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Cellular uptake and trafficking of antisense oligonucleotides. Nat Biotechnol 2017; 35:230-237. [PMID: 28244996 DOI: 10.1038/nbt.3779] [Citation(s) in RCA: 379] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/22/2016] [Indexed: 01/08/2023]
Abstract
Antisense oligonucleotides (ASOs) modified with phosphorothioate (PS) linkages and different 2' modifications can be used either as drugs (e.g., to treat homozygous familial hypercholesterolemia and spinal muscular atrophy) or as research tools to alter gene expression. PS-ASOs can enter cells without additional modification or formulation and can be designed to mediate sequence-specific cleavage of different types of RNA (including mRNA and non-coding RNA) targeted by endogenous RNase H1. Although PS-ASOs function in both the cytoplasm and nucleus, localization to different subcellular regions can affect their therapeutic potency. Cellular uptake and intracellular distribution of PS ASOs are mediated by protein interactions. The main proteins involved in these processes have been identified, and intracellular sites in which PS ASOs are active, or inactive, cataloged.
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2
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Alberini CM. The role of protein synthesis during the labile phases of memory: revisiting the skepticism. Neurobiol Learn Mem 2007; 89:234-46. [PMID: 17928243 DOI: 10.1016/j.nlm.2007.08.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 08/08/2007] [Indexed: 12/23/2022]
Abstract
Despite the fact that extensive evidence supports the view that phases of de novo protein synthesis are necessary for memory formation and maintenance, doubts are still raised. Skeptics generally argue that amnesia and the disruption of long-term synaptic plasticity are caused by "non-specific effects" of the reagents or approaches used to disrupt protein synthesis. This paper attempts to clarify some of these issues by reviewing, discussing and providing results addressing some of the major critiques that argue against the idea that de novo protein synthesis is necessary for the stabilization of long-term memory.
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Affiliation(s)
- Cristina M Alberini
- Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA.
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3
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Federici T, Boulis NM. Ribonucleic acid interference for neurological disorders: candidate diseases, potential targets, and current approaches. Neurosurgery 2007; 60:3-15; discussion 15-6. [PMID: 17228249 DOI: 10.1227/01.neu.0000249214.42461.a5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Ribonucleic acid (RNA) interference (RNAi) is a conserved evolutionary defense mechanism that is gaining utility for therapeutic application by modulating gene expression or silencing disease-causing genes. METHODS This strategy has recently achieved success in mammalian cells via synthetic small interfering RNA or short hairpin RNA expressed in vectors for gene delivery. The vector-based RNAi strategy has particular potential because of the possibility of targeted gene delivery, long-term gene expression, and the potential means of penetrating the blood-brain barrier. RESULTS RNAi-based approaches have been proposed for a variety of neurological disorders, including dominant genetic diseases, neurodegenerative diseases, malignant brain tumors, pain, and viral-induced encephalopathies. CONCLUSION This review summarizes the current approaches of the RNAi strategy for neurological disorders, focusing on potential targets for therapeutic intervention.
