1
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Sarli SL, Fakih HH, Kelly K, Devi G, Rembetsy-Brown J, McEachern H, Ferguson C, Echeverria D, Lee J, Sousa J, Sleiman H, Khvorova A, Watts J. Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo. Nucleic Acids Res 2024; 52:4799-4817. [PMID: 38613388 PMCID: PMC11109979 DOI: 10.1093/nar/gkae260] [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: 01/07/2024] [Revised: 03/06/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Glioblastoma multiforme is a universally lethal brain tumor that largely resists current surgical and drug interventions. Despite important advancements in understanding GBM biology, the invasiveness and heterogeneity of these tumors has made it challenging to develop effective therapies. Therapeutic oligonucleotides-antisense oligonucleotides and small-interfering RNAs-are chemically modified nucleic acids that can silence gene expression in the brain. However, activity of these oligonucleotides in brain tumors remains inadequately characterized. In this study, we developed a quantitative method to differentiate oligonucleotide-induced gene silencing in orthotopic GBM xenografts from gene silencing in normal brain tissue, and used this method to test the differential silencing activity of a chemically diverse panel of oligonucleotides. We show that oligonucleotides chemically optimized for pharmacological activity in normal brain tissue do not show consistent activity in GBM xenografts. We then survey multiple advanced oligonucleotide chemistries for their activity in GBM xenografts. Attaching lipid conjugates to oligonucleotides improves silencing in GBM cells across several different lipid classes. Highly hydrophobic lipid conjugates cholesterol and docosanoic acid enhance silencing but at the cost of higher neurotoxicity. Moderately hydrophobic, unsaturated fatty acid and amphiphilic lipid conjugates still improve activity without compromising safety. These oligonucleotide conjugates show promise for treating glioblastoma.
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Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia M Rembetsy-Brown
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Holly R McEachern
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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2
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Mallette TL, Lidke DS, Lakin MR. Heterochiral modifications enhance robustness and function of DNA in living human cells. Chembiochem 2024; 25:e202300755. [PMID: 38228506 PMCID: PMC10923132 DOI: 10.1002/cbic.202300755] [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: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
Oligonucleotide therapeutics are becoming increasingly important as more are approved by the FDA, both for treatment and vaccination. Similarly, dynamic DNA nanotechnology is a promising technique that can be used to sense exogenous input molecules or endogenous biomarkers and integrate the results of multiple sensing reactions in situ via a programmed cascade of reactions. The combination of these two technologies could be highly impactful in biomedicine by enabling smart oligonucleotide therapeutics that can autonomously sense and respond to a disease state. A particular challenge, however, is the limited lifetime of standard nucleic acid components in living cells and organisms due to degradation by endogenous nucleases. In this work, we address this challenge by incorporating mirror-image, ʟ-DNA nucleotides to produce heterochiral "gapmers". We use dynamic DNA nanotechnology to show that these modifications keep the oligonucleotide intact in living human cells for longer than an unmodified strand. To this end, we used a sequential transfection protocol for delivering multiple nucleic acids into living human cells while providing enhanced confidence that subsequent interactions are actually occurring within the cells. Taken together, this work advances the state of the art of ʟ-nucleic acid protection of oligonucleotides and DNA circuitry for applications in vivo.
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Affiliation(s)
- Tracy L Mallette
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, 87131, USA
| | - Diane S Lidke
- Department of Pathology and Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, 87131, USA
| | - Matthew R Lakin
- Department of Computer Science, Department of Chemical & Biological Engineering, Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, 87131, USA
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3
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Elkhashab M, Dilek Y, Foss M, Creemers LB, Howard KA. A Modular Albumin-Oligonucleotide Biomolecular Assembly for Delivery of Antisense Therapeutics. Mol Pharm 2024; 21:491-500. [PMID: 38214218 PMCID: PMC10848253 DOI: 10.1021/acs.molpharmaceut.3c00561] [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: 06/30/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024]
Abstract
Antisense nucleic acid drugs are susceptible to nuclease degradation, rapid renal clearance, and short circulatory half-life. In this work, we introduce a modular-based recombinant human albumin-oligonucleotide (rHA-cODN) biomolecular assembly that allows incorporation of a chemically stabilized therapeutic gapmer antisense oligonucleotide (ASO) and FcRn-driven endothelial cellular recycling. A phosphodiester ODN linker (cODN) was conjugated to recombinant human albumin (rHA) using maleimide chemistry, after which a complementary gapmer ASO, targeting ADAMTS5 involved in osteoarthritis pathogenesis, was annealed. The rHA-cODN/ASO biomolecular assembly production, fluorescence labeling, and purity were confirmed using polyacrylamide gel electrophoresis. ASO release was triggered by DNase-mediated degradation of the linker strand, reaching 40% in serum after 72 h, with complete release observed following 30 min of incubation with DNase. Cellular internalization and trafficking of the biomolecular assembly using confocal microscopy in C28/I2 cells showed higher uptake and endosomal localization by increasing incubation time from 4 to 24 h. FcRn-mediated cellular recycling of the assembly was demonstrated in FcRn-expressing human microvascular endothelial cells. ADAMTS5 in vitro silencing efficiency reached 40%, which was comparable to free gapmer after 72 h incubation with human osteoarthritis patients' chondrocytes. This work introduces a versatile biomolecular modular-based "Plug-and-Play" platform potentially applicable for albumin-mediated half-life extension for a range of different types of ODN therapeutics.
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Affiliation(s)
- Marwa Elkhashab
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Yeter Dilek
- Department
of Orthopedics, University Medical Center
Utrecht, 3584 CT Utrecht, The Netherlands
| | - Morten Foss
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Laura B. Creemers
- Department
of Orthopedics, University Medical Center
Utrecht, 3584 CT Utrecht, The Netherlands
| | - Kenneth A. Howard
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
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4
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Cimen I, Natarelli L, Abedi Kichi Z, Henderson JM, Farina FM, Briem E, Aslani M, Megens RTA, Jansen Y, Mann-Fallenbuchel E, Gencer S, Duchêne J, Nazari-Jahantigh M, van der Vorst EPC, Enard W, Döring Y, Schober A, Santovito D, Weber C. Targeting a cell-specific microRNA repressor of CXCR4 ameliorates atherosclerosis in mice. Sci Transl Med 2023; 15:eadf3357. [PMID: 37910599 DOI: 10.1126/scitranslmed.adf3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
The CXC chemokine receptor 4 (CXCR4) in endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) is crucial for vascular integrity. The atheroprotective functions of CXCR4 in vascular cells may be counteracted by atherogenic functions in other nonvascular cell types. Thus, strategies for cell-specifically augmenting CXCR4 function in vascular cells are crucial if this receptor is to be useful as a therapeutic target in treating atherosclerosis and other vascular disorders. Here, we identified miR-206-3p as a vascular-specific CXCR4 repressor and exploited a target-site blocker (CXCR4-TSB) that disrupted the interaction of miR-206-3p with CXCR4 in vitro and in vivo. In vitro, CXCR4-TSB enhanced CXCR4 expression in human and murine ECs and VSMCs to modulate cell viability, proliferation, and migration. Systemic administration of CXCR4-TSB in Apoe-deficient mice enhanced Cxcr4 expression in ECs and VSMCs in the walls of blood vessels, reduced vascular permeability and monocyte adhesion to endothelium, and attenuated the development of diet-induced atherosclerosis. CXCR4-TSB also increased CXCR4 expression in B cells, corroborating its atheroprotective role in this cell type. Analyses of human atherosclerotic plaque specimens revealed a decrease in CXCR4 and an increase in miR-206-3p expression in advanced compared with early lesions, supporting a role for the miR-206-3p-CXCR4 interaction in human disease. Disrupting the miR-206-3p-CXCR4 interaction in a cell-specific manner with target-site blockers is a potential therapeutic approach that could be used to treat atherosclerosis and other vascular diseases.
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Affiliation(s)
- Ismail Cimen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Zahra Abedi Kichi
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - James M Henderson
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Floriana M Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Eva Briem
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 85152 Planegg-Martinsried, Germany
| | - Maria Aslani
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biomedical Engineering, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6200 MD Maastricht, Netherlands
| | - Yvonne Jansen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Elizabeth Mann-Fallenbuchel
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Selin Gencer
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Johan Duchêne
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Maliheh Nazari-Jahantigh
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Emiel P C van der Vorst
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, 52074 Aachen, Germany
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52062 Aachen, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 85152 Planegg-Martinsried, Germany
| | - Yvonne Döring
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Angiology, Swiss Cardiovascular Center, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland
| | - Andreas Schober
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Institute of Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council (CNR), 20090 Milan, Italy
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6229 HX Maastricht, Netherlands
- Munich Cluster for Systems Neurology (SyNergy), 81337 Munich, Germany
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5
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Hill AC, Becker JP, Slominski D, Halloy F, Søndergaard C, Ravn J, Hall J. Peptide Conjugates of a 2'- O-Methoxyethyl Phosphorothioate Splice-Switching Oligonucleotide Show Increased Entrapment in Endosomes. ACS OMEGA 2023; 8:40463-40481. [PMID: 37929104 PMCID: PMC10620785 DOI: 10.1021/acsomega.3c05144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Antisense oligonucleotides (ASOs) are short, single-stranded nucleic acid molecules that alter gene expression. However, their transport into appropriate cellular compartments is a limiting factor in their potency. Here, we synthesized splice-switching oligonucleotides (SSOs) previously developed to treat the rare disease erythropoietic protoporphyria. Using chemical ligation-quantitative polymerase chain reaction (CL-qPCR), we quantified the SSOs in cells and subcellular compartments following free uptake. To drive nuclear localization, we covalently conjugated nuclear localization signal (NLS) peptides to a lead 2'-O-methoxyethyl phosphorothioate SSO using thiol-maleimide chemistry. The conjugates and parent SSO displayed similar RNA target-binding affinities. CL-qPCR quantification of the conjugates in cells and subcellular compartments following free uptake revealed one conjugate with better nuclear accumulation relative to the parent SSO. However, compared to the parent SSO, which altered the splicing of the target pre-mRNA, the conjugates were inactive at splice correction under free uptake conditions in vitro. Splice-switching activity could be conferred on the conjugates by delivering them into cells via cationic lipid-mediated transfection or by treating the cells into which the conjugates had been freely taken up with chloroquine, an endosome-disrupting agent. Our results identify the major barrier to the activity of the peptide-oligonucleotide conjugates as endosomal entrapment.
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Affiliation(s)
- Alyssa C. Hill
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - J. Philipp Becker
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - Daria Slominski
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - François Halloy
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | | | - Jacob Ravn
- Roche
Innovation Center Copenhagen (RICC), Hørsholm 2970, Denmark
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
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6
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Anwar S, Mir F, Yokota T. Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies. Pharmaceutics 2023; 15:pharmaceutics15041130. [PMID: 37111616 PMCID: PMC10140998 DOI: 10.3390/pharmaceutics15041130] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.
