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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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2
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Nagata T, Dwyer CA, Yoshida-Tanaka K, Ihara K, Ohyagi M, Kaburagi H, Miyata H, Ebihara S, Yoshioka K, Ishii T, Miyata K, Miyata K, Powers B, Igari T, Yamamoto S, Arimura N, Hirabayashi H, Uchihara T, Hara RI, Wada T, Bennett CF, Seth PP, Rigo F, Yokota T. Cholesterol-functionalized DNA/RNA heteroduplexes cross the blood-brain barrier and knock down genes in the rodent CNS. Nat Biotechnol 2021; 39:1529-1536. [PMID: 34385691 DOI: 10.1038/s41587-021-00972-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
Achieving regulation of endogenous gene expression in the central nervous system (CNS) with antisense oligonucleotides (ASOs) administered systemically would facilitate the development of ASO-based therapies for neurological diseases. We demonstrate that DNA/RNA heteroduplex oligonucleotides (HDOs) conjugated to cholesterol or α-tocopherol at the 5' end of the RNA strand reach the CNS after subcutaneous or intravenous administration in mice and rats. The HDOs distribute throughout the brain, spinal cord and peripheral tissues and suppress the expression of four target genes by up to 90% in the CNS, whereas single-stranded ASOs conjugated to cholesterol have limited activity. Gene knockdown was observed in major CNS cell types and was greatest in neurons and microglial cells. Side effects, such as thrombocytopenia and focal brain necrosis, were limited by using subcutaneous delivery or by dividing intravenous injections. By crossing the blood-brain barrier more effectively, cholesterol-conjugated HDOs may overcome the limited efficacy of ASOs targeting the CNS without requiring intrathecal administration.
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Affiliation(s)
- Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kensuke Ihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Ohyagi
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidetoshi Kaburagi
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Haruka Miyata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoe Ebihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Ishii
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kenichi Miyata
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Tomoko Igari
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Naoto Arimura
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Toshiki Uchihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | | | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. .,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan.
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4
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Cao X, Sun Y, Lu P, Zhao M. Fluorescence imaging of intracellular nucleases-A review. Anal Chim Acta 2020; 1137:225-237. [PMID: 33153605 DOI: 10.1016/j.aca.2020.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Nucleases play crucial roles in maintaining genomic integrity. Visualization of intracellular distribution and translocation of nucleases are of great importance for understanding the in-vivo physiological functions of these enzymes and their roles in DNA repair and other cellular signaling pathways. Here we review the recently developed approaches for fluorescence imaging of nucleases in various eukaryotic cells. We mainly focused on the immunofluorescence techniques, the genetically encoded fluorescent probes and the chemically synthesized fluorescent DNA-substrate probes that enabled in-situ visualization of the subcellular localization of nucleases and their interactions with other protein/DNA molecules within cells. The targeted nucleases included important endonucleases, 3' exonucleases and 5' exonucleases that were involved in the DNA damage repair pathways and the intracellular DNA degradation. The advantages and limitations of the available tools were summarized and discussed.
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Affiliation(s)
- Xiangjian Cao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ying Sun
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peng Lu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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5
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Wu G, Bazer FW. Application of new biotechnologies for improvements in swine nutrition and pork production. J Anim Sci Biotechnol 2019; 10:28. [PMID: 31019685 PMCID: PMC6474057 DOI: 10.1186/s40104-019-0337-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/17/2019] [Indexed: 12/18/2022] Open
Abstract
Meeting the increasing demands for high-quality pork protein requires not only improved diets but also biotechnology-based breeding to generate swine with desired production traits. Biotechnology can be classified as the cloning of animals with identical genetic composition or genetic engineering (via recombinant DNA technology and gene editing) to produce genetically modified animals or microorganisms. Cloning helps to conserve species and breeds, particularly those with excellent biological and economical traits. Recombinant DNA technology combines genetic materials from multiple sources into single cells to generate proteins. Gene (genome) editing involves the deletion, insertion or silencing of genes to produce: (a) genetically modified pigs with important production traits; or (b) microorganisms without an ability to resist antimicrobial substances. Current gene-editing tools include the use of zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), or clustered regularly interspaced short palindromic repeats-associated nuclease-9 (CRISPR/Cas9) as editors. ZFN, TALEN, or CRISPR/Cas9 components are delivered into target cells through transfection (lipid-based agents, electroporation, nucleofection, or microinjection) or bacteriophages, depending on cell type and plasmid. Compared to the ZFN and TALEN, CRISPR/Cas9 offers greater ease of design and greater flexibility in genetic engineering, but has a higher frequency of off-target effects. To date, genetically modified pigs have been generated to express bovine growth hormone, bacterial phytase, fungal carbohydrases, plant and C. elagan fatty acid desaturases, and uncoupling protein-1; and to lack myostatin, α-1,3-galactosyltransferase, or CD163 (a cellular receptor for the "blue ear disease" virus). Biotechnology holds promise in improving the efficiency of swine production and developing alternatives to antibiotics in the future.