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Affiliation(s)
- Thais Federici
- Department of Neuroscience The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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4
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Chauhan NB, Siegel GJ. Antisense inhibition at the beta-secretase-site of beta-amyloid precursor protein reduces cerebral amyloid and acetyl cholinesterase activity in Tg2576. Neuroscience 2007; 146:143-51. [PMID: 17303345 PMCID: PMC1955231 DOI: 10.1016/j.neuroscience.2007.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 12/27/2006] [Accepted: 01/05/2007] [Indexed: 12/29/2022]
Abstract
Misprocessing of beta-amyloid precursor protein (APP) leading to the formation of elevated quantities of beta-amyloid peptide (Abeta), derived by a cleavage at the beta-secretase site (N-671/673aa) and by a cleavage at the gamma-secretase site (C-711/713aa) of APP, is considered a key event in the pathogenesis of Alzheimer disease (AD). Point mutations near the beta-secretase site in the human gene for APP, such as in the Swedish mutation-KM670/671NL, lead to a form of dominantly inherited AD. These mutations are known to promote beta-site cleavage and to increase levels of Abeta. Abeta has been shown previously to increase acetyl cholinesterase (AChE) activity in vitro. We wished to test whether translational blocking of APP-mRNA at the mutated beta-site by antisense (AS) oligodeoxynucleotides (ODNs) directed to the mutated site will reduce cerebral amyloid in the Swedish transgenic mouse model (Tg2576). Mice were injected i.c.v. with AS-ODNs directed at the mutated beta-site (AS-beta site) or with AS-ODNs directed at the normal gamma-site (AS-gamma site) of human APP-mRNA, and compared with procedural controls that received i.c.v. injections of sense ODNs at the beta-site (S-beta site), sense ODNs at the gamma-site (S-gamma site) or mismatched ODNs, and with untreated littermates (Lt) and untreated transgenic mice (Tgs). ODNs were injected into the 3rd ventricle once a week for 4 weeks. Brains were processed for enzyme-linked immunosorbent assay analysis of beta- and gamma-cleaved soluble Abeta40 (sAbeta40), beta- and gamma-cleaved soluble Abeta42 (sAbeta42) and alpha-cleaved soluble beta-amyloid precursor protein (sAPPalpha). The physiological relevance of AS ODNs was tested by evaluating the cerebral distribution of AChE before and after the treatment. AChE was found increased about fivefold in Tg cortex as compared with control brain. Results show that compared with untreated and procedural controls, AS-beta increased cerebral levels of sAPPalpha by 43% and reduced sAbeta40/42 by approximately 39%; while simultaneously reducing the cortical density of AChE by approximately fourfold in the treated Tg animals, almost to the level found in the control brain (all values P<0.0001, analysis of variance, unpaired two-tailed Student's t-test), while AS-gamma did not have any effect. These results indicate that AS directed to the mutated beta-site may be an effective approach to treat familial AD.
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Affiliation(s)
- Neelima B Chauhan
- Department of Anesthesiology, University of Illinois at Chicago 60612, and Neurology Service (127), Edward Hines, Jr., VA Hospital, Hines, IL 60614, USA.
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5
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Fichou Y, Férec C. The potential of oligonucleotides for therapeutic applications. Trends Biotechnol 2006; 24:563-70. [PMID: 17045686 DOI: 10.1016/j.tibtech.2006.10.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 08/21/2006] [Accepted: 10/03/2006] [Indexed: 12/15/2022]
Abstract
Viral-derived particles have been widely used and described in gene therapy clinical trials. Although substantial results have been achieved, major safety issues have also arisen. For more than a decade, oligonucleotides have been seen as an alternative to gene complementation by viral vectors or DNA plasmids, either to correct the genetic defect or to silence gene expression. The development of RNA interference has strengthened the potential of this approach. Recent clinical trials have also tested the ability of aptamer molecules and decoy oligonucleotides to sequestrate pathogenic proteins. Here, we review the potential of oligonucleotides in gene therapy, outline what has already been accomplished, and consider what remains to be done.
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Affiliation(s)
- Yann Fichou
- Inserm U613, Université de Bretagne Occidentale, 46 rue Félix Le Dantec, 29275 Brest Cedex, France
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6
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Abstract
Within the course of only the last few years, RNA interference (RNAi) has been established as a standard technology for investigation of protein function and target validation. The present review summarizes recent progress made in the application of RNAi in neurosciences with special emphasis on pain research. RNAi is a straightforward method to generate loss-of-function phenotypes for any gene of interest. In mammals, silencing is induced by small interfering RNAs (siRNAs), which have been shown to surpass traditional antisense molecules. Due to its high specificity, RNAi has the potential for subtype selective silencing of even closely related genes. One of the major challenges for in vivo investigations of RNAi remains efficient delivery of siRNA molecules to the relevant tissues and cells, particularly to the central nervous system. Various examples will be given to demonstrate that intrathecal application of siRNAs is a suitable approach to analyse the function of receptors or other proteins that are hypothesized to play an important role in pain signalling. Intensive efforts are currently ongoing to solve remaining problems such as the risk of off-target effects, the stability of siRNA molecules and their efficient delivery to the CNS. RNAi has thus demonstrated that it is an extremely valuable tool for the development of new analgesic drugs.