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Affiliation(s)
- Saeed Anwar
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Farin Mir
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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7
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Aartsma-Rus A, Garanto A, van Roon-Mom W, McConnell EM, Suslovitch V, Yan WX, Watts JK, Yu TW. Consensus Guidelines for the Design and In Vitro Preclinical Efficacy Testing N-of-1 Exon Skipping Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:17-25. [PMID: 36516128 PMCID: PMC9940807 DOI: 10.1089/nat.2022.0060] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Antisense oligonucleotides (ASOs) can modulate pre-mRNA splicing. This offers therapeutic opportunities for numerous genetic diseases, often in a mutation-specific and sometimes even individual-specific manner. Developing therapeutic ASOs for as few as even a single patient has been shown feasible with the development of Milasen for an individual with Batten disease. Efforts to develop individualized ASOs for patients with different genetic diseases are ongoing globally. The N = 1 Collaborative (N1C) is an umbrella organization dedicated to supporting the nascent field of individualized medicine. N1C recently organized a workshop to discuss and advance standards for the rigorous design and testing of splice-switching ASOs. In this study, we present guidelines resulting from that meeting and the key recommendations: (1) dissemination of standardized experimental designs, (2) use of standardized reference ASOs, and (3) a commitment to data sharing and exchange.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,N = 1 Collaborative
| | - Alejandro Garanto
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Pediatrics and Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willeke van Roon-Mom
- Dutch Center for RNA Therapeutics, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Victoria Suslovitch
- N = 1 Collaborative.,Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Jonathan K Watts
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Timothy W Yu
- N = 1 Collaborative.,Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Division of Genetics and Genomics, Boston, Massachusetts, USA
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8
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Pulido-Quetglas C, Johnson R. Designing libraries for pooled CRISPR functional screens of long noncoding RNAs. Mamm Genome 2022; 33:312-327. [PMID: 34533605 PMCID: PMC9114037 DOI: 10.1007/s00335-021-09918-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/09/2021] [Indexed: 02/01/2023]
Abstract
Human and other genomes encode tens of thousands of long noncoding RNAs (lncRNAs), the vast majority of which remain uncharacterised. High-throughput functional screening methods, notably those based on pooled CRISPR-Cas perturbations, promise to unlock the biological significance and biomedical potential of lncRNAs. Such screens are based on libraries of single guide RNAs (sgRNAs) whose design is critical for success. Few off-the-shelf libraries are presently available, and lncRNAs tend to have cell-type-specific expression profiles, meaning that library design remains in the hands of researchers. Here we introduce the topic of pooled CRISPR screens for lncRNAs and guide readers through the three key steps of library design: accurate annotation of transcript structures, curation of optimal candidate sets, and design of sgRNAs. This review is a starting point and reference for researchers seeking to design custom CRISPR screening libraries for lncRNAs.
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Affiliation(s)
- Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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9
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Wang Y, Luo W, Huang L, Xiao J, Song X, Li F, Ma Y, Wang X, Jin F, Liu P, Zhu Y, Kitazato K, Wang Y, Ren Z. A novel lncRNA linc-AhRA negatively regulates innate antiviral response in murine microglia upon neurotropic herpesvirus infection. Am J Cancer Res 2021; 11:9623-9651. [PMID: 34646390 PMCID: PMC8490526 DOI: 10.7150/thno.64880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Microglia are the primary cellular source of type I interferons (I-IFNs) in the brain upon neurotropic virus infection. Although the I-IFN-based antiviral innate immune response is crucial for eliminating viruses, overproduction led to immune disorders. Therefore, the relatively long-lasting I-IFNs must be precisely controlled, but the regulatory mechanism for the innate antiviral response in microglia remains largely unknown. Long non-coding RNAs (lncRNAs) are being recognized as crucial factors in numerous diseases, but their regulatory roles in the innate antiviral response in microglia are undefined. Methods: The high-throughput RNA sequencing was performed to obtain differentially expressed lncRNAs (DELs) in primary microglia infected with or without the neurotropic herpes simplex virus type 1 (HSV-1). We selected four DELs ranked in the top 15 in basic level and their fold change induced by HSV-1, i.e., FPKMHSV-1/FPKMCells.We subsequently found a key lncRNA affecting the innate antiviral response of microglia significantly. We next used dual-luciferase reporter assays, bioinformatical tools, and truncation mutants of both lncRNA and targeted proteins to elucidate the downstream and upstream mechanism of action of lncRNA. Further, we established microglia-specific knock-in (KI) mice to investigate the role of lncRNA in vivo. Results: We identified a long intergenic non-coding RNA, linc-AhRA, involved in regulating the innate antiviral response in murine microglia. linc-AhRA is activated by aryl hydrocarbon receptor (AhR) and restricts I-IFN production in microglia upon neurotropic herpesvirus infection and innate immune stimulation. Mechanistically, linc-AhRA binds to both tripartite motif-containing 27 (TRIM27) and TANK-binding kinase 1 (TBK1) through its conserved 117nt fragment as a molecular scaffold to enhance TRIM27-TBK1 interaction. This interaction facilitates the TRIM27-mediated ubiquitination of TBK1 and results in ubiquitin-proteasome-dependent degradation of TBK1. Consequently, linc-AhRA suppresses I-IFN production through facilitating TBK1 degradation and limits the microglial innate immune response against neurotropic herpesvirus infection. Microglia-specific KI of linc-AhRA mice shows a weakened antiviral immune response upon neurotropic herpesvirus challenge due to a reduction of TBK1 in microglia. Conclusion: Our findings indicate that linc-AhRA is a negative regulator of I-IFN production in microglia to avoid excessive autoimmune responses. These findings uncover a previously unappreciated role for lncRNA conserved fragments in the innate antiviral response, providing a strong foundation for developing nucleotide drugs based on conserved functional fragments within lncRNAs.
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10
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Ducoli L, Agrawal S, Hon CC, Ramilowski JA, Sibler E, Tagami M, Itoh M, Kondo N, Abugessaisa I, Hasegawa A, Kasukawa T, Suzuki H, Carninci P, Shin JW, de Hoon MJL, Detmar M. The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background. BMC Genom Data 2021; 22:33. [PMID: 34521352 PMCID: PMC8439024 DOI: 10.1186/s12863-021-00992-1] [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: 03/09/2021] [Accepted: 08/29/2021] [Indexed: 11/18/2022] Open
Abstract
Background The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism’s physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner. Results To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background. Conclusion In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00992-1.
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Affiliation(s)
- Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Eliane Sibler
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan.,Human Technopole, Via Cristina Belgioioso 171, 20157, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
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11
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Fernández-Garibay X, Ortega MA, Cerro-Herreros E, Comelles J, Martínez E, Artero R, Fernández-Costa JM, Ramón-Azcón J. Bioengineered in vitro3D model of myotonic dystrophy type 1 human skeletal muscle. Biofabrication 2021; 13. [PMID: 33836519 DOI: 10.1088/1758-5090/abf6ae] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/09/2021] [Indexed: 02/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is the most common hereditary myopathy in the adult population. The disease is characterized by progressive skeletal muscle degeneration that produces severe disability. At present, there is still no effective treatment for DM1 patients, but the breakthroughs in understanding the molecular pathogenic mechanisms in DM1 have allowed the testing of new therapeutic strategies. Animal models andin vitrotwo-dimensional cell cultures have been essential for these advances. However, serious concerns exist regarding how faithfully these models reproduce the biological complexity of the disease. Biofabrication tools can be applied to engineer human three-dimensional (3D) culture systems that complement current preclinical research models. Here, we describe the development of the firstin vitro3D model of DM1 human skeletal muscle. Transdifferentiated myoblasts from patient-derived fibroblasts were encapsulated in micromolded gelatin methacryloyl-carboxymethyl cellulose methacrylate hydrogels through photomold patterning on functionalized glass coverslips. These hydrogels present a microstructured topography that promotes myoblasts alignment and differentiation resulting in highly aligned myotubes from both healthy and DM1 cells in a long-lasting cell culture. The DM1 3D microtissues recapitulate the molecular alterations detected in patient biopsies. Importantly, fusion index analyses demonstrate that 3D micropatterning significantly improved DM1 cell differentiation into multinucleated myotubes compared to standard cell cultures. Moreover, the characterization of the 3D cultures of DM1 myotubes detects phenotypes as the reduced thickness of myotubes that can be used for drug testing. Finally, we evaluated the therapeutic effect of antagomiR-23b administration on bioengineered DM1 skeletal muscle microtissues. AntagomiR-23b treatment rescues both molecular DM1 hallmarks and structural phenotype, restoring myotube diameter to healthy control sizes. Overall, these new microtissues represent an improvement over conventional cell culture models and can be used as biomimetic platforms to establish preclinical studies for myotonic dystrophy.
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Affiliation(s)
- Xiomara Fernández-Garibay
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - María A Ortega
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - Estefanía Cerro-Herreros
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Translational Genomics Group, Incliva Health Research Institute, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Joint Unit Incliva- CIPF, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
| | - Jordi Comelles
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain.,Department of Electronics and Biomedical Engineering, University of Barcelona (UB), c/Martí i Franquès 1-11, E08028 Barcelona, Spain
| | - Elena Martínez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain.,Department of Electronics and Biomedical Engineering, University of Barcelona (UB), c/Martí i Franquès 1-11, E08028 Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER), Av. Monforte de Lemos 3-5, Pabellón 11, Planta 0, E28029 Madrid, Spain
| | - Rubén Artero
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Translational Genomics Group, Incliva Health Research Institute, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Joint Unit Incliva- CIPF, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
| | - Juan M Fernández-Costa
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - Javier Ramón-Azcón
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain.,Institució Catalana de Reserca I Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, E08010 Barcelona, Spain
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12
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Garcia A, Dunoyer-Geindre S, Fish RJ, Neerman-Arbez M, Reny JL, Fontana P. Methods to Investigate miRNA Function: Focus on Platelet Reactivity. Thromb Haemost 2021; 121:409-421. [PMID: 33124028 PMCID: PMC8263142 DOI: 10.1055/s-0040-1718730] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs modulating protein production. They are key players in regulation of cell function and are considered as biomarkers in several diseases. The identification of the proteins they regulate, and their impact on cell physiology, may delineate their role as diagnostic or prognostic markers and identify new therapeutic strategies. During the last 3 decades, development of a large panel of techniques has given rise to multiple models dedicated to the study of miRNAs. Since plasma samples are easily accessible, circulating miRNAs can be studied in clinical trials. To quantify miRNAs in numerous plasma samples, the choice of extraction and purification techniques, as well as normalization procedures, are important for comparisons of miRNA levels in populations and over time. Recent advances in bioinformatics provide tools to identify putative miRNAs targets that can then be validated with dedicated assays. In vitro and in vivo approaches aim to functionally validate candidate miRNAs from correlations and to understand their impact on cellular processes. This review describes the advantages and pitfalls of the available techniques for translational research to study miRNAs with a focus on their role in regulating platelet reactivity.
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Affiliation(s)
- Alix Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Richard J. Fish
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics in Geneva, Geneva, Switzerland
| | - Jean-Luc Reny
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of General Internal Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Pierre Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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13
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Albumin-Binding Fatty Acid-Modified Gapmer Antisense Oligonucleotides for Modulation of Pharmacokinetics. Methods Mol Biol 2021; 2176:163-174. [PMID: 32865790 DOI: 10.1007/978-1-0716-0771-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Prolonged circulation and modulation of the pharmacokinetic profile are important to improve the clinical potential of antisense oligonucleotides (ASOs). Gapmer ASOs demonstrate excellent nuclease stability and robust gene silencing activity without the requirement of transfection agents. A major challenge for in vivo applications, however, is the short blood circulatory half-life. This work describes utilization of the long circulation of serum albumin to increase the blood residence time of gapmer ASOs. The method introduces fatty acid modifications into the gapmer ASOs design to exploit the binding and transport property of serum albumin for endogenous ligands. The level of albumin-gapmer ASOs interaction, blood circulatory half-life and biodistribution was dependent on number, position, and fatty acid type (palmitic or myristic acid) within the gapmer ASO sequence and either phosphorothioate or phosphodiester backbone modifications. This work offers a strategy to optimize gapmer ASO pharmacokinetics by a proposed endogenous assembly process with serum albumin that can be tuned by gapmer ASO design modifications.
