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Ren W, Duan S, Dai C, Xie C, Jiang L, Shi Y. Nanotechnology Lighting the Way for Gene Therapy in Ophthalmopathy: From Opportunities toward Applications. Molecules 2023; 28:molecules28083500. [PMID: 37110734 PMCID: PMC10141718 DOI: 10.3390/molecules28083500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Hereditary ophthalmopathy is a well-described threat to human visual health affecting millions of people. Gene therapy for ophthalmopathy has received widespread attention with the increasing understanding of pathogenic genes. Effective and safe delivery of accurate nucleic acid drugs (NADs) is the core of gene therapy. Efficient nanodelivery and nanomodification technologies, appropriate targeted genes, and the choice of drug injection methods are the guiding lights of gene therapy. Compared with traditional drugs, NADs can specifically change the expression of specific genes or restore the normal function of mutant genes. Nanodelivery carriers can improve targeting and nanomodification can improve the stability of NADs. Therefore, NADs, which can fundamentally solve pathogeny, hold great promise in the treatment of ophthalmopathy. This paper reviews the limitations of ocular disease treatment, discusses the classification of NADs in ophthalmology, reveals the delivery strategies of NADs to improve bioavailability, targeting, and stability, and summarizes the mechanisms of NADs in ophthalmopathy.
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Affiliation(s)
- Weiming Ren
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Suyang Duan
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chao Dai
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chunbao Xie
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Lingxi Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 610072, China
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
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Czapik T, Piasecka J, Kierzek R, Kierzek E. Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:64-74. [PMID: 35784013 PMCID: PMC9217987 DOI: 10.1016/j.omtn.2022.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/26/2022] [Indexed: 11/16/2022]
Abstract
The naturally occurring structure and biological functions of RNA are correlated, which includes hammerhead ribozymes. We proposed new variants of hammerhead ribozymes targeting conserved structural motifs of segment 5 of influenza A virus (IAV) (+)RNA. The variants carry structural and chemical modifications aiming to improve the RNA cleavage activity of ribozymes. We introduced an additional hairpin motif and attempted to select ribozyme-target pairs with sequence features that enable the potential formation of the trans-Hoogsteen interactions that are present in full-length, highly active hammerhead ribozymes. We placed structurally defined guanosine analogs into the ribozyme catalytic core. Herein, the significantly improved synthesis of 2′-deoxy-2′-fluoroarabinoguanosine derivatives is described. The most potent hammerhead ribozymes were applied to chimeric short hairpin RNA (shRNA)-ribozyme plasmid constructs to improve the antiviral activity of the two components. The modified hammerhead ribozymes showed moderate cleavage activity. Treatment of IAV-infected Madin-Darby canine kidney (MDCK) cells with the plasmid constructs resulted in significant inhibition of virus replication. Real-time PCR analysis revealed a significant (80%–88%) reduction in viral RNA when plasmids carriers were used. A focus formation assay (FFA) for chimeric plasmids showed inhibition of virus replication by 1.6–1.7 log10 units, whereas the use of plasmids carrying ribozymes or shRNAs alone resulted in lower inhibition.
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Rouge JL, Sita TL, Hao L, Kouri FM, Briley WE, Stegh AH, Mirkin CA. Ribozyme-Spherical Nucleic Acids. J Am Chem Soc 2015; 137:10528-10531. [PMID: 26271335 DOI: 10.1021/jacs.5b07104] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ribozymes are highly structured RNA sequences that can be tailored to recognize and cleave specific stretches of mRNA. Their current therapeutic efficacy remains low due to their large size and structural instability compared to shorter therapeutically relevant RNA such as small interfering RNA (siRNA) and microRNA (miRNA). Herein, a synthetic strategy that makes use of the spherical nucleic acid (SNA) architecture to stabilize ribozymes and transfect them into live cells is reported. The properties of this novel ribozyme-SNA are characterized in the context of the targeted knockdown of O(6)-methylguanine-DNA methyltransferase (MGMT), a DNA repair protein involved in chemotherapeutic resistance of solid tumors, foremost glioblastoma multiforme (GBM). Data showing the direct cleavage of full-length MGMT mRNA, knockdown of MGMT protein, and increased sensitization of GBM cells to therapy-mediated apoptosis, independent of transfection agents, provide compelling evidence for the promising properties of this new chemical architecture.