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Affiliation(s)
- Thomas Röhl
- Institute of Chemistry and Biochemistry, Free University Berlin, Germany
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Zhang Z, Weinschenk T, Guo K, Schluesener HJ. siRNA binding proteins of microglial cells: PKR is an unanticipated ligand. J Cell Biochem 2006; 97:1217-29. [PMID: 16315288 DOI: 10.1002/jcb.20716] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Small interfering RNA (siRNA), double-stranded RNA (dsRNA) 21-23 nucleotides (nt) long with two nt 3' overhangs, has been shown to mediate powerful sequence-specific gene silence in mammalian cells through RNA interference (RNAi). Due to its high efficiency and high specificity siRNA has been used as a powerful post genomic tool and a potent therapeutic candidate. However, there is still a lot to learn about the mobility of siRNA inside cells and the cellular factors that might interfere with the specificity and activity of siRNA. Microglia are the brain's effector cells of the innate immune system and suitable targets in the development of novel therapeutic strategies. Here, we show the cellular uptake and intracellular distribution of siRNA in murine microglial N9 cells. siRNA was internalized by microglial N9 cells without transfection reagent and mainly localized to the endosomes However, no significant gene silencing effects were observed. Its cellular uptake and cellular distribution pattern were similar with that of a same length single stranded DNA (ssDNA). Further, cellular binding proteins of siRNA were purified and identified by mass spectrometry. Negative control siRNA and siRNA targeted to beta-actin were used in this part of experiment. Most of the siRNA binding proteins for negative control siRNA and siRNA targeted to beta-actin were dsRNA-binding proteins, such as dsRNA-dependent protein kinase R (PKR). Furthermore, both control siRNA and siRNA targeted to beta-actin activated PKR in N9 cells, which suggest that siRNA might cause off-target effects through activation of PKR.
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Affiliation(s)
- Zhiren Zhang
- Institute of Brain Research, University of Tuebingen, Calwer Str. 3, D-72076 Tuebingen, Germany.
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8
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Silverman SK. In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res 2005; 33:6151-63. [PMID: 16286368 PMCID: PMC1283523 DOI: 10.1093/nar/gki930] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Over the last decade, many catalytically active DNA molecules (deoxyribozymes; DNA enzymes) have been identified by in vitro selection from random-sequence DNA pools. This article focuses on deoxyribozymes that cleave RNA substrates. The first DNA enzyme was reported in 1994 and cleaves an RNA linkage. Since that time, many other RNA-cleaving deoxyribozymes have been identified. Most but not all of these deoxyribozymes require a divalent metal ion cofactor such as Mg2+ to catalyze attack by a specific RNA 2′-hydroxyl group on the adjacent phosphodiester linkage, forming a 2′,3′-cyclic phosphate and a 5′-hydroxyl group. Several deoxyribozymes that cleave RNA have utility for in vitro RNA biochemistry. Some DNA enzymes have been applied in vivo to degrade mRNAs, and others have been engineered into sensors. The practical impact of RNA-cleaving deoxyribozymes should continue to increase as additional applications are developed.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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9
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Sim ACN, Luhur A, Tan TMC, Chow VTK, Poh CL. RNA interference against enterovirus 71 infection. Virology 2005; 341:72-9. [PMID: 16083932 DOI: 10.1016/j.virol.2005.06.047] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 06/13/2005] [Accepted: 06/20/2005] [Indexed: 01/30/2023]
Abstract
Enterovirus 71 (EV71) is a highly infectious major causative agent of hand, foot, and mouth disease (HFMD) which could lead to severe neurological complications. There is currently no effective therapy against EV71. In this study, RNA interference (RNAi) is employed as a therapeutic approach for specific viral inhibition. Various regions of the EV71 genome were targeted for inhibition by chemically synthesized siRNAs. Transfection of rhabdomyosarcoma (RD) cells with siRNA targeting the 3'UTR, 2C, 3C, or 3D region significantly alleviated cytopathic effects of EV71. The inhibitory effect was dosage-dependent with a corresponding decrease in viral RNA, viral proteins, and plaque formations by EV71. Viral inhibition of siRNA transfected RD cells was still evident after 48 h. In addition, no significant adverse off-target silencing effects were observed. These results demonstrated the potential and feasibility for the use of siRNA as an antiviral therapy for EV71 infections.
