression in vivo.
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Affiliation(s)
- Eric Rovira
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
| | - Beatriz Moreno
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
| | - Nerea Razquin
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
| | - Lorea Blázquez
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031 Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ruben Hernández-Alcoceba
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid 28029, Spain
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid 28029, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid 28029, Spain
| | - Fernando Pastor
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona 31008, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona 31008, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid 28029, Spain
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11
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Düchs M, Blazevic D, Rechtsteiner P, Kenny C, Lamla T, Low S, Savistchenko J, Neumann M, Melki R, Schönberger T, Stierstorfer B, Wyatt D, Igney F, Ciossek T. AAV-mediated expression of a new conformational anti-aggregated α-synuclein antibody prolongs survival in a genetic model of α-synucleinopathies. NPJ Parkinsons Dis 2023; 9:91. [PMID: 37322068 DOI: 10.1038/s41531-023-00542-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Prion-like transmission of pathology in α-synucleinopathies like Parkinson's disease or multiple system atrophy is increasingly recognized as one potential mechanism to address disease progression. Active and passive immunotherapies targeting insoluble, aggregated α-synuclein are already being actively explored in the clinic with mixed outcomes so far. Here, we report the identification of 306C7B3, a highly selective, aggregate-specific α-synuclein antibody with picomolar affinity devoid of binding to the monomeric, physiologic protein. 306C7B3 binding is Ser129-phosphorylation independent and shows high affinity to several different aggregated α-synuclein polymorphs, increasing the likelihood that it can also bind to the pathological seeds assumed to drive disease progression in patients. In support of this, highly selective binding to pathological aggregates in postmortem brains of MSA patients was demonstrated, with no staining in samples from other human neurodegenerative diseases. To achieve CNS exposure of 306C7B3, an adeno-associated virus (AAV) based approach driving expression of the secreted antibody within the brain of (Thy-1)-[A30P]-hα-synuclein mice was used. Widespread central transduction after intrastriatal inoculation was ensured by using the AAV2HBKO serotype, with transduction being spread to areas far away from the inoculation site. Treatment of (Thy-1)-[A30P]-hα-synuclein mice at the age of 12 months demonstrated significantly increased survival, with 306C7B3 concentration reaching 3.9 nM in the cerebrospinal fluid. These results suggest that AAV-mediated expression of 306C7B3, targeting extracellular, presumably disease-propagating aggregates of α-synuclein, has great potential as a disease-modifying therapy for α-synucleinopathies as it ensures CNS exposure of the antibody, thereby mitigating the selective permeability of the blood-brain barrier.
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Affiliation(s)
- Matthias Düchs
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany
| | - Dragica Blazevic
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany
| | | | | | - Thorsten Lamla
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany
| | - Sarah Low
- Boehringer Ingelheim USA, Ridgefield, CT, USA
| | | | - Manuela Neumann
- Molecular Neuropathology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tübingen, Germany
- Department of Neuropathology, University Hospital of Tübingen, Tübingen, Germany
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA, CNRS, Fontenay-aux-Roses, France
| | - Tanja Schönberger
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany
| | | | - David Wyatt
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany
| | - Frederik Igney
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany
| | - Thomas Ciossek
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riss, Germany.
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12
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Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
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13
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Shitik EM, Shalik IK, Yudkin DV. AAV- based vector improvements unrelated to capsid protein modification. Front Med (Lausanne) 2023; 10:1106085. [PMID: 36817775 PMCID: PMC9935841 DOI: 10.3389/fmed.2023.1106085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) is the leading platform for delivering genetic constructs in vivo. To date, three AAV-based gene therapeutic agents have been approved by the FDA and are used in clinical practice. Despite the distinct advantages of gene therapy development, it is clear that AAV vectors need to be improved. Enhancements in viral vectors are mainly associated with capsid protein modifications. However, there are other structures that significantly affect the AAV life cycle and transduction. The Rep proteins, in combination with inverted terminal repeats (ITRs), determine viral genome replication, encapsidation, etc. Moreover, transgene cassette expression in recombinant variants is directly related to AAV production and transduction efficiency. This review discusses the ways to improve AAV vectors by modifying ITRs, a transgene cassette, and the Rep proteins.