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14
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Ghidini A, Cléry A, Halloy F, Allain FHT, Hall J. RNA‐PROTACs: Degraders of RNA‐Binding Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alice Ghidini
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Antoine Cléry
- Department of Biology ETH Zurich Hönggerbergring 64 8093 Zurich Switzerland
| | - François Halloy
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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15
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Ghidini A, Cléry A, Halloy F, Allain FHT, Hall J. RNA-PROTACs: Degraders of RNA-Binding Proteins. Angew Chem Int Ed Engl 2021; 60:3163-3169. [PMID: 33108679 PMCID: PMC7898822 DOI: 10.1002/anie.202012330] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Indexed: 12/19/2022]
Abstract
Defects in the functions of RNA binding proteins (RBPs) are at the origin of many diseases; however, targeting RBPs with conventional drugs has proven difficult. PROTACs are a new class of drugs that mediate selective degradation of a target protein through a cell's ubiquitination machinery. PROTACs comprise a moiety that binds the selected protein, conjugated to a ligand of an E3 ligase. Herein, we introduce RNA-PROTACs as a new concept in the targeting of RBPs. These chimeric structures employ small RNA mimics as targeting groups that dock the RNA-binding site of the RBP, whereupon a conjugated E3-recruiting peptide derived from the HIF-1α protein directs the RBP for proteasomal degradation. We performed a proof-of-concept demonstration with the degradation of two RBPs-a stem cell factor LIN28 and a splicing factor RBFOX1-and showed their use in cancer cell lines. The RNA-PROTAC approach opens the way to rapid, selective targeting of RBPs in a rational and general fashion.
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Affiliation(s)
- Alice Ghidini
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Antoine Cléry
- Department of BiologyETH ZurichHönggerbergring 648093ZurichSwitzerland
| | - François Halloy
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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16
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Deprey K, Batistatou N, Kritzer JA. A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics. Nucleic Acids Res 2020; 48:7623-7639. [PMID: 32644123 PMCID: PMC7430645 DOI: 10.1093/nar/gkaa576] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
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17
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Lazar S, Wurtzel JGT, Chen X, Ma P, Goldfinger LE. High-efficiency unassisted transfection of platelets with naked double-stranded miRNAs modulates signal-activated translation and platelet function. Platelets 2020; 32:794-806. [PMID: 32838617 DOI: 10.1080/09537104.2020.1809642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We sought novel approaches to improve transfection efficiencies of microRNAs (miRNAs) in platelets, and to apply these approaches to investigate the roles of miRNAs in regulating signal-activated protein translation and functional effects. We found that ex vivo human platelets support gymnosis---internalization of ectopic miRNAs following co-incubation in the absence of conventional transfection reagents or schemes---and subsequently incorporate transfected miRNA into ARGONAUTE2 (AGO2)-based RNA-induced silencing complexes (RISC). Thrombin/fibrinogen stimulation activated translation of miR-223-3p target SEPTIN2, which was suppressed by miR-223-3p transfection in an AGO2/RISC-dependent manner. Thrombin/fibrinogen-induced exosome and microvesicle generation was inhibited by miR-223-3p transfection, and this effect was reversed with a RISC inhibitor. Platelet gymnosis of naked miRNAs appeared to be mediated in part by endocytic pathways including clathrin-dependent and fluid-phase endocytosis and caveolae. These results demonstrate the ability of ex vivo platelets to internalize ectopic miRNAs by unassisted transfection, and utilize them to modulate signal-activated translation and platelet function. Our results identify new roles for miR-223-3p in extracellular vesicle generation in stimulated platelets. High-efficiency gymnotic transfection of miRNAs in ex vivo platelets may be a broadly useful tool for exploring molecular genetic regulation of platelet function.
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Affiliation(s)
- Sophia Lazar
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jeremy G T Wurtzel
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Xi Chen
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Peisong Ma
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Lawrence E Goldfinger
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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18
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Aguti S, Bolduc V, Ala P, Turmaine M, Bönnemann CG, Muntoni F, Zhou H. Exon-Skipping Oligonucleotides Restore Functional Collagen VI by Correcting a Common COL6A1 Mutation in Ullrich CMD. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:205-216. [PMID: 32585628 PMCID: PMC7321786 DOI: 10.1016/j.omtn.2020.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 11/19/2022]
Abstract
Collagen VI-related congenital muscular dystrophies (COL6-CMDs) are the second most common form of congenital muscular dystrophy. Currently, there is no effective treatment available. COL6-CMDs are caused by recessive or dominant mutations in one of the three genes encoding for the α chains of collagen type VI (COL6A1, COL6A2, and COL6A3). One of the most common mutations in COL6-CMD patients is a de novo deep intronic c.930+189C > T mutation in COL6A1 gene. This mutation creates a cryptic donor splice site and induces incorporation of a novel in-frame pseudo-exon in the mature transcripts. In this study, we systematically evaluated the splice switching approach using antisense oligonucleotides (ASOs) to correct this mutation. Fifteen ASOs were designed using the RNA-tiling approach to target the misspliced pseudo-exon and its flanking sequences. The efficiency of ASOs was evaluated at RNA, protein, and structural levels in skin fibroblasts established from four patients carrying the c.930+189C > T mutation. We identified two additional lead ASO candidates that efficiently induce pseudo-exon exclusion from the mature transcripts, thus allowing for the restoration of a functional collagen VI microfibrillar matrix. Our findings provide further evidence for ASO exon skipping as a therapeutic approach for COL6-CMD patients carrying this common intronic mutation.
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Affiliation(s)
- Sara Aguti
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neurosciences Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Véronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Pierpaolo Ala
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neurosciences Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Mark Turmaine
- Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neurosciences Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.
| | - Haiyan Zhou
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK; Genetics and Genomic Medicine Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.
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19
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Abewe H, Deshmukh S, Mukim A, Beliakova-Bethell N. Use of GapmeRs for gene expression knockdowns in human primary resting CD4+ T cells. J Immunol Methods 2020; 476:112674. [PMID: 31629740 PMCID: PMC6939142 DOI: 10.1016/j.jim.2019.112674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022]
Abstract
Human primary resting CD4+ T cells are difficult to transfect while preserving viability. The present study evaluated gymnotic delivery and RNase H1-dependent gene expression knockdown mediated by antisense oligonucleotides, called GapmeRs. Exposure of primary resting CD4+ T cells to GapmeRs did not cause cell activation or affect cell viability. Gene expression knockdowns were stable at least up to 48 h after removal of GapmeRs from culture. Exposure to GapmeRs resulted in comparable levels of degradation along the entire transcript, which could be important when studying function of regulatory long non-coding RNAs. Efficiency of transcript degradation was not solely dependent on the dose of GapmeR, RNA target and its localization. When using GapmeRs, some optimization is required, and all targets have to be individually tested; however, using GapmeRs is advantageous in experiments where preservation of the resting state of the human primary CD4+ T cells and targeting nuclear RNAs are desired. In certain cases, combining GapmeR with siRNA for the same target may improve knockdown efficiency.
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Affiliation(s)
- Hosiana Abewe
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; University of California San Diego, La Jolla, CA 92093, USA
| | - Savitha Deshmukh
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA
| | - Amey Mukim
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA
| | - Nadejda Beliakova-Bethell
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; University of California San Diego, La Jolla, CA 92093, USA.
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20
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Crespo D, Assis LHC, van de Kant HJG, de Waard S, Safian D, Lemos MS, Bogerd J, Schulz RW. Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: follicle-stimulating hormone, retinoic acid and androgens. Development 2019; 146:dev.178665. [PMID: 31597660 DOI: 10.1242/dev.178665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/01/2019] [Indexed: 01/07/2023]
Abstract
Retinoic acid (RA) is crucial for mammalian spermatogonia differentiation, and stimulates Stra8 expression, a gene required for meiosis. Certain fish species, including zebrafish, have lost the stra8 gene. While RA still seems important for spermatogenesis in fish, it is not known which stage(s) respond to RA or whether its effects are integrated into the endocrine regulation of spermatogenesis. In zebrafish, RA promoted spermatogonia differentiation, supported androgen-stimulated meiosis, and reduced spermatocyte and spermatid apoptosis. Follicle-stimulating hormone (Fsh) stimulated RA production. Expressing a dominant-negative RA receptor variant in germ cells clearly disturbed spermatogenesis but meiosis and spermiogenesis still took place, although sperm quality was low in 6-month-old adults. This condition also activated Leydig cells. Three months later, spermatogenesis apparently had recovered, but doubling of testis weight demonstrated hypertrophy, apoptosis/DNA damage among spermatids was high and sperm quality remained low. We conclude that RA signaling is important for zebrafish spermatogenesis but is not of crucial relevance. As Fsh stimulates androgen and RA production, germ cell-mediated, RA-dependent reduction of Leydig cell activity may form a hitherto unknown intratesticular negative-feedback loop.
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Affiliation(s)
- Diego Crespo
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Luiz H C Assis
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Henk J G van de Kant
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Sjors de Waard
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Diego Safian
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Moline S Lemos
- Laboratory of Cellular Biology, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Jan Bogerd
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Rüdiger W Schulz
- Reproductive Biology Group, Division Developmental Biology, Department Biology, Science Faculty, Utrecht University, Utrecht 3584 CH, The Netherlands .,Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen NO-5817, Norway
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21
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Buntz A, Killian T, Schmid D, Seul H, Brinkmann U, Ravn J, Lindholm M, Knoetgen H, Haucke V, Mundigl O. Quantitative fluorescence imaging determines the absolute number of locked nucleic acid oligonucleotides needed for suppression of target gene expression. Nucleic Acids Res 2019; 47:953-969. [PMID: 30462278 PMCID: PMC6344898 DOI: 10.1093/nar/gky1158] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022] Open
Abstract
Locked nucleic acid based antisense oligonucleotides (LNA-ASOs) can reach their intracellular RNA targets without delivery modules. Functional cellular uptake involves vesicular accumulation followed by translocation to the cytosol and nucleus. However, it is yet unknown how many LNA-ASO molecules need to be delivered to achieve target knock down. Here we show by quantitative fluorescence imaging combined with LNA-ASO microinjection into the cytosol or unassisted uptake that ∼105 molecules produce >50% knock down of their targets, indicating that a substantial amount of LNA-ASO escapes from endosomes. Microinjected LNA-ASOs redistributed within minutes from the cytosol to the nucleus and remained bound to nuclear components. Together with the fact that RNA levels for a given target are several orders of magnitude lower than the amounts of LNA-ASO, our data indicate that only a minor fraction is available for RNase H1 mediated reduction of target RNA. When non-specific binding sites were blocked by co-administration of non-related LNA-ASOs, the amount of target LNA-ASO required was reduced by an order of magnitude. Therefore, dynamic processes within the nucleus appear to influence the distribution and activity of LNA-ASOs and may represent important parameters for improving their efficacy and potency.