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Affiliation(s)
- Guoyao Wu
- Department of Animal Science and Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, TX 77843-2471 USA
| | - Fuller W Bazer
- Department of Animal Science and Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, TX 77843-2471 USA
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7
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Rosazza C, Deschout H, Buntz A, Braeckmans K, Rols MP, Zumbusch A. Endocytosis and Endosomal Trafficking of DNA After Gene Electrotransfer In Vitro. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e286. [PMID: 26859199 PMCID: PMC4884790 DOI: 10.1038/mtna.2015.59] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 01/08/2023]
Abstract
DNA electrotransfer is a successful technique for gene delivery into cells and represents an attractive alternative to virus-based methods for clinical applications including gene therapy and DNA vaccination. However, little is currently known about the mechanisms governing DNA internalization and its fate inside cells. The objectives of this work were to investigate the role of endocytosis and to quantify the contribution of different routes of cellular trafficking during DNA electrotransfer. To pursue these objectives, we performed flow cytometry and single-particle fluorescence microscopy experiments using inhibitors of endocytosis and endosomal markers. Our results show that ~50% of DNA is internalized by caveolin/raft-mediated endocytosis, 25% by clathrin-mediated endocytosis, and 25% by macropinocytosis. During active transport, DNA is routed through multiple endosomal compartments with, in the hour following electrotransfer, 70% found in Rab5 structures, 50% in Rab11-containing organelles and 30% in Rab9 compartments. Later, 60% of DNA colocalizes with Lamp1 vesicles. Because these molecular markers can overlap while following organelles through several steps of trafficking, the percentages do not sum up to 100%. We conclude that electrotransferred DNA uses the classical endosomal trafficking pathways. Our results are important for a generalized understanding of gene electrotransfer, which is crucial for its safe use in clinics.
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Affiliation(s)
- Christelle Rosazza
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Department of Structural Biology and Biophysics, Institute of Pharmacology and Structural Biology (IPBS), CNRS UMR5089, Toulouse, France.,University of Toulouse III, UPS, Toulouse, France
| | - Hendrik Deschout
- Laboratory of General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, University of Ghent, Ghent, Belgium
| | - Annette Buntz
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, University of Ghent, Ghent, Belgium
| | - Marie-Pierre Rols
- Department of Structural Biology and Biophysics, Institute of Pharmacology and Structural Biology (IPBS), CNRS UMR5089, Toulouse, France.,University of Toulouse III, UPS, Toulouse, France
| | - Andreas Zumbusch
- Department of Chemistry, University of Konstanz, Konstanz, Germany
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8
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Stacey KJ, Idris A, Sagulenko V, Vitak N, Sester DP. Methods for Delivering DNA to Intracellular Receptors. Methods Mol Biol 2016; 1390:93-106. [PMID: 26803624 DOI: 10.1007/978-1-4939-3335-8_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cytosolic DNA can indicate infection and induces type I interferon (IFN) and AIM2 inflammasome responses. Characterization of these responses has required introduction of DNA into the cytosol of macrophages by either chemical transfection or electroporation, each of which has advantages in different applications. We describe here optimized procedures for both electroporation and chemical transfection, including the centrifugation of chemical transfection reagent onto cells, which greatly increases the speed and strength of responses. Appropriate choice of DNA and use of these methods allow study of either the cytosolic DNA responses in isolation or the simultaneous stimulation of cytosolic receptors and the CpG DNA receptor toll-like receptor 9 (TLR9) in the endosomes.
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Affiliation(s)
- Katryn J Stacey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Adi Idris
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Vitaliya Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nazarii Vitak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David P Sester
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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