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14
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Kelvin D, Suess B. Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer. RNA Biol 2023; 20:457-468. [PMID: 37459466 DOI: 10.1080/15476286.2023.2234732] [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: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
Synthetic riboswitches are a versatile class of regulatory elements that are becoming increasingly established in synthetic biology applications. They are characterized by their compact size and independence from auxiliary protein factors. While naturally occurring riboswitches were mostly discovered in bacteria, synthetic riboswitches have been designed for all domains of life. Published design strategies far exceed the number of riboswitches found in nature. A core element of any riboswitch is a binding domain, called an aptamer, which is characterized by high specificity and affinity for its ligand. Aptamers can be selected de novo, allowing the design of synthetic riboswitches against a broad spectrum of targets. The tetracycline aptamer has proven to be well suited for riboswitch engineering. Since its selection, it has been used in a variety of applications and is considered to be well established and characterized. Using the tetracycline aptamer as an example, we aim to discuss a large variety of design approaches for synthetic riboswitch engineering and their application. We aim to demonstrate the versatility of riboswitches in general and the high potential of synthetic RNA devices for creating new solutions in both the scientific and medical fields.
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Affiliation(s)
- Daniel Kelvin
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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15
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Lennon SR, Batey RT. Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches. J Mol Biol 2022; 434:167585. [PMID: 35427633 PMCID: PMC9474592 DOI: 10.1016/j.jmb.2022.167585] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
Abstract
Riboswitches are an outstanding example of genetic regulation mediated by RNA conformational switching. In these non-coding RNA elements, the occupancy status of a ligand-binding domain governs the mRNA's decision to form one of two mutually exclusive structures in the downstream expression platform. Temporal constraints upon the function of many riboswitches, requiring folding of complex architectures and conformational switching in a limited co-transcriptional timeframe, make them ideal model systems for studying these processes. In this review, we focus on the mechanism of ligand-directed conformational changes in one of the most widely distributed riboswitches in bacteria: the cobalamin family. We describe the architectural features of cobalamin riboswitches whose structures have been determined by x-ray crystallography, which suggest a direct physical role of cobalamin in effecting the regulatory switch. Next, we discuss a series of experimental approaches applied to several model cobalamin riboswitches that interrogate these structural models. As folding is central to riboswitch function, we consider the differences in folding landscapes experienced by RNAs that are produced in vitro and those that are allowed to fold co-transcriptionally. Finally, we highlight a set of studies that reveal the difficulties of studying cobalamin riboswitches outside the context of transcription and that co-transcriptional approaches are essential for developing a more accurate picture of their structure-function relationships in these switches. This understanding will be essential for future advancements in the use of small-molecule guided RNA switches in a range of applications such as biosensors, RNA imaging tools, and nucleic acid-based therapies.
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Affiliation(s)
- Shelby R Lennon
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA.
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16
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Time and phenotype-dependent transcriptome analysis in AAV-TGFβ1 and Bleomycin-induced lung fibrosis models. Sci Rep 2022; 12:12190. [PMID: 35842487 PMCID: PMC9288451 DOI: 10.1038/s41598-022-16344-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/08/2022] [Indexed: 11/19/2022] Open
Abstract
We have previously established a novel mouse model of lung fibrosis based on Adeno-associated virus (AAV)-mediated pulmonary overexpression of TGFβ1. Here, we provide an in-depth characterization of phenotypic and transcriptomic changes (mRNA and miRNA) in a head-to-head comparison with Bleomycin-induced lung injury over a 4-week disease course. The analyses delineate the temporal state of model-specific and commonly altered pathways, thereby providing detailed insights into the processes underlying disease development. They further guide appropriate model selection as well as interventional study design. Overall, Bleomycin-induced fibrosis resembles a biphasic process of acute inflammation and subsequent transition into fibrosis (with partial resolution), whereas the TGFβ1-driven model is characterized by pronounced and persistent fibrosis with concomitant inflammation and an equally complex disease phenotype as observed upon Bleomycin instillation. Finally, based on an integrative approach combining lung function data, mRNA/miRNA profiles, their correlation and miRNA target predictions, we identify putative drug targets and miRNAs to be explored as therapeutic candidates for fibrotic diseases. Taken together, we provide a comprehensive analysis and rich data resource based on RNA-sequencing, along with a strategy for transcriptome-phenotype coupling. The results will be of value for TGFβ research, drug discovery and biomarker identification in progressive fibrosing interstitial lung diseases.