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Affiliation(s)
- Annette Buntz
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Tobias Killian
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Daniela Schmid
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Heike Seul
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Ulrich Brinkmann
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Jacob Ravn
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Marie Lindholm
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Hendrik Knoetgen
- Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Volker Haucke
- Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin 13125, Germany
| | - Olaf Mundigl
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
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22
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Zhang X, Castanotto D, Liu X, Shemi A, Stein CA. Ammonium and arsenic trioxide are potent facilitators of oligonucleotide function when delivered by gymnosis. Nucleic Acids Res 2019. [PMID: 29522198 DOI: 10.1093/nar/gky150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Oligonucleotide (ON) concentrations employed for therapeutic applications vary widely, but in general are high enough to raise significant concerns for off target effects and cellular toxicity. However, lowering ON concentrations reduces the chances of a therapeutic response, since typically relatively small amounts of ON are taken up by targeted cells in tissue culture. It is therefore imperative to identify new strategies to improve the concentration dependence of ON function. In this work, we have identified ammonium ion (NH4+) as a non-toxic potent enhancer of ON activity in the nucleus and cytoplasm following delivery by gymnosis. NH4+ is a metabolite that has been extensively employed as diuretic, expectorant, for the treatment of renal calculi and in a variety of other diseases. Enhancement of function can be found in attached and suspension cells, including in difficult-to-transfect Jurkat T and CEM T cells. We have also demonstrated that NH4+ can synergistically interact with arsenic trioxide (arsenite) to further promote ON function without producing any apparent increased cellular toxicity. These small, inexpensive, widely distributed molecules could be useful not only in laboratory experiments but potentially in therapeutic ON-based combinatorial strategy for clinical applications.
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Affiliation(s)
- Xiaowei Zhang
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Daniela Castanotto
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Xueli Liu
- Department of Information Science, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Amotz Shemi
- Silenseed, 2 HaMa'ayan Street, Modi'in Technology Park, Modi'in 7177871, Israel
| | - Cy A Stein
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
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23
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Takahashi M, Li H, Zhou J, Chomchan P, Aishwarya V, Damha MJ, Rossi JJ. Dual Mechanisms of Action of Self-Delivering, Anti-HIV-1 FANA Oligonucleotides as a Potential New Approach to HIV Therapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:615-625. [PMID: 31394430 PMCID: PMC6695270 DOI: 10.1016/j.omtn.2019.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/27/2022]
Abstract
Currently, the most effective and durable therapeutic option for HIV-1 infection is combination antiretroviral therapy (cART). Although cART is powerful and can delay viral evolution of drug resistance for decades, it is associated with limitations, including an inability to eradicate the virus and a potential for adverse effects. Therefore, it is imperative to discover new HIV therapeutic modalities. In this study, we designed, characterized, and evaluated the in vitro potency of 2′-deoxy-2′-fluoroarabinonucleotide (FANA) modified antisense oligonucleotides (ASOs) targeting highly conserved regions in the HIV-1 genome. Carrier-free cellular internalization of FANA ASOs resulted in strong suppression of HIV-1 replication in HIV-1-infected human primary cells. In vitro mechanistic studies suggested that the inhibitory effect of FANA ASOs can be attributed to RNase H1 activation and steric hindrance of dimerization. Using 5′-RACE PCR and sequencing analysis, we confirmed the presence of human RNase H1-mediated target RNA cleavage products in cells treated with FANA ASOs. We observed no overt cytotoxicity or immune responses upon FANA ASO treatment. Together, our results strongly suggest that FANA ASOs hold great promise for antiretroviral therapy. The dual ability of FANA ASOs to target RNA by recruiting RNase H1 and/or sterically blocking RNA dimerization further enhances their therapeutic potential.
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Affiliation(s)
- Mayumi Takahashi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Haitang Li
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Pritsana Chomchan
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | | | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA; Irell and Manella Graduate School of Biological Science, Beckman Institute of City of Hope, Duarte, CA 91010, USA.
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24
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Tsoumpra MK, Fukumoto S, Matsumoto T, Takeda S, Wood MJA, Aoki Y. Peptide-conjugate antisense based splice-correction for Duchenne muscular dystrophy and other neuromuscular diseases. EBioMedicine 2019; 45:630-645. [PMID: 31257147 PMCID: PMC6642283 DOI: 10.1016/j.ebiom.2019.06.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/31/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked disorder characterized by progressive muscle degeneration, caused by the absence of dystrophin. Exon skipping by antisense oligonucleotides (ASOs) has recently gained recognition as therapeutic approach in DMD. Conjugation of a peptide to the phosphorodiamidate morpholino backbone (PMO) of ASOs generated the peptide-conjugated PMOs (PPMOs) that exhibit a dramatically improved pharmacokinetic profile. When tested in animal models, PPMOs demonstrate effective exon skipping in target muscles and prolonged duration of dystrophin restoration after a treatment regime. Herein we summarize the main pathophysiological features of DMD and the emergence of PPMOs as promising exon skipping agents aiming to rescue defective gene expression in DMD and other neuromuscular diseases. The listed PPMO laboratory findings correspond to latest trends in the field and highlight the obstacles that must be overcome prior to translating the animal-based research into clinical trials tailored to the needs of patients suffering from neuromuscular diseases.
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Key Words
- aso, antisense oligonucleotides
- cns, central nervous system
- cpp, cell penetrating peptide
- dgc, dystrophin glyco-protein complex
- dmd, duchenne muscular dystrophy
- fda, us food and drug administration
- pmo, phosphorodiamidate morpholino
- ppmo, peptide-conjugated pmos
- ps, phosphorothioate
- sma, spinal muscular atrophy
- 2ʹ-ome, 2ʹ-o-methyl
- 2ʹ-moe, 2ʹ-o-methoxyethyl
- 6mwt, 6-minute walk test
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Affiliation(s)
- Maria K Tsoumpra
- Department of Molecular Therapy, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, Kodaira-shi, Tokyo, Japan
| | - Seiji Fukumoto
- Fujii Memorial Institute of Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Toshio Matsumoto
- Fujii Memorial Institute of Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, Kodaira-shi, Tokyo, Japan
| | | | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, Kodaira-shi, Tokyo, Japan.
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25
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Soler-Bistué A, Zorreguieta A, Tolmasky ME. Bridged Nucleic Acids Reloaded. Molecules 2019; 24:E2297. [PMID: 31234313 PMCID: PMC6630285 DOI: 10.3390/molecules24122297] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, has led to the design of nucleotide analogs that, when part of these oligomers, enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs is the first-generation bridged nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second-generation BNA, BNANC (2'-O,4'-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but, in some cases, also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds have been researched, the promising results warrant more effort in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future, offering great hope to oligonucleotide-based fields of research and applications.
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Affiliation(s)
- Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús, CONICET, Universidad Nacional de San Martín, San Martín 1650, Argentina.
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires C1405BWE, Argentina.
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA.
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26
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Pfund E, Dupouy C, Rouanet S, Legay R, Lebargy C, Vasseur JJ, Lequeux T. Difluorophosphonylated Allylic Ether Moiety as a 2′-Modification of RNA-Type Molecules: Synthesis, Thermal, and Metabolic Studies. Org Lett 2019; 21:4803-4807. [DOI: 10.1021/acs.orglett.9b01689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuel Pfund
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
| | - Christelle Dupouy
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, 34060 Montpellier, France
| | - Sonia Rouanet
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, 34060 Montpellier, France
| | - Rémi Legay
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
| | - Cyril Lebargy
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, 34060 Montpellier, France
| | - Thierry Lequeux
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique, UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, 14050 Caen, France
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27
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Garcia JP, Stein J, Cai Y, Riemers F, Wexselblatt E, Wengel J, Tryfonidou M, Yayon A, Howard KA, Creemers LB. Fibrin-hyaluronic acid hydrogel-based delivery of antisense oligonucleotides for ADAMTS5 inhibition in co-delivered and resident joint cells in osteoarthritis. J Control Release 2018; 294:247-258. [PMID: 30572032 DOI: 10.1016/j.jconrel.2018.12.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 02/06/2023]
Abstract
To date no disease-modifying drugs for osteoarthritis (OA) are available, with treatment limited to the use of pain killers and prosthetic replacement. The ADAMTS (A Disintegrin and Metallo Proteinase with Thrombospondin Motifs) enzyme family is thought to be instrumental in the loss of proteoglycans during cartilage degeneration in OA, and their inhibition was shown to reverse osteoarthritic cartilage degeneration. Locked Nucleic Acid (LNA)-modified antisense oligonucleotides (gapmers) released from biomaterial scaffolds for specific and prolonged ADAMTS inhibition in co-delivered and resident chondrocytes, is an attractive therapeutic strategy. Here, a gapmer sequence identified from a gapmer screen showed 90% ADAMTS5 silencing in a monolayer culture of human OA chondrocytes. Incorporation of the gapmer in a fibrin-hyaluronic acid hydrogel exhibited a sustained release profile up to 14 days. Gapmers loaded in hydrogels were able to transfect both co-embedded chondrocytes and chondrocytes in a neighboring gapmer-free hydrogel, as demonstrated by flow cytometry and confocal microscopy. Efficient knockdown of ADAMTS5 was shown up to 14 days in both cell populations, i.e. the gapmer-loaded and gapmer-free hydrogel. This work demonstrates the use applicability of a hydrogel as a platform for combined local delivery of chondrocytes and an ADAMTS-targeting gapmer for catabolic gene modulation in OA.
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Affiliation(s)
- João Pedro Garcia
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Jeroen Stein
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Yunpeng Cai
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Frank Riemers
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Jesper Wengel
- Nucleic Acid Center, University of Southern Denmark, Denmark
| | - Marianna Tryfonidou
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Laura B Creemers
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands.
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28
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Järver P, Dondalska A, Poux C, Sandberg A, Bergenstråhle J, Sköld AE, Dereuddre-Bosquet N, Martinon F, Pålsson S, Zaghloul E, Brodin D, Sander B, Lennox KA, Behlke MA, El-Andaloussi S, Lehtiö J, Lundeberg J, LeGrand R, Spetz AL. Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis. Sci Rep 2018; 8:15841. [PMID: 30367171 PMCID: PMC6203749 DOI: 10.1038/s41598-018-33960-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/26/2018] [Indexed: 12/19/2022] Open
Abstract
Recognition of nucleic acids by endosomal Toll-like receptors (TLR) is essential to combat pathogens, but requires strict control to limit inflammatory responses. The mechanisms governing this tight regulation are unclear. We found that single-stranded oligonucleotides (ssON) inhibit endocytic pathways used by cargo destined for TLR3/4/7 signaling endosomes. Both ssDNA and ssRNA conferred the endocytic inhibition, it was concentration dependent, and required a certain ssON length. The ssON-mediated inhibition modulated signaling downstream of TLRs that localized within the affected endosomal pathway. We further show that injection of ssON dampens dsRNA-mediated inflammatory responses in the skin of non-human primates. These studies reveal a regulatory role for extracellular ssON in the endocytic uptake of TLR ligands and provide a mechanistic explanation of their immunomodulation. The identified ssON-mediated interference of endocytosis (SOMIE) is a regulatory process that temporarily dampens TLR3/4/7 signaling, thereby averting excessive immune responses.
