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Hedlund H, Du Rietz H, Johansson JM, Eriksson HC, Zedan W, Huang L, Wallin J, Wittrup A. Single-cell quantification and dose-response of cytosolic siRNA delivery. Nat Commun 2023; 14:1075. [PMID: 36841822 PMCID: PMC9968291 DOI: 10.1038/s41467-023-36752-1] [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: 10/14/2021] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Endosomal escape and subsequent cytosolic delivery of small interfering RNA (siRNA) therapeutics is believed to be highly inefficient. Since it has not been possible to quantify cytosolic amounts of delivered siRNA at therapeutic doses, determining delivery bottlenecks and total efficiency has been difficult. Here, we present a confocal microscopy-based method to quantify cytosolic delivery of fluorescently labeled siRNA during lipid-mediated delivery. This method enables detection and quantification of sub-nanomolar cytosolic siRNA release amounts from individual release events with measures of quantitation confidence for each event. Single-cell kinetics of siRNA-mediated knockdown in cells expressing destabilized eGFP unveiled a dose-response relationship with respect to knockdown induction, depth and duration in the range from several hundred to thousands of cytosolic siRNA molecules. Accurate quantification of cytosolic siRNA, and the establishment of the intracellular dose-response relationships, will aid the development and characterization of novel delivery strategies for nucleic acid therapeutics.
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Affiliation(s)
- Hampus Hedlund
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hampus Du Rietz
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johanna M Johansson
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hanna C Eriksson
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Wahed Zedan
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Linfeng Huang
- Wang-Cai Biochemistry Lab, Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Jonas Wallin
- Department of Mathematical Statistics, Lund University, Lund, Sweden
| | - Anders Wittrup
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden. .,Skane University Hospital, Oncology, Lund, Sweden. .,Wallenberg Center for Molecular Medicine, Lund, Sweden.
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Dornseifer S, Willkomm S, Far RKK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T. RNAi revised--target mRNA-dependent enhancement of gene silencing. Nucleic Acids Res 2015; 43:10623-32. [PMID: 26578554 PMCID: PMC4678823 DOI: 10.1093/nar/gkv1200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/26/2015] [Indexed: 01/11/2023] Open
Abstract
The discovery of RNA interference (RNAi) gave rise to the development of new nucleic acid-based technologies as powerful investigational tools and potential therapeutics. Mechanistic key details of RNAi in humans need to be deciphered yet, before such approaches take root in biomedicine and molecular therapy. We developed and validated an in silico-based model of siRNA-mediated RNAi in human cells in order to link in vitro-derived pre-steady state kinetic data with a quantitative and time-resolved understanding of RNAi on the cellular level. The observation that product release by Argonaute 2 is accelerated in the presence of an excess of target RNA in vitro inspired us to suggest an associative mechanism for the RNA slicer reaction where incoming target mRNAs actively promote dissociation of cleaved mRNA fragments. This novel associative model is compatible with high multiple turnover rates of RNAi-based gene silencing in living cells and accounts for target mRNA concentration-dependent enhancement of the RNAi machinery.
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Affiliation(s)
- Simon Dornseifer
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Sarah Willkomm
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | | | - Janine Liebschwager
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Foteini Beltsiou
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Kirsten Frank
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Sandra D Laufer
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Thomas Martinetz
- Institute for Neuro- and Bioinformatics, University of Lübeck, 23538 Lübeck, Germany
| | - Georg Sczakiel
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | | | - Tobias Restle
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
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Lundin KE, Højland T, Hansen BR, Persson R, Bramsen JB, Kjems J, Koch T, Wengel J, Smith CIE. Biological activity and biotechnological aspects of locked nucleic acids. ADVANCES IN GENETICS 2013; 82:47-107. [PMID: 23721720 DOI: 10.1016/b978-0-12-407676-1.00002-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Locked nucleic acid (LNA) is one of the most promising new nucleic acid analogues that has been produced under the past two decades. In this chapter, we have tried to cover many of the different areas, where this molecule has been used to improve the function of synthetic oligonucleotides (ONs). The use of LNA in antisense ONs, including gapmers, splice-switching ONs, and siLNA, as well as antigene ONs, is reviewed. Pharmacokinetics as well as pharmacodynamics of LNA ONs and a description of selected compounds in, or close to, clinical testing are described. In addition, new LNA modifications and the adaptation of enzymes for LNA incorporation are reviewed. Such enzymes may become important for the development of stabilized LNA-containing aptamers.
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Affiliation(s)
- Karin E Lundin
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Novum, Huddinge, Stockholm, Sweden.
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Järver P, Coursindel T, Andaloussi SEL, Godfrey C, Wood MJA, Gait MJ. Peptide-mediated Cell and In Vivo Delivery of Antisense Oligonucleotides and siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e27. [PMID: 23344079 PMCID: PMC3390225 DOI: 10.1038/mtna.2012.18] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/26/2012] [Accepted: 04/26/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Peter Järver
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Samir EL Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- Department of Laboratory Medicine, Karolinska Institute, Hudidnge, Sweden
| | - Caroline Godfrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Matthew JA Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Michael J Gait
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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Cell penetrating peptides in the delivery of biopharmaceuticals. Biomolecules 2012; 2:187-202. [PMID: 24970133 PMCID: PMC4030843 DOI: 10.3390/biom2020187] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/16/2012] [Accepted: 03/23/2012] [Indexed: 01/10/2023] Open
Abstract
The cell membrane is a highly selective barrier. This limits the cellular uptake of molecules including DNA, oligonucleotides, peptides and proteins used as therapeutic agents. Different approaches have been employed to increase the membrane permeability and intracellular delivery of these therapeutic molecules. One such approach is the use of Cell Penetrating Peptides (CPPs). CPPs represent a new and innovative concept, which bypasses the problem of bioavailability of drugs. The success of CPPs lies in their ability to unlock intracellular and even intranuclear targets for the delivery of agents ranging from peptides to antibodies and drug-loaded nanoparticles. This review highlights the development of cell penetrating peptides for cell-specific delivery strategies involving biomolecules that can be triggered spatially and temporally within a cell transport pathway by change in physiological conditions. The review also discusses conjugations of therapeutic agents to CPPs for enhanced intracellular delivery and bioavailability that are at the clinical stage of development.