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17
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MSD-based assays facilitate a rapid and quantitative serostatus profiling for the presence of anti-AAV antibodies. Mol Ther Methods Clin Dev 2022; 25:360-369. [PMID: 35573045 PMCID: PMC9065051 DOI: 10.1016/j.omtm.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 04/14/2022] [Indexed: 11/22/2022]
Abstract
Adeno-associated virus (AAV) vector applications are often limited by capsid-directed humoral immune responses, mainly through neutralizing antibodies (NAbs), which are present throughout the human population due to natural AAV infections. Currently, antibody levels are often quantified via ELISA-based protocols or by cellular NAb assays and less frequently by in vivo NAb assays in mice. These methods need optimization for each serotype and are often not applicable to AAV variants with poor in vitro transduction. To tackle these limitations, we have established Meso Scale Discovery (MSD)-based assays for the quantification of binding antibodies (BAbs) and NAbs against the three most commonly used AAV serotypes, AAV2, AAV8, and AAV9. Both assays detect anti-AAV-IgG1–3 with high sensitivity and consistency as shown in a screen of sera from 40 healthy human donors. Subsequently, BAb and NAb titers were determined for identification of seronegative animals in a non-human primate (NHP) cohort. Moreover, the MSD-based BAb assay protocol was extended to a panel of 14 different AAV serotypes. In summary, our platform allows a rapid and quantitative assessment of the immunological properties of any natural or engineered AAV variant irrespective of transduction efficiency and enables high-throughput screens.
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18
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Dykstra PB, Kaplan M, Smolke CD. Engineering synthetic RNA devices for cell control. Nat Rev Genet 2022; 23:215-228. [PMID: 34983970 PMCID: PMC9554294 DOI: 10.1038/s41576-021-00436-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
The versatility of RNA in sensing and interacting with small molecules, proteins and other nucleic acids while encoding genetic instructions for protein translation makes it a powerful substrate for engineering biological systems. RNA devices integrate cellular information sensing, processing and actuation of specific signals into defined functions and have yielded programmable biological systems and novel therapeutics of increasing sophistication. However, challenges centred on expanding the range of analytes that can be sensed and adding new mechanisms of action have hindered the full realization of the field's promise. Here, we describe recent advances that address these limitations and point to a significant maturation of synthetic RNA-based devices.
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Affiliation(s)
- Peter B. Dykstra
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matias Kaplan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,
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19
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Ender A, Stadler PF, Mörl M, Findeiß S. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing. Methods Mol Biol 2022; 2518:179-202. [PMID: 35666446 DOI: 10.1007/978-1-0716-2421-0_11] [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] [Indexed: 06/15/2023]
Abstract
Riboswitches are an attractive target for the directed design of RNA-based regulators by in silico prediction. These noncoding RNA elements consist of an aptamer platform for the highly selective ligand recognition and an expression platform which controls gene activity typically at the level of transcription or translation. In previous work, we could successfully apply RNA folding prediction to implement a new riboswitch mechanism regulating processing of a tRNA by RNase P. In this contribution, we present detailed information about our pipeline consisting of in silico design combined with the biochemical analysis for the verification of the implemented mechanism. Furthermore, we discuss the applicability of the presented biochemical in vivo and in vitro methods for the characterization of other artificial riboswitches.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Santa Fe Institute, Santa Fe, NM, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.