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Affiliation(s)
- Peter Järver
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden.
| | - Aleksandra Dondalska
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Candice Poux
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - AnnSofi Sandberg
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Joseph Bergenstråhle
- Department of Gene Technology, Science for Life Laboratory, Royal Institute of Technology, 171 65, Solna, Sweden
| | - Annette E Sköld
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Nathalie Dereuddre-Bosquet
- CEA, -Université Paris Sud-Inserm U1184, IDMIT Department, Institut de Biologie Francois Jacob (IBFJ), 922 60, Fontenay-aux-Roses, France
| | - Fréderic Martinon
- CEA, -Université Paris Sud-Inserm U1184, IDMIT Department, Institut de Biologie Francois Jacob (IBFJ), 922 60, Fontenay-aux-Roses, France
| | - Sandra Pålsson
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Eman Zaghloul
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
| | - David Brodin
- Bioinformatics and Expression Analysis core facility, Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Stockholm, Sweden
| | - Birgitta Sander
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
| | - Kim A Lennox
- Integrated DNA Technologies Inc, Coralville, 52241, Iowa, USA
| | - Mark A Behlke
- Integrated DNA Technologies Inc, Coralville, 52241, Iowa, USA
| | - Samir El-Andaloussi
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden.,Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3PT, Oxford, UK
| | - Janne Lehtiö
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Joakim Lundeberg
- Department of Gene Technology, Science for Life Laboratory, Royal Institute of Technology, 171 65, Solna, Sweden
| | - Roger LeGrand
- CEA, -Université Paris Sud-Inserm U1184, IDMIT Department, Institut de Biologie Francois Jacob (IBFJ), 922 60, Fontenay-aux-Roses, France
| | - Anna-Lena Spetz
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden.
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29
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Cai Y, Makarova AM, Wengel J, Howard KA. Palmitoylated phosphodiester gapmer designs with albumin binding capacity and maintained in vitro gene silencing activity. J Gene Med 2018; 20:e3025. [PMID: 29800498 DOI: 10.1002/jgm.3025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Antisense gapmer oligonucleotide drugs require delivery and biodistribution enabling technologies to increase in vivo efficacy. An attractive approach is their binding and consequent transport by the endogenous human serum albumin pool as mediated by fatty acid incorporation into the gapmer design. METHODS The present study investigated the effect of palmitoyl modification and position on albumin-binding, cellular uptake and in vitro gene silencing of gapmers with either a phosphorothioate (PS) or phosphodiester (PO) backbone. RESULTS Two palmitoyls positioned exclusively at the 5' end, or a single palmitoyl at both the 3' and 5' positions, showed similar binding to human serum albumin as demonstrated by a gel-shift assay. Decreased cellular uptake determined by flow cytometry (27% compared to nonpalmitoyl gapmers) was observed for palmitoylated Cy5.5 labelled gapmers. However, HER3 (human epidermal growth factor receptor 3) gene silencing was exhibited by the palmitoylated gapmers with transfection agent in PC-3 and Caco-2 cells (68% and 62%, respectively), which was comparable to nonpalmitoyl gapmers (68% and 82%, respectively). Importantly, PO gapmers with a single palmitoyl positioned at both the 3' and 5' positions showed high silencing efficiencies (68% and 66% in PC-3 and Caco-2 cells, respectively) similar to those of PS nonpalmitoylated gapmers (67% and 66% in PC-3 and Caco-2 cells, respectively) in the absence of a transfection agent. CONCLUSIONS The present study defines phosphodiester gapmer design criteria exhibiting high gene silencing activity and albumin binding that may be utilized with potentially less in vivo toxicity that can be associated with phosphorothioate gapmer designs.
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Affiliation(s)
- Yunpeng Cai
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Kenneth A Howard
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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30
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Zhu L, Bi J, Zheng L, Zhao Q, Shu X, Guo G, Liu J, Yang G, Liu J, Yin G. In vitro inhibition of porcine reproductive and respiratory syndrome virus replication by short antisense oligonucleotides with locked nucleic acid modification. BMC Vet Res 2018; 14:109. [PMID: 29580234 PMCID: PMC5870238 DOI: 10.1186/s12917-018-1432-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 03/15/2018] [Indexed: 12/14/2022] Open
Abstract
Background Porcine reproductive and respiratory syndrome virus (PRRSV) causes porcine reproductive and respiratory syndrome (PRRS), which is currently insufficiently controlled. From a previous small-scale screen we identified an effective DNA-based short antisense oligonucleotide (AS-ON) targeting viral NSP9, which could inhibit PRRSV replication in both Marc-145 cells and pulmonary alveolar macrophages (PAMs). The objective of this study was to explore the strategy of incorporating locked nucleic acids (LNAs) to achieve better inhibition of PRRSV replication in vitro. Methods The effective DNA-based AS-ON (YN8) was modified with LNAs at both ends as gap-mer (LNA-YN8-A) or as mix-mer (LNA-YN8-B). Marc-145 cells or PAMs were infected with PRRSV and subsequently transfected. Results Compared with the DNA-based YN8 control, the two AS-ONs modified with LNAs were found to be significantly more effective in decreasing the cytopathic effect (CPE) induced by PRRSV and thus in maintaining cell viability. LNA modifications conferred longer lifetimes to the AS-ON in the cell culture model. Viral ORF7 levels were more significantly reduced at both RNA and protein levels as shown by quantitative PCR, western blot and indirect immunofluorescence staining. Moreover, transfection with LNA modified AS-ON reduced the PRRSV titer by 10-fold compared with the YN8 control. Conclusion Taken together, incorporation of LNA into AS-ON technology holds higher therapeutic promise for PRRS control.
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Affiliation(s)
- Lingyun Zhu
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China
| | - Junlong Bi
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China.,Present address: Center for Animal Disease Control and Prevention, City, 675000, Yunnan province, Chuxiong, China
| | - Longlong Zheng
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China.,Present address: College of Animal Science and Technology, Shanxi Agricultural University, Shanxi province, Taigu, 030801, China
| | - Qian Zhao
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China
| | - Xianghua Shu
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China
| | - Gang Guo
- Haikou Experimental Station/Hainan Key Laboratory of Banana Genetic Improvement, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, Hainan, People's Republic of China
| | - Jia Liu
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China
| | - Guishu Yang
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China
| | - Jianping Liu
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, -17177, Stockholm, SE, Sweden.
| | - Gefen Yin
- Department of Veterinary Medicine, College of Animal Science and Technology, Yunnan Agricultural University, Yunnan province, Kunming, 650201, China.
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Uemura Y, Hagiwara K, Kobayashi K. The intratracheal administration of locked nucleic acid containing antisense oligonucleotides induced gene silencing and an immune-stimulatory effect in the murine lung. PLoS One 2017; 12:e0187286. [PMID: 29107995 PMCID: PMC5673232 DOI: 10.1371/journal.pone.0187286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Locked nucleic acid containing antisense oligonucleotides (LNA-ASOs) have the potential to modulate the disease-related gene expression by the RNaseH-dependent degradation of mRNAs. Pulmonary drug delivery has been widely used for the treatment of lung disease. Thus, the inhalation of LNA-ASOs is expected to be an efficient therapy that can be applied to several types of lung disease. Because the lung has a distinct immune system against pathogens, the immune-stimulatory effect of LNA-ASOs should be considered for the development of novel inhaled LNA-ASOs therapies. However, there have been no reports on the relationship between knock-down (KD) and the immune-stimulatory effects of inhaled LNA-ASOs in the lung. In this report, LNA-ASOs targeting Scarb1 (Scarb1-ASOs) or negative control LNA-ASOs targeting ApoB (ApoB-ASOs) were intratracheally administered to mice to investigate the KD of the gene expression and the immune-stimulatory effects in the lung. We confirmed that the intratracheal administration of Scarb1-ASOs exerted a KD effect in the lung without a drug delivery system. On the other hand, both Scarb1-ASOs and ApoB-ASOs induced neutrophilic infiltration in the alveoli and increased the expression levels of G-CSF and CXCL1 in the lung. The dose required for KD was the same as the dose that induced the neutrophilic immune response. In addition, in our in vitro experiments, Scarb1-ASOs did not increase the G-CSF or CXCL1 expression in primary lung cells, even though Scarb1-ASOs exerted a strong KD effect. Hence, we hypothesize that inhaled LNA-ASOs have the potential to exert a KD effect in the lung, but that they may be associated with a risk of immune stimulation. Further studies about the mechanism underlying the immune-stimulatory effect of LNA-ASOs is necessary for the development of novel inhaled LNA-ASO therapies.
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Affiliation(s)
- Yasunori Uemura
- Immunology & Allergy R&D Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., Nagaizumi-cho, Shizuoka, Japan
- * E-mail:
| | - Kenji Hagiwara
- Innovative Technology Labs, Research Functions Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., Machida, Tokyo, Japan
| | - Katsuya Kobayashi
- Immunology & Allergy R&D Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., Nagaizumi-cho, Shizuoka, Japan
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Zaghloul EM, Gissberg O, Moreno PMD, Siggens L, Hällbrink M, Jørgensen AS, Ekwall K, Zain R, Wengel J, Lundin KE, Smith CIE. CTG repeat-targeting oligonucleotides for down-regulating Huntingtin expression. Nucleic Acids Res 2017; 45:5153-5169. [PMID: 28334749 PMCID: PMC5435994 DOI: 10.1093/nar/gkx111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
Huntington's disease (HD) is a fatal, neurodegenerative disorder in which patients suffer from mobility, psychological and cognitive impairments. Existing therapeutics are only symptomatic and do not significantly alter the disease progression or increase life expectancy. HD is caused by expansion of the CAG trinucleotide repeat region in exon 1 of the Huntingtin gene (HTT), leading to the formation of mutant HTT transcripts (muHTT). The toxic gain-of-function of muHTT protein is a major cause of the disease. In addition, it has been suggested that the muHTT transcript contributes to the toxicity. Thus, reduction of both muHTT mRNA and protein levels would ideally be the most useful therapeutic option. We herein present a novel strategy for HD treatment using oligonucleotides (ONs) directly targeting the HTT trinucleotide repeat DNA. A partial, but significant and potentially long-term, HTT knock-down of both mRNA and protein was successfully achieved. Diminished phosphorylation of HTT gene-associated RNA-polymerase II is demonstrated, suggestive of reduced transcription downstream the ON-targeted repeat. Different backbone chemistries were found to have a strong impact on the ON efficiency. We also successfully use different delivery vehicles as well as naked uptake of the ONs, demonstrating versatility and possibly providing insights for in vivo applications.
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Affiliation(s)
- Eman M Zaghloul
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, El-Khartoum square, Azareeta, 21 521 Alexandria, Egypt
| | - Olof Gissberg
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Lee Siggens
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, SE-141 86, Huddinge, Stockholm, Sweden
| | - Mattias Hällbrink
- Department of Neurochemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Anna S Jørgensen
- Department of Physics and Chemistry, Nucleic Acid Centre University of Southern Denmark, DK-5230 Odense, Denmark
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, SE-141 86, Huddinge, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Jesper Wengel
- Department of Physics and Chemistry, Nucleic Acid Centre University of Southern Denmark, DK-5230 Odense, Denmark
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
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Pendergraff HM, Krishnamurthy PM, Debacker AJ, Moazami MP, Sharma VK, Niitsoo L, Yu Y, Tan YN, Haitchi HM, Watts JK. Locked Nucleic Acid Gapmers and Conjugates Potently Silence ADAM33, an Asthma-Associated Metalloprotease with Nuclear-Localized mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:158-168. [PMID: 28918018 PMCID: PMC5498289 DOI: 10.1016/j.omtn.2017.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 12/22/2022]
Abstract
Two mechanisms dominate the clinical pipeline for oligonucleotide-based gene silencing, namely, the antisense approach that recruits RNase H to cleave target RNA and the RNAi approach that recruits the RISC complex to cleave target RNA. Multiple chemical designs can be used to elicit each pathway. We compare the silencing of the asthma susceptibility gene ADAM33 in MRC-5 lung fibroblasts using four classes of gene silencing agents, two that use each mechanism: traditional duplex small interfering RNAs (siRNAs), single-stranded small interfering RNAs (ss-siRNAs), locked nucleic acid (LNA) gapmer antisense oligonucleotides (ASOs), and novel hexadecyloxypropyl conjugates of the ASOs. Of these designs, the gapmer ASOs emerged as lead compounds for silencing ADAM33 expression: several gapmer ASOs showed subnanomolar potency when transfected with cationic lipid and low micromolar potency with no toxicity when delivered gymnotically. The preferential susceptibility of ADAM33 mRNA to silencing by RNase H may be related to the high degree of nuclear retention observed for this mRNA. Dynamic light scattering data showed that the hexadecyloxypropyl ASO conjugates self-assemble into clusters. These conjugates showed reduced potency relative to unconjugated ASOs unless the lipophilic tail was conjugated to the ASO using a biocleavable linkage. Finally, based on the lead ASOs from (human) MRC-5 cells, we developed a series of homologous ASOs targeting mouse Adam33 with excellent activity. Our work confirms that ASO-based gene silencing of ADAM33 is a useful tool for asthma research and therapy.