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Zaghloul EM, Viola JR, Zuber G, Smith CIE, Lundin KE. Formulation and delivery of splice-correction antisense oligonucleotides by amino acid modified polyethylenimine. Mol Pharm 2010; 7:652-63. [PMID: 20128628 DOI: 10.1021/mp900220p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Splice-correcting phosphorothioate RNA antisense oligonucleotides with 2'-O-methyl modifications (ASO) are promising therapeutic agents for several disorders caused by aberrant splicing. However, their usefulness is hindered by the lack of efficient delivery. Unmodified 25 kDa polyethylenimine (PEI) has shown potential for plasmid delivery but seems to be less efficient for short nucleic acid sequences. Herein, we have evaluated several amino acid modified PEI molecules as carriers for ASO. By characterization of their properties, such as size, stability and transfection into mammalian cells, we have identified tyrosine-modified PEI (PEIY) as an efficient ASO delivery system. HeLa705 cells containing an aberrant luciferase gene, interrupted by a mutated beta-globin intron, were used to assess the splice correction effectiveness mediated by the various modified PEI/ASO polyplexes. PEIY has a self-assembly nature, as opposed to the highly cationic parent polymer, which is relevant for the stability of the PEIY/ASO complexes. As a result, at an optimal ratio of 20:1 (+/-), the complexes that formed significantly corrected the splicing on both the mRNA and the protein levels. ASO formulated with PEIY enhanced luciferase activity up to 450-fold. This increase was three times higher than that produced by the commercially available transfection agent Lipofectamine. PEIY/ASO polyplexes resulted in at least 80% correct splicing of the transcript. Moreover, extremely low doses of ASO (0.025 microM) showed significant splice correction represented by 150-fold increase of luciferase activity and 47% mRNA correction. Our findings suggest key parameters for formulating active complexes and reveal a new platform that can be further developed for ASO in vivo targeting.
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Affiliation(s)
- Eman M Zaghloul
- Department of Laboratory Medicine, Karolinska Institute, Sweden.
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Trabulo S, Cardoso AL, Mano M, De Lima MCP. Cell-Penetrating Peptides-Mechanisms of Cellular Uptake and Generation of Delivery Systems. Pharmaceuticals (Basel) 2010; 3:961-993. [PMID: 27713284 PMCID: PMC4034016 DOI: 10.3390/ph3040961] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/20/2010] [Accepted: 03/29/2010] [Indexed: 01/13/2023] Open
Abstract
The successful clinical application of nucleic acid-based therapeutic strategies has been limited by the poor delivery efficiency achieved by existing vectors. The development of alternative delivery systems for improved biological activity is, therefore, mandatory. Since the seminal observations two decades ago that the Tat protein, and derived peptides, can translocate across biological membranes, cell-penetrating peptides (CPPs) have been considered one of the most promising tools to improve non-invasive cellular delivery of therapeutic molecules. Despite extensive research on the use of CPPs for this purpose, the exact mechanisms underlying their cellular uptake and that of peptide conjugates remain controversial. Over the last years, our research group has been focused on the S413-PV cell-penetrating peptide, a prototype of this class of peptides that results from the combination of 13-amino-acid cell penetrating sequence derived from the Dermaseptin S4 peptide with the SV40 large T antigen nuclear localization signal. By performing an extensive biophysical and biochemical characterization of this peptide and its analogs, we have gained important insights into the mechanisms governing the interaction of CPPs with cells and their translocation across biological membranes. More recently, we have started to explore this peptide for the intracellular delivery of nucleic acids (plasmid DNA, siRNA and oligonucleotides). In this review we discuss the current knowledge of the mechanisms responsible for the cellular uptake of cell-penetrating peptides, including the S413-PV peptide, and the potential of peptide-based formulations to mediate nucleic acid delivery.
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Affiliation(s)
- Sara Trabulo
- Center for Neuroscience and Cell Biology of Coimbra, Department of Zoology, University of Coimbra, Portugal
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Apartado 3126, 3001-401 Coimbra, Portugal
| | - Ana Luísa Cardoso
- Center for Neuroscience and Cell Biology of Coimbra, Department of Zoology, University of Coimbra, Portugal
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Apartado 3126, 3001-401 Coimbra, Portugal
| | - Miguel Mano
- Center for Neuroscience and Cell Biology of Coimbra, Department of Zoology, University of Coimbra, Portugal
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Apartado 3126, 3001-401 Coimbra, Portugal
| | - Maria C Pedroso De Lima
- Center for Neuroscience and Cell Biology of Coimbra, Department of Zoology, University of Coimbra, Portugal.
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Apartado 3126, 3001-401 Coimbra, Portugal.
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