1
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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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Song G, Lv F, Huang Y, Bai H, Wang S. Conjugated Polymers for Gene Delivery and Photothermal Gene Expression. Chempluschem 2022; 87:e202200073. [DOI: 10.1002/cplu.202200073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/26/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Gang Song
- Institute of Chemistry CAS: Institute of Chemistry Chinese Academy of Sciences Organic Solids CHINA
| | - Fengting Lv
- Institute of Chemistry Chinese Academy of Sciences Zhongguancun North First Street 2 CHINA
| | - Yiming Huang
- Institute of Chemistry CAS: Institute of Chemistry Chinese Academy of Sciences Organic Solids CHINA
| | - Haotian Bai
- Institute of Chemistry CAS: Institute of Chemistry Chinese Academy of Sciences Organic Solids CHINA
| | - Shu Wang
- Institute of Chemistry CAS: Institute of Chemistry Chinese Academy of Sciences Organic Solids CHINA
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3
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Di Blasi R, Marbiah MM, Siciliano V, Polizzi K, Ceroni F. A call for caution in analysing mammalian co-transfection experiments and implications of resource competition in data misinterpretation. Nat Commun 2021; 12:2545. [PMID: 33953169 PMCID: PMC8099865 DOI: 10.1038/s41467-021-22795-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 02/08/2023] Open
Abstract
Transient transfections are routinely used in basic and synthetic biology studies to unravel pathway regulation and to probe and characterise circuit designs. As each experiment has a component of intrinsic variability, reporter gene expression is usually normalized with co-delivered genes that act as transfection controls. Recent reports in mammalian cells highlight how resource competition for gene expression leads to biases in data interpretation, with a direct impact on co-transfection experiments. Here we define the connection between resource competition and transient transfection experiments and discuss possible alternatives. Our aim is to raise awareness within the community and stimulate discussion to include such considerations in future experimental designs, for the development of better transfection controls.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Masue M Marbiah
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Velia Siciliano
- Synthetic and Systems Biology lab for Biomedicine, Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples (ITA), Italy
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK. .,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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4
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Blokpoel Ferreras LA, Chan SY, Vazquez Reina S, Dixon JE. Rapidly Transducing and Spatially Localized Magnetofection Using Peptide-Mediated Non-Viral Gene Delivery Based on Iron Oxide Nanoparticles. ACS APPLIED NANO MATERIALS 2021; 4:167-181. [PMID: 33763629 PMCID: PMC7978400 DOI: 10.1021/acsanm.0c02465] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/06/2020] [Indexed: 05/03/2023]
Abstract
Non-viral delivery systems are generally of low efficiency, which limits their use in gene therapy and editing applications. We previously developed a technology termed glycosaminoglycan (GAG)-binding enhanced transduction (GET) to efficiently deliver a variety of cargos intracellularly; our system employs GAG-binding peptides, which promote cell targeting, and cell penetrating peptides (CPPs), which enhance endocytotic cell internalization. Herein, we describe a further modification by combining gene delivery and magnetic targeting with the GET technology. We associated GET peptides, plasmid (p)DNA, and iron oxide superparamagnetic nanoparticles (MNPs), allowing rapid and targeted GET-mediated uptake by application of static magnetic fields in NIH3T3 cells. This produced effective transfection levels (significantly higher than the control) with seconds to minutes of exposure and localized gene delivery two orders of magnitude higher in targeted over non-targeted cell monolayers using magnetic fields (in 15 min exposure delivering GFP reporter pDNA). More importantly, high cell membrane targeting by GET-DNA and MNP co-complexes and magnetic fields allowed further enhancement to endocytotic uptake, meaning that the nucleic acid cargo was rapidly internalized beyond that of GET complexes alone (GET-DNA). Magnetofection by MNPs combined with GET-mediated delivery allows magnetic field-guided local transfection in vitro and could facilitate focused gene delivery for future regenerative and disease-targeted therapies in vivo.