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Affiliation(s)
- Hannah M Pendergraff
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Pranathi Meda Krishnamurthy
- RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Alexandre J Debacker
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Michael P Moazami
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Vivek K Sharma
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA
| | - Liisa Niitsoo
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yong Yu
- Institute of Materials Research and Engineering, A*STAR, Singapore 138634, Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, A*STAR, Singapore 138634, Singapore
| | - Hans Michael Haitchi
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit at University Hospital Southampton NHS Foundation Trust, Southampton, Southampton SO16 6YD, UK.
| | - Jonathan K Watts
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; RNA Therapeutics Institute, UMass Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA 01605, USA.
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34
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The Race of 10 Synthetic RNAi-Based Drugs to the Pharmaceutical Market. Pharm Res 2017; 34:1339-1363. [PMID: 28389707 DOI: 10.1007/s11095-017-2134-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/27/2017] [Indexed: 02/08/2023]
Abstract
Ten years after Fire and Melo's Nobel Prize for discovery of gene silencing by double-stranded RNA, a remarkable progress was achieved in RNA interference (RNAi). Changes in the chemical structure of synthetic oligonucleotides make them more stable and specific, and new delivery strategies became progressively available. The attention of pharmaceutical industry rapidly turned to RNAi, as an opportunity to explore new drug targets. This review addresses nine small-interfering RNAs (siRNAs) and one unique microRNA (miRNA) inhibitor, which entered the phase 2-3 clinical trials. The siRNAs in focus are PF-04523655, TKM-080301, Atu027, SYL040012, SYL1001, siG12D-LODER (phase 2), QPI-1002, QPI-1007, and patisiran (phase 3). Regarding miRNAs, their content can be down- or up-regulated, by using miRNA inhibitors (AntimiRs) or miRNA mimics. Miravirsen is an AntimiR-122 for hepatitis C virus infection. The flexibility of RNAi technology is easily understood taking into account: (i) the different drug targets (i.e. p53, caspase 2, PKN3, β2-adrenergic receptor, mutated KRAS, microRNAs); (ii) therapeutic conditions, including ophthalmic diseases, kidney injury, amyloidosis, pancreatic cancer, viral hepatitis; and (iii) routes of administration (ocular, intravenous, subcutaneous, intratumoral). Although some issues are still matters of concern (delivery, toxicity, cost, and biological barriers), RNAi definitively opens a wide avenue for drug development.
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35
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Kropp J, Carrillo JA, Namous H, Daniels A, Salih SM, Song J, Khatib H. Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos. BMC Genomics 2017; 18:280. [PMID: 28381255 PMCID: PMC5382486 DOI: 10.1186/s12864-017-3673-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/31/2017] [Indexed: 11/12/2022] Open
Abstract
Background Infertility in dairy cattle is a concern where reduced fertilization rates and high embryonic loss are contributing factors. Studies of the paternal contribution to reproductive performance are limited. However, recent discoveries have shown that, in addition to DNA, sperm delivers transcription factors and epigenetic components that are required for fertilization and proper embryonic development. Hence, characterization of the paternal contribution at the time of fertilization is warranted. We hypothesized that sire fertility is associated with differences in DNA methylation patterns in sperm and that the embryonic transcriptomic profiles are influenced by the fertility status of the bull. Embryos were generated in vitro by fertilization with either a high or low fertility Holstein bull. Blastocysts derived from each high and low fertility bulls were evaluated for morphology, development, and transcriptomic analysis using RNA-Sequencing. Additionally, DNA methylation signatures of sperm from high and low fertility sires were characterized by performing whole-genome DNA methylation binding domain sequencing. Results Embryo morphology and developmental capacity did not differ between embryos generated from either a high or low fertility bull. However, RNA-Sequencing revealed 98 genes to be differentially expressed at a false discovery rate < 1%. A total of 65 genes were upregulated in high fertility bull derived embryos, and 33 genes were upregulated in low fertility derived embryos. Expression of the genes CYCS, EEA1, SLC16A7, MEPCE, and TFB2M was validated in three new pairs of biological replicates of embryos. The role of the differentially expressed gene TFB2M in embryonic development was further assessed through expression knockdown at the zygotic stage, which resulted in decreased development to the blastocyst stage. Assessment of the epigenetic signature of spermatozoa between high and low fertility bulls revealed 76 differentially methylated regions. Conclusions Despite similar morphology and development to the blastocyst stage, preimplantation embryos derived from high and low fertility bulls displayed significant transcriptomic differences. The relationship between the paternal contribution and the embryonic transcriptome is unclear, although differences in methylated regions were identified which could influence the reprogramming of the early embryo. Further characterization of paternal factors delivered to the oocyte could lead to the identification of biomarkers for better selection of sires to improve reproductive efficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3673-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenna Kropp
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - José A Carrillo
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Hadjer Namous
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alyssa Daniels
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sana M Salih
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792, USA.,Present address: Department of Obstetrics and Gynecology, West Virginia University, Morgantown, WV, 26508, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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36
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González-Barriga A, Nillessen B, Kranzen J, van Kessel IDG, Croes HJE, Aguilera B, de Visser PC, Datson NA, Mulders SAM, van Deutekom JCT, Wieringa B, Wansink DG. Intracellular Distribution and Nuclear Activity of Antisense Oligonucleotides After Unassisted Uptake in Myoblasts and Differentiated Myotubes In Vitro. Nucleic Acid Ther 2017; 27:144-158. [PMID: 28375678 PMCID: PMC5467152 DOI: 10.1089/nat.2016.0641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Clinical efficacy of antisense oligonucleotides (AONs) for the treatment of neuromuscular disorders depends on efficient cellular uptake and proper intracellular routing to the target. Selection of AONs with highest in vitro efficiencies is usually based on chemical or physical methods for forced cellular delivery. Since these methods largely bypass existing natural mechanisms for membrane passage and intracellular trafficking, spontaneous uptake and distribution of AONs in cells are still poorly understood. Here, we report on the unassisted uptake of naked AONs, so-called gymnosis, in muscle cells in culture. We found that gymnosis works similarly well for proliferating myoblasts as for terminally differentiated myotubes. Cell biological analyses combined with microscopy imaging showed that a phosphorothioate backbone promotes efficient gymnosis, that uptake is clathrin mediated and mainly results in endosomal-lysosomal accumulation. Nuclear localization occurred at a low level, but the gymnotically delivered AONs effectively modulated the expression of their nuclear RNA targets. Chloroquine treatment after gymnotic delivery helped increase nuclear AON levels. In sum, we demonstrate that gymnosis is feasible in proliferating and non-proliferating muscle cells and we confirm the relevance of AON chemistry for uptake and intracellular trafficking with this method, which provides a useful means for bio-activity screening of AONs in vitro.
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Affiliation(s)
- Anchel González-Barriga
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands .,2 BioMarin Nederland B.V., Leiden, the Netherlands
| | - Bram Nillessen
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Julia Kranzen
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Ingeborg D G van Kessel
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Huib J E Croes
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | | | | | | | | | | | - Bé Wieringa
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Derick G Wansink
- 1 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, the Netherlands
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37
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Cai Y, López-Ruiz E, Wengel J, Creemers LB, Howard KA. A hyaluronic acid-based hydrogel enabling CD44-mediated chondrocyte binding and gapmer oligonucleotide release for modulation of gene expression in osteoarthritis. J Control Release 2017; 253:153-159. [PMID: 28274742 DOI: 10.1016/j.jconrel.2017.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/25/2022]
Abstract
Hyaluronic acid (HA) is an attractive biomaterial for osteoarthritis (OA) treatment due to inherent functional and compatibility properties as an endogenous knee joint component. In this work, we describe a HA-based hydrogel with the dual functionality of increased CD44-dependent chondrocyte binding and controlled release of gapmer antisense oligonucleotides for unassisted cellular entry and subsequent gene silencing activity. A Schiff base-mediated gelation method was used to produce a panel of hydrogels varying in the aldehyde-modified HA (900kDa) to chitosan ratios (3:7, 5:5 and 7:3) for identifying designs displaying optimal engagement of OA patient-derived CD44-expressing chondrocytes. Correlation was found between cell binding and CD44 expression, with maximal binding exhibited at a HA/chitosan ratio of 7:3, that was 181% higher than CD44-negative MCF-7 cell control cells. Transfection agent-free uptake into OA chondrocytes of fluorescent 13-mer DNA oligonucleotides with a flanked locked nucleic acid (LNA) gapmer design, in contrast to naked siRNA, was demonstrated by confocal and flow cytometric analysis. A sustained and complete release over 5days was found with the 7:3 hydrogel, in contrast, the 5:5 and 3:7 hydrogel released 60% and 43% of loaded gapmers, respectively over the same period. A COX-2-specific gapmer designed with maximal chondrocyte gene silencing (~70% silencing efficiency at 500nM compared with a mismatch gapmer sequence) resulted in effective COX-2 silencing over 14days in hydrogels seeded with OA chondrocytes, with significant difference exhibited between day 3 and 10. This work introduces a novel HA-based CD44-mediated cellular binding and gapmer controlled release platform to modulate cellular gene expression.
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Affiliation(s)
- Yunpeng Cai
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Elena López-Ruiz
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark; Department of Health Sciences, University of Jaén, Jaén E-23071, Spain
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Laura B Creemers
- Department of Orthopaedics, University Medical Center Utrecht, 3584 CX, Utrecht, Netherlands
| | - Kenneth A Howard
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.
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38
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Zhang X, Castanotto D, Nam S, Horne D, Stein C. 6BIO Enhances Oligonucleotide Activity in Cells: A Potential Combinatorial Anti-androgen Receptor Therapy in Prostate Cancer Cells. Mol Ther 2017; 25:79-91. [PMID: 28129131 DOI: 10.1016/j.ymthe.2016.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 12/22/2022] Open
Abstract
Approximately 15%-25% of men diagnosed with prostate cancer do not survive their disease. The American Cancer Society estimated that for the year 2016 the number of prostate cancer deaths will be 26,120. Thus, there is a critical need for novel approaches to treat this deadly disease. Using high-throughput small-molecule screening, we found that the small molecule 6-bromo-indirubin-3'-oxime (6BIO) significantly improves the targeting of antisense oligonucleotides (ASOs) delivered by gymnosis (i.e., in the absence of any transfection reagents) in both the cell cytoplasm and the nucleus. Furthermore, as a single agent, 6BIO had the unexpected ability to simultaneously downregulate androgen receptor (AR) expression and AR signaling in prostate cancer cells. This includes downregulating levels of the AR-V7, a drug-resistance-related AR splice variant that is important in the progression of prostate cancer. Combining 6BIO and an anti-AR oligonucleotide (AR-ASO) can augment the downregulation of AR expression. We also demonstrated that 6BIO enhances ASO function and represses AR expression through the inhibition of the two main glycogen synthase kinase 3 (GSK-3) isoforms: GSK-3α and GSK-3β activity. Our findings provide a rationale for the use of 6BIO as a single agent or as part of a combinatorial ASO-based therapy in the treatment of human prostate cancer.