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20
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Eriksson RAE, Nieminen T, Galibert L, Peltola SK, Tikkanen P, Käyhty P, Lesch HP, Ylä-Herttuala S, Airenne KJ. Optimized riboswitch-regulated AAV vector for VEGF-B gene therapy. Front Med (Lausanne) 2022; 9:1052318. [PMID: 36582287 PMCID: PMC9792491 DOI: 10.3389/fmed.2022.1052318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022] Open
Abstract
Gene therapy would greatly benefit from a method to regulate therapeutic gene expression temporally. Riboswitches are small RNA elements that have been studied for their potential use in turning transgene expression on or off by ligand binding. We compared several tetracycline and toyocamycin-inducible ON-riboswitches for a drug responsive transgene expression. The tetracycline-dependent K19 riboswitch showed the best control and we successfully applied it to different transgenes. The induction of gene expression was 6- to 10-fold, dose-dependent, reversible, and occurred within hours after the addition of a clinically relevant tetracycline dose, using either plasmid or adeno-associated virus (AAV) vectors. To enhance the switching capacity, we further optimized the gene cassette to control the expression of a potential therapeutic gene for cardiovascular diseases, VEGF-B. Using two or three riboswitches simultaneously reduced leakiness and improved the dynamic range, and a linker sequence between the riboswitches improved their functionality. The riboswitch function was promoter-independent, but a post-transcriptional WPRE element in the expression cassette reduced its functionality. The optimized construct was a dual riboswitch at the 3' end of the transgene with a 100 bp linker sequence. Our study reveals significant differences in the function of riboswitches and provides important aspects on optimizing expression cassette designs. The findings will benefit further research and development of riboswitches.
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Affiliation(s)
- Reetta A E Eriksson
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tiina Nieminen
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | | | | | - Petra Tikkanen
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Piia Käyhty
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Hanna P Lesch
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.,Gene Therapy Unit and Research Center, Kuopio University Hospital, Kuopio, Finland
| | - Kari J Airenne
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
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21
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Chen L, Chen W, Liu G, Li J, Lu C, Li J, Tan W, Yang H. Nucleic acid-based molecular computation heads towards cellular applications. Chem Soc Rev 2021; 50:12551-12575. [PMID: 34604889 DOI: 10.1039/d0cs01508c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids, with the advantages of programmability and biocompatibility, have been widely used to design different kinds of novel biocomputing devices. Recently, nucleic acid-based molecular computing has shown promise in making the leap from the test tube to the cell. Such molecular computing can perform logic analysis within the confines of the cellular milieu with programmable modulation of biological functions at the molecular level. In this review, we summarize the development of nucleic acid-based biocomputing devices that are rationally designed and chemically synthesized, highlighting the ability of nucleic acid-based molecular computing to achieve cellular applications in sensing, imaging, biomedicine, and bioengineering. Then we discuss the future challenges and opportunities for cellular and in vivo applications. We expect this review to inspire innovative work on constructing nucleic acid-based biocomputing to achieve the goal of precisely rewiring, even reconstructing cellular signal networks in a prescribed way.
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Affiliation(s)
- Lanlan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Wanzhen Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Guo Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Jingying Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China. .,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Weihong Tan
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
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22
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Achberger K, Cipriano M, Düchs MJ, Schön C, Michelfelder S, Stierstorfer B, Lamla T, Kauschke SG, Chuchuy J, Roosz J, Mesch L, Cora V, Pars S, Pashkovskaia N, Corti S, Hartmann SM, Kleger A, Kreuz S, Maier U, Liebau S, Loskill P. Human stem cell-based retina on chip as new translational model for validation of AAV retinal gene therapy vectors. Stem Cell Reports 2021; 16:2242-2256. [PMID: 34525384 PMCID: PMC8452599 DOI: 10.1016/j.stemcr.2021.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 01/04/2023] Open
Abstract
Gene therapies using adeno-associated viruses (AAVs) are among the most promising strategies to treat or even cure hereditary and acquired retinal diseases. However, the development of new efficient AAV vectors is slow and costly, largely because of the lack of suitable non-clinical models. By faithfully recreating structure and function of human tissues, human induced pluripotent stem cell (iPSC)-derived retinal organoids could become an essential part of the test cascade addressing translational aspects. Organ-on-chip (OoC) technology further provides the capability to recapitulate microphysiological tissue environments as well as a precise control over structural and temporal parameters. By employing our recently developed retina on chip that merges organoid and OoC technology, we analyzed the efficacy, kinetics, and cell tropism of seven first- and second-generation AAV vectors. The presented data demonstrate the potential of iPSC-based OoC models as the next generation of screening platforms for future gene therapeutic studies.