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Affiliation(s)
- Lia A. Blokpoel Ferreras
- Regenerative
Medicine & Cellular Therapies Division, The University of Nottingham
Biodiscovery Institute (BDI), School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Sze Yan Chan
- Regenerative
Medicine & Cellular Therapies Division, The University of Nottingham
Biodiscovery Institute (BDI), School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Saul Vazquez Reina
- School
of Veterinary Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - James E. Dixon
- Regenerative
Medicine & Cellular Therapies Division, The University of Nottingham
Biodiscovery Institute (BDI), School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
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5
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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6
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Toga T, Kuraoka I, Watanabe S, Nakano E, Takeuchi S, Nishigori C, Sugasawa K, Iwai S. Fluorescence detection of cellular nucleotide excision repair of damaged DNA. Sci Rep 2014; 4:5578. [PMID: 24993089 PMCID: PMC4081890 DOI: 10.1038/srep05578] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/18/2014] [Indexed: 12/31/2022] Open
Abstract
To maintain genetic integrity, ultraviolet light-induced photoproducts in DNA must be removed by the nucleotide excision repair (NER) pathway, which is initiated by damage recognition and dual incisions of the lesion-containing strand. We intended to detect the dual-incision step of cellular NER, by using a fluorescent probe. A 140-base pair linear duplex containing the (6-4) photoproduct and a fluorophore-quencher pair was prepared first. However, this type of DNA was found to be degraded rapidly by nucleases in cells. Next, a plasmid was used as a scaffold. In this case, the fluorophore and the quencher were attached to the same strand, and we expected that the dual-incision product containing them would be degraded in cells. At 3 h after transfection of HeLa cells with the plasmid-type probes, fluorescence emission was detected at the nuclei by fluorescence microscopy only when the probe contained the (6-4) photoproduct, and the results were confirmed by flow cytometry. Finally, XPA fibroblasts and the same cells expressing the XPA gene were transfected with the photoproduct-containing probe. Although the transfer of the probe into the cells was slow, fluorescence was detected depending on the NER ability of the cells.
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Affiliation(s)
- Tatsuya Toga
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Isao Kuraoka
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shun Watanabe
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Eiji Nakano
- Division of Dermatology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Seiji Takeuchi
- Division of Dermatology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Chikako Nishigori
- Division of Dermatology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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7
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Rombouts K, Martens TF, Zagato E, Demeester J, De Smedt SC, Braeckmans K, Remaut K. Effect of Covalent Fluorescence Labeling of Plasmid DNA on Its Intracellular Processing and Transfection with Lipid-Based Carriers. Mol Pharm 2014; 11:1359-68. [DOI: 10.1021/mp4003078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Koen Rombouts
- Laboratory
for General Biochemistry and Physical Pharmacy, Ghent University, Ghent 9000, Belgium
- Centre
for Nano- and Biophotonics, Ghent University, Ghent 9000, Belgium
| | - Thomas F. Martens
- Laboratory
for General Biochemistry and Physical Pharmacy, Ghent University, Ghent 9000, Belgium
- Centre
for Nano- and Biophotonics, Ghent University, Ghent 9000, Belgium
| | - Elisa Zagato
- Laboratory
for General Biochemistry and Physical Pharmacy, Ghent University, Ghent 9000, Belgium
- Centre
for Nano- and Biophotonics, Ghent University, Ghent 9000, Belgium
| | - Jo Demeester
- Laboratory
for General Biochemistry and Physical Pharmacy, Ghent University, Ghent 9000, Belgium
| | - Stefaan C. De Smedt
- Laboratory
for General Biochemistry and Physical Pharmacy, Ghent University, Ghent 9000, Belgium
| | - Kevin Braeckmans
- Laboratory
for General Biochemistry and Physical Pharmacy, Ghent University, Ghent 9000, Belgium
- Centre
for Nano- and Biophotonics, Ghent University, Ghent 9000, Belgium
| | - Katrien Remaut
- Laboratory
for General Biochemistry and Physical Pharmacy, Ghent University, Ghent 9000, Belgium
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