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Affiliation(s)
- Xiaowei Zhang
- Departments of Medical Oncology and Experimental Therapeutics and Molecular and Cellular Biology, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Daniela Castanotto
- Departments of Medical Oncology and Experimental Therapeutics and Molecular and Cellular Biology, City of Hope Medical Center, Duarte, CA 91010, USA; Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA.
| | - Sangkil Nam
- Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA
| | - David Horne
- Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Cy Stein
- Departments of Medical Oncology and Experimental Therapeutics and Molecular and Cellular Biology, City of Hope Medical Center, Duarte, CA 91010, USA; Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA.
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GapmeR cellular internalization by macropinocytosis induces sequence-specific gene silencing in human primary T-cells. Sci Rep 2016; 6:37721. [PMID: 27883055 PMCID: PMC5121623 DOI: 10.1038/srep37721] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/27/2016] [Indexed: 12/21/2022] Open
Abstract
Post-transcriptional gene silencing holds great promise in discovery research for addressing intricate biological questions and as therapeutics. While various gene silencing approaches, such as siRNA and CRISPR-Cas9 techniques, are available, these cannot be effectively applied to “hard-to-transfect” primary T-lymphocytes. The locked nucleic acid-conjugated chimeric antisense oligonucleotide, called “GapmeR”, is an emerging new class of gene silencing molecule. Here, we show that GapmeR internalizes into human primary T-cells through macropinocytosis. Internalized GapmeR molecules can associate with SNX5-positive macropinosomes in T-cells, as detected by super-resolution microscopy. Utilizing the intrinsic self-internalizing capability of GapmeR, we demonstrate significant and specific depletion (>70%) of the expression of 5 different endogenous proteins with varying molecular weights (18 kDa Stathmin, 80 kDa PKCε, 180 kDa CD11a, 220 kDa Talin1 and 450 kDa CG-NAP/AKAP450) in human primary and cultured T-cells. Further functional analysis confirms CG-NAP and Stathmin as regulators of T-cell motility. Thus, in addition to screening, identifying or verifying critical roles of various proteins in T-cell functioning, this study provides novel opportunities to silence individual or multiple genes in a subset of purified human primary T-cells that would be exploited as future therapeutics.
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40
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Hiding in the Shadows: CPOX Expression and 5-ALA Induced Fluorescence in Human Glioma Cells. Mol Neurobiol 2016; 54:5699-5708. [PMID: 27644131 DOI: 10.1007/s12035-016-0109-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/06/2016] [Indexed: 10/21/2022]
Abstract
Protoporphyrin IX (PpIX) is widely used in photodynamic diagnosis. To date, the details of molecular mechanisms underlying PpIX accumulation in malignant cells after 5-ALA administration remain unclear. The fluorescence of PpIX was studied in human glioma cells. Several cell cultures were established from glioma tumor tissue to study the differences between fluorescence-positive and fluorescence-negative human glioma tumors. The cell cultures demonstrated fluorescence profiles similar to those of source tumor tissues, which allows us to use these cultures in experimental research. Dynamics of the rates of synthesis and degradation of fluorescent protoporphyrin IX was studied in the cultures obtained. In addition, the expression of CPOX, an enzyme involved in PpIX synthesis, was evaluated. mRNA levels of heme biosynthesis enzymes were analyzed, and PpIX fluorescence proved to correlate with the CPOX protein level, whereas no such correlation was observed at the mRNA level. Fluorescence intensity decreased at low levels of the enzyme, which indicates its critical role in PpIX fluorescence. Finally, the fluorescence intensity proved to correlate with the proliferative activity.
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41
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Rocha CSJ, Lundin KE, Behlke MA, Zain R, El Andaloussi S, Smith CIE. Four Novel Splice-Switch Reporter Cell Lines: Distinct Impact of Oligonucleotide Chemistry and Delivery Vector on Biological Activity. Nucleic Acid Ther 2016; 26:381-391. [PMID: 27629437 DOI: 10.1089/nat.2016.0631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
New advances in oligonucleotide (ON) chemistry emerge continuously, and over the last few years, several aspects of ON delivery have been improved. However, clear knowledge regarding how certain chemistries behave alone, or in combination with various delivery vectors, is limited. Moreover, characterization is frequently limited to a single reporter cell line and, when different cell types are studied, experiments are commonly not carried out under similar conditions, hampering comparative analysis. To address this, we have developed a small "tissue" library of new, stable, pLuc/705 splice-switching reporter cell lines (named HuH7_705, U-2 OS_705, C2C12_705, and Neuro-2a_705). Our data show that, indeed, the cell type used in activity screenings influences the efficiency of ONs of different chemistry (phosphorothioate with locked nucleic acid or 2'-O-methyl with or without N,N-diethyl-4-(4-nitronaphthalen-1-ylazo)-phenylamine). Likewise, the delivery method, Lipofectamine® 2000, PepFect14 nanoparticles, or "naked" uptake, also demonstrates cell-type-dependent outcomes. Taken together, these cell lines can potentially become useful tools for future in vitro evaluation of new nucleic acid-based oligomers as well as delivery compounds for splice-switching approaches and cell-specific therapies.
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Affiliation(s)
- Cristina S J Rocha
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Karin E Lundin
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Mark A Behlke
- 2 Integrated DNA Technologies, Inc. , Coralville, Iowa
| | - Rula Zain
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,3 Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital , Stockholm, Sweden
| | - Samir El Andaloussi
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,4 Department of Physiology, Anatomy and Genetics, University of Oxford , Oxford, United Kingdom
| | - C I Edvard Smith
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
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Protein Kinase C-α is a Critical Protein for Antisense Oligonucleotide-mediated Silencing in Mammalian Cells. Mol Ther 2016; 24:1117-1125. [PMID: 26961407 DOI: 10.1038/mt.2016.54] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/18/2016] [Indexed: 01/08/2023] Open
Abstract
We have identified the existence of a productive, PKC-α-dependent endocytotic silencing pathway that leads gymnotically-delivered locked nucleic acid (LNA)-gapmer phosphorothioate antisense oligonucleotides (ASOs) into late endosomes. By blocking the maturation of early endosomes to late endosomes, silencing the expression of PKC-α results in the potent reduction of ASO silencing ability in the cell. We have also demonstrated that silencing of gene expression in the cytoplasm is vitiated when PKC-α expression is reduced. Restoring PKC-α expression via a reconstitution experiment reinstates the ability of ASOs to silence. These results advance our understanding of intracellular ASO trafficking and activity following gymnotic delivery, and further demonstrate the existence of two distinct silencing pathways in mammalian cells, one in the cytoplasmic and the other in the nuclear compartment.
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Jaschinski F, Korhonen H, Janicot M. Design and Selection of Antisense Oligonucleotides Targeting Transforming Growth Factor Beta (TGF-β) Isoform mRNAs for the Treatment of Solid Tumors. Methods Mol Biol 2016; 1317:137-51. [PMID: 26072406 DOI: 10.1007/978-1-4939-2727-2_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transforming growth factor beta isoforms (TGF-β1, -β2, and -β3) are cytokines associated with a wide range of biological processes in oncology including tumor cell invasion and migration, angiogenesis, immunosuppression, as well as regulation of tumor stem cell properties. Hence, blocking the TGF-β signaling pathways may have a multifold therapeutic benefit for the treatment of solid tumors. Here, we describe the identification and selection processes for the development of highly potent and selective chemically modified antisense oligodeoxynucleotides (fully phosphorothioate locked nucleic acid gapmers) allowing effective and selective suppression of TGF-β isoform expression in cell-based assays and in vivo preclinical models.
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Affiliation(s)
- Frank Jaschinski
- Isarna Therapeutics. Preclinical Research and Development Department, Leopoldstrasse 254-256, 80807, Munich, Germany
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44
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Castanotto D, Lin M, Kowolik C, Wang L, Ren XQ, Soifer HS, Koch T, Hansen BR, Oerum H, Armstrong B, Wang Z, Bauer P, Rossi J, Stein CA. A cytoplasmic pathway for gapmer antisense oligonucleotide-mediated gene silencing in mammalian cells. Nucleic Acids Res 2015; 43:9350-61. [PMID: 26433227 PMCID: PMC4627093 DOI: 10.1093/nar/gkv964] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 09/04/2015] [Indexed: 11/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are known to trigger mRNA degradation in the nucleus via an RNase H-dependent mechanism. We have now identified a putative cytoplasmic mechanism through which ASO gapmers silence their targets when transfected or delivered gymnotically (i.e. in the absence of any transfection reagent). We have shown that the ASO gapmers can interact with the Ago-2 PAZ domain and can localize into GW-182 mRNA-degradation bodies (GW-bodies). The degradation products of the targeted mRNA, however, are not generated by Ago-2-directed cleavage. The apparent identification of a cytoplasmic pathway complements the previously known nuclear activity of ASOs and concurrently suggests that nuclear localization is not an absolute requirement for gene silencing.
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Affiliation(s)
- Daniela Castanotto
- Department of Medical Oncology, City of Hope, 1500 East Duarte Road, Duarte CA 91010, USA
| | - Min Lin
- Department of Cancer Immunotherapeutics and Tumor Immunology, City of Hope, 1500 East Duarte Road, Duarte CA 91010, USA
| | - Claudia Kowolik
- Department of Molecular Medicine, City of Hope, 1500 East Duarte Road, Duarte CA 91010, USA
| | - LiAnn Wang
- Pfizer Research Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
| | - Xiao-Qin Ren
- Pfizer Research Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
| | - Harris S Soifer
- bioTheranostics, 9640 Towne Center Dr., Suite 100, San Diego, CA 92121, USA
| | - Troels Koch
- Roche, Fremtidsvej 3, Horsholm, DK 2970, Denmark
| | | | - Henrik Oerum
- Roche, Fremtidsvej 3, Horsholm, DK 2970, Denmark
| | - Brian Armstrong
- Department of Neuroscience, City of Hope, 1500 East Duarte Road, Duarte CA 91010, USA
| | - Zhigang Wang
- Pfizer Research Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
| | - Paul Bauer
- Pfizer Research Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, City of Hope, 1500 East Duarte Road, Duarte CA 91010, USA
| | - C A Stein
- Department of Medical Oncology, City of Hope, 1500 East Duarte Road, Duarte CA 91010, USA
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45
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Kropp J, Khatib H. mRNA fragments in in vitro culture media are associated with bovine preimplantation embryonic development. Front Genet 2015; 6:273. [PMID: 26379701 PMCID: PMC4547040 DOI: 10.3389/fgene.2015.00273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
In vitro production (IVP) systems have been used to bypass problems of fertilization and early embryonic development. However, embryos produced by IVP are commonly selected for implantation based on morphological assessment, which is not a strong indicator of establishment and maintenance of pregnancy. Thus, there is a need to identify additional indicators of embryonic developmental potential. Previous studies have identified microRNA expression in in vitro culture media to be indicative of embryo quality in both bovine and human embryos. Like microRNAs, mRNAs have been shown to be secreted from cells into the extracellular environment, but it is unknown whether or not these RNAs are secreted by embryos. Thus, the objective of the present study was to determine whether mRNAs are secreted into in vitro culture media and if their expression in the media is indicative of embryo quality. In vitro culture medium was generated and collected from both blastocyst and degenerate (those which fail to develop from the morula to blastocyst stage) embryos. Small-RNA sequencing revealed that many mRNA fragments were present in the culture media. A total of 17 mRNA fragments were differentially expressed between blastocyst and degenerate conditioned media. Differential expression was confirmed by quantitative real-time PCR for fragments of mRNA POSTN and VSNL-1, in four additional biological replicates of media. To better understand the mechanisms of mRNA secretion into the media, the expression of a predicted RNA binding protein of POSTN, PUM2, was knocked down using an antisense oligonucleotide gapmer. Supplementation of a PUM2 gapmer significantly reduced blastocyst development and decreased secretion of POSTN mRNA into the media. Overall, differential mRNA expression in the media was repeatable and sets the framework for future study of mRNA biomarkers in in vitro culture media to improve predictability of reproductive performance.