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Affiliation(s)
- Jessica L Rouge
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.,International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy L Sita
- Interdisciplinary Biological Sciences Graduate Program, Evanston, Illinois 60208, United States.,International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States.,The Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States
| | - Liangliang Hao
- Interdisciplinary Biological Sciences Graduate Program, Evanston, Illinois 60208, United States.,International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Fotini M Kouri
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States.,The Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States.,Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - William E Briley
- Interdisciplinary Biological Sciences Graduate Program, Evanston, Illinois 60208, United States.,International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander H Stegh
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States.,The Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States.,Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Chad A Mirkin
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.,International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
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Liu B, Zhang YJ, Yang BS. Two novel Cr(III) complexes [Cr(SA)2(en)]TBA and [Cr(SA)(en)2]Br: Synthesis, characterization and spectral studies. INORG CHEM COMMUN 2013. [DOI: 10.1016/j.inoche.2013.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lévesque MV, Rouleau SG, Perreault JP. Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Ther 2011; 21:241-52. [PMID: 21793786 DOI: 10.1089/nat.2011.0301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Hepatitis Delta Virus (HDV) ribozyme, which is well adapted to the environment of the human cell, is an excellent candidate for the future development of gene-inactivation systems. On top of this, a new generation of HDV ribozymes now exists that benefits from the addition of a specific on/off adaptor (specifically the SOFA-HDV ribozymes) which greatly increases both the ribozyme's specificity and its cleavage activity. Unlike RNAi and hammerhead ribozymes, the designing of SOFA-HDV ribozymes to cleave, in trans, given RNA species has never been the object of a systematic optimization study, even with their recent use for the gene knockdown of various targets. This report aims at both improving and clarifying the design process of SOFA-HDV ribozymes. Both the ribozyme and the targeted RNA substrate were analyzed in order to provide new criteria that are useful in the selection of the most potent SOFA-HDV ribozymes. The crucial features present in both the ribozyme's biosensor and blocker, as well as at the target site, were identified and characterized. Simple rules were derived and tested using hepatitis C virus NS5B RNA as a model target. Overall, this method should promote the use of the SOFA-HDV ribozymes in a plethora of applications in both functional genomics and gene therapy.
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Affiliation(s)
- Michel V Lévesque
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke , Sherbrooke, Québec, Canada
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Drug delivery of siRNA therapeutics: potentials and limits of nanosystems. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2009; 5:8-20. [DOI: 10.1016/j.nano.2008.06.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 05/21/2008] [Accepted: 06/04/2008] [Indexed: 11/21/2022]
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Rasmussen LCV, Sperling-Petersen HU, Mortensen KK. Hitting bacteria at the heart of the central dogma: sequence-specific inhibition. Microb Cell Fact 2007; 6:24. [PMID: 17692125 PMCID: PMC1995221 DOI: 10.1186/1475-2859-6-24] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Accepted: 08/10/2007] [Indexed: 12/16/2022] Open
Abstract
An important objective in developing new drugs is the achievement of high specificity to maximize curing effect and minimize side-effects, and high specificity is an integral part of the antisense approach. The antisense techniques have been extensively developed from the application of simple long, regular antisense RNA (asRNA) molecules to highly modified versions conferring resistance to nucleases, stability of hybrid formation and other beneficial characteristics, though still preserving the specificity of the original nucleic acids. These new and improved second- and third-generation antisense molecules have shown promising results. The first antisense drug has been approved and more are in clinical trials. However, these antisense drugs are mainly designed for the treatment of different human cancers and other human diseases. Applying antisense gene silencing and exploiting RNA interference (RNAi) are highly developed approaches in many eukaryotic systems. But in bacteria RNAi is absent, and gene silencing by antisense compounds is not nearly as well developed, despite its great potential and the intriguing possibility of applying antisense molecules in the fight against multiresistant bacteria. Recent breakthrough and current status on the development of antisense gene silencing in bacteria including especially phosphorothioate oligonucleotides (PS-ODNs), peptide nucleic acids (PNAs) and phosphorodiamidate morpholino oligomers (PMOs) will be presented in this review.
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Affiliation(s)
| | - Hans Uffe Sperling-Petersen
- Laboratory of BioDesign, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Kim Kusk Mortensen
- Laboratory of BioDesign, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
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Christiansen JK, Lobedanz S, Arar K, Wengel J, Vester B. LNA nucleotides improve cleavage efficiency of singular and binary hammerhead ribozymes. Bioorg Med Chem 2007; 15:6135-43. [PMID: 17624789 DOI: 10.1016/j.bmc.2007.06.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 06/13/2007] [Indexed: 11/21/2022]
Abstract
Variants of trans-acting hammerhead ribozymes were modified with Locked Nucleic Acid (LNA) nucleotides to reduce their size, to improve access to their RNA target and to explore combinational properties of binary constructs. Using low Mg(2+) concentrations and low substrate and ribozyme concentrations, it was found that insertion of LNA monomers into the substrate binding arms allowed these to be shortened and results in a very active enzyme under both single and multiple turnover conditions. Incorporation of a mix of LNA and DNA residues further increased the multiple turnover cleavage activity. At high Mg(2+) concentrations or high substrate and ribozyme concentrations, the enhancing effect of LNA incorporation was even more prominent. Using LNA in the stem of Helix II diminished cleavage activity, but allowed deletion of the tetra-loop and thus separating the ribozyme into two molecules with each half binding to the substrate. Efficient, binary hammerhead ribozymes were pursued in a combinatorial approach using a 6-times 5 library, which was analysed concerning the best combinations, buffer conditions and fragment ratios.