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Affiliation(s)
- Kevin Achberger
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Madalena Cipriano
- Department of Biomedical Engineering, Faculty of Medicine, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Matthias J Düchs
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christian Schön
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | | | | | - Thorsten Lamla
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Stefan G Kauschke
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Johanna Chuchuy
- Department of Biomedical Engineering, Faculty of Medicine, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Julia Roosz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Lena Mesch
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Virginia Cora
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Selin Pars
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Natalia Pashkovskaia
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Serena Corti
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Sophia-Marie Hartmann
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Alexander Kleger
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Sebastian Kreuz
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Udo Maier
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Peter Loskill
- Department of Biomedical Engineering, Faculty of Medicine, Eberhard Karls University Tübingen, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; 3R-Center for In vitro Models and Alternatives to Animal Testing, Eberhard Karls University Tübingen, Tübingen, Germany.
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23
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Regulated control of gene therapies by drug-induced splicing. Nature 2021; 596:291-295. [PMID: 34321659 PMCID: PMC8966400 DOI: 10.1038/s41586-021-03770-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/23/2021] [Indexed: 01/13/2023]
Abstract
So far, gene therapies have relied on complex constructs that cannot be finely controlled1,2. Here we report a universal switch element that enables precise control of gene replacement or gene editing after exposure to a small molecule. The small-molecule inducers are currently in human use, are orally bioavailable when given to animals or humans and can reach both peripheral tissues and the brain. Moreover, the switch system, which we denote Xon, does not require the co-expression of any regulatory proteins. Using Xon, the translation of the desired elements for controlled gene replacement or gene editing machinery occurs after a single oral dose of the inducer, and the robustness of expression can be controlled by the drug dose, protein stability and redosing. The ability of Xon to provide temporal control of protein expression can be adapted for cell-biology applications and animal studies. Additionally, owing to the oral bioavailability and safety of the drugs used, the Xon switch system provides an unprecedented opportunity to refine and tailor the application of gene therapies in humans.
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24
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Finke M, Brecht D, Stifel J, Gense K, Gamerdinger M, Hartig JS. Efficient splicing-based RNA regulators for tetracycline-inducible gene expression in human cell culture and C. elegans. Nucleic Acids Res 2021; 49:e71. [PMID: 33893804 PMCID: PMC8266659 DOI: 10.1093/nar/gkab233] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/17/2021] [Accepted: 04/23/2021] [Indexed: 01/07/2023] Open
Abstract
Synthetic riboswitches gain increasing interest for controlling transgene expression in diverse applications ranging from synthetic biology, functional genomics, and pharmaceutical target validation to potential therapeutic approaches. However, existing systems often lack the pharmaceutically suited ligands and dynamic responses needed for advanced applications. Here we present a series of synthetic riboswitches for controlling gene expression through the regulation of alternative splicing. Placing the 5′-splice site into a stem structure of a tetracycline-sensing aptamer allows us to regulate the accessibility of the splice site. In the presence of tetracycline, an exon with a premature termination codon is skipped and gene expression can occur, whereas in its absence the exon is included into the coding sequence, repressing functional protein expression. We were able to identify RNA switches controlling protein expression in human cells with high dynamic ranges and different levels of protein expression. We present minimalistic versions of this system that circumvent the need to insert an additional exon. Further, we demonstrate the robustness of our approach by transferring the devices into the important research model organism Caenorhabditis elegans, where high levels of functional protein with very low background expression could be achieved.