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Affiliation(s)
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin–Madison, MadisonWI, USA
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46
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Ezzat K, Aoki Y, Koo T, McClorey G, Benner L, Coenen-Stass A, O'Donovan L, Lehto T, Garcia-Guerra A, Nordin J, Saleh AF, Behlke M, Morris J, Goyenvalle A, Dugovic B, Leumann C, Gordon S, Gait MJ, El-Andaloussi S, Wood MJA. Self-Assembly into Nanoparticles Is Essential for Receptor Mediated Uptake of Therapeutic Antisense Oligonucleotides. NANO LETTERS 2015; 15:4364-73. [PMID: 26042553 PMCID: PMC6415796 DOI: 10.1021/acs.nanolett.5b00490] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Antisense oligonucleotides (ASOs) have the potential to revolutionize medicine due to their ability to manipulate gene function for therapeutic purposes. ASOs are chemically modified and/or incorporated within nanoparticles to enhance their stability and cellular uptake, however, a major challenge is the poor understanding of their uptake mechanisms, which would facilitate improved ASO designs with enhanced activity and reduced toxicity. Here, we study the uptake mechanism of three therapeutically relevant ASOs (peptide-conjugated phosphorodiamidate morpholino (PPMO), 2'Omethyl phosphorothioate (2'OMe), and phosphorothioated tricyclo DNA (tcDNA) that have been optimized to induce exon skipping in models of Duchenne muscular dystrophy (DMD). We show that PPMO and tcDNA have high propensity to spontaneously self-assemble into nanoparticles. PPMO forms micelles of defined size and their net charge (zeta potential) is dependent on the medium and concentration. In biomimetic conditions and at low concentrations, PPMO obtains net negative charge and its uptake is mediated by class A scavenger receptor subtypes (SCARAs) as shown by competitive inhibition and RNAi silencing experiments in vitro. In vivo, the activity of PPMO was significantly decreased in SCARA1 knockout mice compared to wild-type animals. Additionally, we show that SCARA1 is involved in the uptake of tcDNA and 2'OMe as shown by competitive inhibition and colocalization experiments. Surface plasmon resonance binding analysis to SCARA1 demonstrated that PPMO and tcDNA have higher binding profiles to the receptor compared to 2'OMe. These results demonstrate receptor-mediated uptake for a range of therapeutic ASO chemistries, a mechanism that is dependent on their self-assembly into nanoparticles.
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MESH Headings
- Animals
- Base Sequence
- Cell Line
- Exons
- Genetic Therapy
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Micelles
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/therapy
- Nanoparticles/chemistry
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/pharmacokinetics
- Oligonucleotides, Antisense/therapeutic use
- Scavenger Receptors, Class A/genetics
- Scavenger Receptors, Class A/metabolism
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Affiliation(s)
- Kariem Ezzat
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
| | - Yoshitsugu Aoki
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
- ●Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8551, Japan
| | - Taeyoung Koo
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
- ‡Center for Genome Engineering, Institute for Basic Science, Seoul 151-747, South Korea
- §Functional Genomics, University of Science and Technology, Daejeon 305-338, South Korea
| | - Graham McClorey
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
| | - Leif Benner
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
| | - Anna Coenen-Stass
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
| | - Liz O'Donovan
- ∥Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Taavi Lehto
- ⊥Department of Laboratory Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Antonio Garcia-Guerra
- #Clarendon Laboratory, Department of Physics, University of Oxford, OX13PU, Oxford, United Kingdom
| | - Joel Nordin
- ⊥Department of Laboratory Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Amer F Saleh
- ∥Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Mark Behlke
- ∇Integrated DNA Technologies (IDT), Coralville, Iowa 55241, United States
| | - John Morris
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
| | - Aurelie Goyenvalle
- ○Université de Versailles Saint Quentin, Montigny le Bretonneux 78180, France
| | - Branislav Dugovic
- ◆Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Christian Leumann
- ◆Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Siamon Gordon
- ¶Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, United Kingdom
| | - Michael J Gait
- ∥Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Samir El-Andaloussi
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
- ⊥Department of Laboratory Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Matthew J A Wood
- †Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX, Oxford, United Kingdom
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47
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MicroRNA-17-92 controls T-cell responses in graft-versus-host disease and leukemia relapse in mice. Blood 2015; 126:1314-23. [PMID: 26138686 DOI: 10.1182/blood-2015-02-627356] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/25/2015] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRs) play important roles in orchestrating many aspects of the immune response. The miR-17-92 cluster, which encodes 6 miRs including 17, 18a, 19a, 20a, 19b-1, and 92-1, is among the best characterized of these miRs. The miR-17-92 cluster has been shown to regulate a variety of immune responses including infection, tumor, and autoimmunity, but the role of this cluster in T-cell response to alloantigens has not been previously explored. By using major histocompatibility complex (MHC)-matched, -mismatched, and haploidentical murine models of allogeneic bone marrow transplantation (allo-BMT), we demonstrate that the expression of miR-17-92 on donor T cells is essential for the induction of graft-versus-host disease (GVHD), but dispensable for the graft-versus-leukemia (GVL) effect. The miR-17-92 plays a major role in promoting CD4 T-cell activation, proliferation, survival, and Th1 differentiation, while inhibiting Th2 and iTreg differentiation. Alternatively, miR-17-92 may promote migration of CD8 T cells to GVHD target organs, but has minimal impact on CD8 T-cell proliferation, survival, or cytolytic function, which could contribute to the preserved GVL effect mediated by T cells deficient for miR-17-92. Furthermore, we evaluated a translational approach and found that systemic administration of antagomir to block miR-17 or miR-19b in this cluster significantly inhibited alloreactive T-cell expansion and interferon-γ (IFNγ) production, and prolonged the survival in recipients afflicted with GVHD while preserving the GVL effect. Taken together, the current work provides a strong rationale and demonstrates the feasibility to target miR-17-92 for the control of GVHD while preserving GVL activity after allo-BMT.
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48
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Shoeneman JK, Ehrhart EJ, Charles JB, Thamm DH. Survivin inhibition via EZN-3042 in canine lymphoma and osteosarcoma. Vet Comp Oncol 2014; 14:e45-57. [PMID: 24923332 DOI: 10.1111/vco.12104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/08/2014] [Accepted: 05/15/2014] [Indexed: 12/21/2022]
Abstract
Canine lymphoma (LSA) and osteosarcoma (OS) have high mortality rates and remain in need of more effective therapeutic approaches. Survivin, an inhibitor of apoptosis (IAP) family member protein that inhibits apoptosis and drives cell proliferation, is commonly elevated in human and canine cancer. Survivin expression is a negative prognostic factor in dogs with LSA and OS, and canine LSA and OS cell lines express high levels of survivin. In this study, we demonstrate that survivin downregulation in canine LSA and OS cells using a clinically applicable locked nucleic acid antisense oligonucleotide (EZN-3042, Enzon Pharmaceuticals, Piscataway Township, NJ, USA) inhibits growth, induces apoptosis and enhances chemosensitivity in vitro, and inhibits survivin transcription and protein production in orthotopic canine OS xenografts. Our findings strongly suggest that survivin-directed therapies might be effective in treatment of canine LSA and OS and support evaluation of EZN-3042 in dogs with cancer.
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Affiliation(s)
- J K Shoeneman
- Flint Animal Cancer Center, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA
| | - E J Ehrhart
- Flint Animal Cancer Center, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - J B Charles
- Flint Animal Cancer Center, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - D H Thamm
- Flint Animal Cancer Center, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA
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49
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Cheng CJ, Saltzman WM, Slack FJ. Canonical and non-canonical barriers facing antimiR cancer therapeutics. Curr Med Chem 2014; 20:3582-93. [PMID: 23745563 DOI: 10.2174/0929867311320290004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 12/14/2022]
Abstract
Once considered genetic "oddities", microRNAs (miRNAs) are now recognized as key epigenetic regulators of numerous biological processes, including some with a causal link to the pathogenesis, maintenance, and treatment of cancer. The crux of small RNA-based therapeutics lies in the antagonism of potent cellular targets; the main shortcoming of the field in general, lies in ineffective delivery. Inhibition of oncogenic miRNAs is a relatively nascent therapeutic concept, but as with predecessor RNA-based therapies, success hinges on delivery efficacy. This review will describes the canonical (e.g. pharmacokinetics and clearance, cellular uptake, endosome escape, etc.) and non-canonical (e.g. spatial localization and accessibility of miRNA, technical limitations of miRNA inhibition, off-target impacts, etc.) challenges to the delivery of antisense-based anti-miRNA therapeutics (i.e. antimiRs) for the treatment of cancer. Emphasis will be placed on how the current leading antimiR platforms-ranging from naked chemically modified oligonucleotides to nanoscale delivery vehicles-are affected by and overcome these barriers. The perplexity of antimiR delivery presents both engineering and biological hurdles that must be overcome in order to capitalize on the extensive pharmacological benefits of antagonizing tumor-associated miRNAs.
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Affiliation(s)
- Christopher J Cheng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
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50
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Koch T, Shim I, Lindow M, Ørum H, Bohr HG. Quantum mechanical studies of DNA and LNA. Nucleic Acid Ther 2014; 24:139-48. [PMID: 24491259 DOI: 10.1089/nat.2013.0465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Quantum mechanical (QM) methodology has been employed to study the structure activity relations of DNA and locked nucleic acid (LNA). The QM calculations provide the basis for construction of molecular structure and electrostatic surface potentials from molecular orbitals. The topologies of the electrostatic potentials were compared among model oligonucleotides, and it was observed that small structural modifications induce global changes in the molecular structure and surface potentials. Since ligand structure and electrostatic potential complementarity with a receptor is a determinant for the bonding pattern between molecules, minor chemical modifications may have profound changes in the interaction profiles of oligonucleotides, possibly leading to changes in pharmacological properties. The QM modeling data can be used to understand earlier observations of antisense oligonucleotide properties, that is, the observation that small structural changes in oligonucleotide composition may lead to dramatic shifts in phenotypes. These observations should be taken into account in future oligonucleotide drug discovery, and by focusing more on non RNA target interactions it should be possible to utilize the exhibited property diversity of oligonucleotides to produce improved antisense drugs.
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