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Affiliation(s)
- Janne K Christiansen
- Department of Biochemistry and Molecular Biology, The Nucleic Acid Center, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Peter JU, Alenina N, Bader M, Walther DJ. Development of antithrombotic miniribozymes that target peripheral tryptophan hydroxylase. Mol Cell Biochem 2006; 295:205-15. [PMID: 16924415 DOI: 10.1007/s11010-006-9290-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 07/24/2006] [Indexed: 01/01/2023]
Abstract
Serotonin is not only a neurotransmitter in the central nervous system, but also a ubiquitous hormone in the periphery involved in vasoconstriction and platelet function. Tryptophan hydroxylase is the rate-limiting enzyme in serotonin biosynthesis. By gene targeting, we have shown that serotonin is synthesized independently by two different tryptophan hydroxylase isoenzymes in peripheral tissues and neurons and identified a neuronal tryptophan hydroxylase isoform. Mice deficient in peripheral tryptophan hydroxylase (TPH1) and serotonin exhibit a reduced risk of thrombosis and thromboembolism. Therefore, we designed several antitph1 hammerhead miniribozymes and tested their cleavage activity against short synthetic Tph1 RNA substrates. In vitro cleavage studies demonstrated site-specific cleavage of Tph1 mRNA that was dependent on substrate/miniribozyme ratio and duration of exposure to miniribozyme. Interestingly, we detected different in vitro cleavage rates after we had cloned the miniribozymes into tRNA expression constructs, and found one with a high cleavage rate. We also demonstrated that this active tRNA-miniribozyme chimera is capable of selectively cleaving native Tph1 mRNA in vivo, with concomitant downregulation of the serotonin biosynthesis. Therefore, this Tph1-specific miniribozyme may provide a novel and effective form of gene therapy that may be applicable to a variety of thrombotic diseases.
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Affiliation(s)
- Jens-Uwe Peter
- Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195, Berlin, Germany
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Ng EWM, Shima DT, Calias P, Cunningham ET, Guyer DR, Adamis AP. Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat Rev Drug Discov 2006; 5:123-32. [PMID: 16518379 DOI: 10.1038/nrd1955] [Citation(s) in RCA: 1019] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers are oligonucleotide ligands that are selected for high-affinity binding to molecular targets. Pegaptanib sodium (Macugen; Eyetech Pharmaceuticals/Pfizer) is an RNA aptamer directed against vascular endothelial growth factor (VEGF)-165, the VEGF isoform primarily responsible for pathological ocular neovascularization and vascular permeability. After nearly a decade of preclinical development to optimize and characterize its biological effects, pegaptanib was shown in clinical trials to be effective in treating choroidal neovascularization associated with age-related macular degeneration. Pegaptanib therefore has the notable distinction of being the first aptamer therapeutic approved for use in humans, paving the way for future aptamer applications.
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Affiliation(s)
- Eugene W M Ng
- Eyetech Pharmaceuticals, Inc., 3 Times Square, 12th Floor, New York, New York 10036, USA
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Hendry P, McCall MJ, Lockett TJ. Influence of Helix Length on Cleavage Efficiency of Hammerhead Ribozymes. Aust J Chem 2005. [DOI: 10.1071/ch05196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cleavage rates of RNA substrates by trans-acting, hammerhead ribozymes are controlled by interactions between helices I and II. The interactions are affected by the relative lengths of these two double helices and by unpaired nucleotides protruding beyond helix I, either in the substrate or the ribozyme strand. Maximum cleavage rates are observed for ribozyme–substrate complexes with three or more base pairs in helix II and six or less base pairs in helix I. However, for these helix combinations, rates fall sharply with unpaired nucleotides at the end of helix I. Cleavage rates by ribozymes with one or two base pairs in helix II increase as helix I is lengthened, and are unaffected by unpaired nucleotides on the end. Since miniribozymes, with one base pair in helix II, efficiently cleave long RNA transcripts under physiological conditions, they represent the optimal design for the simple hammerheads for application in vivo.
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