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Affiliation(s)
- Monika Finke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dominik Brecht
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Julia Stifel
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karina Gense
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Martin Gamerdinger
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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25
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26
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von Jonquieres G, Rae CD, Housley GD. Emerging Concepts in Vector Development for Glial Gene Therapy: Implications for Leukodystrophies. Front Cell Neurosci 2021; 15:661857. [PMID: 34239416 PMCID: PMC8258421 DOI: 10.3389/fncel.2021.661857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Central Nervous System (CNS) homeostasis and function rely on intercellular synchronization of metabolic pathways. Developmental and neurochemical imbalances arising from mutations are frequently associated with devastating and often intractable neurological dysfunction. In the absence of pharmacological treatment options, but with knowledge of the genetic cause underlying the pathophysiology, gene therapy holds promise for disease control. Consideration of leukodystrophies provide a case in point; we review cell type – specific expression pattern of the disease – causing genes and reflect on genetic and cellular treatment approaches including ex vivo hematopoietic stem cell gene therapies and in vivo approaches using adeno-associated virus (AAV) vectors. We link recent advances in vectorology to glial targeting directed towards gene therapies for specific leukodystrophies and related developmental or neurometabolic disorders affecting the CNS white matter and frame strategies for therapy development in future.
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Affiliation(s)
- Georg von Jonquieres
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Caroline D Rae
- Neuroscience Research Australia, Randwick, NSW, Australia
| | - Gary D Housley
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
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Tickner ZJ, Farzan M. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors. Pharmaceuticals (Basel) 2021; 14:ph14060554. [PMID: 34200913 PMCID: PMC8230432 DOI: 10.3390/ph14060554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation.
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Affiliation(s)
- Zachary J. Tickner
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Correspondence:
| | - Michael Farzan
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Emmune, Inc., Jupiter, FL 33458, USA
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Hass DT, Barnstable CJ. Uncoupling proteins in the mitochondrial defense against oxidative stress. Prog Retin Eye Res 2021; 83:100941. [PMID: 33422637 DOI: 10.1016/j.preteyeres.2021.100941] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 02/06/2023]
Abstract
Oxidative stress is a major component of most major retinal diseases. Many extrinsic anti-oxidative strategies have been insufficient at counteracting one of the predominant intrinsic sources of reactive oxygen species (ROS), mitochondria. The proton gradient across the inner mitochondrial membrane is a key driving force for mitochondrial ROS production, and this gradient can be modulated by members of the mitochondrial uncoupling protein (UCP) family. Of the UCPs, UCP2 shows a widespread distribution and has been shown to uncouple oxidative phosphorylation, with concomitant decreases in ROS production. Genetic studies using transgenic and knockout mice have documented the ability of increased UCP2 activity to provide neuroprotection in models of a number of diseases, including retinal diseases, indicating that it is a strong candidate for a therapeutic target. Molecular studies have identified the structural mechanism of action of UCP2 and have detailed the ways in which its expression and activity can be controlled at the transcriptional, translational and posttranslational levels. These studies suggest a number of ways in control of UCP2 expression and activity can be used therapeutically for both acute and chronic conditions. The development of such therapeutic approaches will greatly increase the tools available to combat a broad range of serious retinal diseases.
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Affiliation(s)
- Daniel T Hass
- Department of Biochemistry, The University of Washington, Seattle, WA, 98109, USA
| | - Colin J Barnstable
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, 17033, USA.
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Spöring M, Boneberg R, Hartig JS. Aptamer-Mediated Control of Polyadenylation for Gene Expression Regulation in Mammalian Cells. ACS Synth Biol 2020; 9:3008-3018. [PMID: 33108164 DOI: 10.1021/acssynbio.0c00222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Small aptamer-based regulatory devices can be designed to control a range of RNA-dependent cellular processes and emerged as promising tools for fine-tuning gene expression in synthetic biology. Here, we design a conceptually new riboswitch device that allows for the conditional regulation of polyadenylation. By making use of ligand-induced sequence occlusion, the system efficiently controls the accessibility of the eukaryotic polyadenylation signal. Undesirable 3'-extended read-through products are counteracted by the downstream insertion of a microRNA target site. We demonstrate the modularity of the system with regard to sensor aptamers and polyadenylation signals used and combine the newly designed riboswitch with well-known aptazymes to yield superior composite systems. In addition, we show that the switches can be used to control alternative polyadenylation. The presented genetic switches require very little coding space and can be easily optimized by rational adjustments of the thermodynamic stability. The polyadenylation riboswitch extends the repertoire of RNA-based regulators and opens new possibilities for the generation of complex synthetic circuits.
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Affiliation(s)
- Maike Spöring
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Ronja Boneberg
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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