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Affiliation(s)
- Adrian Chong Nyi Sim
- Department of Microbiology, Faculty of Medicine, National University of Singapore, MD4A, 5 Science Drive 2, 117597, Singapore.
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Luo MC, Zhang DQ, Ma SW, Huang YY, Shuster SJ, Porreca F, Lai J. An efficient intrathecal delivery of small interfering RNA to the spinal cord and peripheral neurons. Mol Pain 2005; 1:29. [PMID: 16191203 PMCID: PMC1253531 DOI: 10.1186/1744-8069-1-29] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 09/28/2005] [Indexed: 12/29/2022] Open
Abstract
We have developed a highly effective method for in vivo gene silencing in the spinal cord and dorsal root ganglia (DRG) by a cationic lipid facilitated delivery of synthetic, small interfering RNA (siRNA). A siRNA to the delta opioid receptor (DOR), or a mismatch RNA, was mixed with the transfection reagent, i-Fect (vehicle), and delivered as repeated daily bolus doses (0.5 microg to 4 microg) via implanted intrathecal catheter to the lumbar spinal cord of rats. Twenty-four hours after the last injection, rats were tested for antinociception by the DOR selective agonist, [D-Ala(2), Glu(4)]deltorphin II (DELT), or the mu opioid receptor (MOR) selective agonist, [D-Ala(2), N-Me-Phe(4), Gly-ol(5)]enkephalin (DAMGO). Pretreatment with the siRNA, but not the mismatch RNA or vehicle alone, blocked DELT antinociception dose-dependently. The latter was concomitant with a reduction in the spinal immunoreactivity and receptor density of DOR, and in DOR transcripts in the lumbar DRG and spinal dorsal horn. Neither siRNA nor mismatch RNA pretreatment altered spinal immunoreactivity of MOR or antinociception by spinal DAMGO, and had no effect on the baseline thermal nociceptive threshold. The inhibition of function and expression of DOR by siRNA was reversed by 72 hr after the last RNA injection. The uptake of fluorescence-tagged siRNA was detected in both DRG and spinal cord. The low effective dose of siRNA/i-Fect complex reflects an efficient delivery of the siRNA to peripheral and spinal neurons, produced no behavioral signs of toxicity. This delivery method may be optimized for other gene targets.
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MESH Headings
- Animals
- Cell Line
- Ganglia, Spinal/cytology
- Ganglia, Spinal/drug effects
- Ganglia, Spinal/metabolism
- Gene Expression Regulation/drug effects
- Gene Knockdown Techniques
- Injections, Spinal
- Lumbar Vertebrae/cytology
- Lumbar Vertebrae/drug effects
- Lumbar Vertebrae/metabolism
- Naltrexone/analogs & derivatives
- Naltrexone/metabolism
- Neurons/metabolism
- Nociceptors/metabolism
- Oligopeptides/pharmacology
- Pain Measurement
- Peripheral Nervous System/cytology
- Peripheral Nervous System/metabolism
- Posterior Horn Cells/cytology
- Posterior Horn Cells/drug effects
- Posterior Horn Cells/metabolism
- Quinolinium Compounds/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/administration & dosage
- Rats
- Rats, Sprague-Dawley
- Receptors, Opioid, delta/genetics
- Receptors, Opioid, delta/metabolism
- Receptors, Opioid, mu/metabolism
- Spinal Cord/drug effects
- Spinal Cord/metabolism
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Affiliation(s)
- Miaw-Chyi Luo
- Department of Pharmacology, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA
| | - Dong-Qin Zhang
- Department of Pharmacology, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA
| | - Shou-Wu Ma
- Department of Pharmacology, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA
| | - Yuan-Yuan Huang
- Department of Pharmacology, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA
| | | | - Frank Porreca
- Department of Pharmacology, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA
| | - Josephine Lai
- Department of Pharmacology, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA
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11
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Akaneya Y, Jiang B, Tsumoto T. RNAi-Induced Gene Silencing by Local Electroporation in Targeting Brain Region. J Neurophysiol 2005; 93:594-602. [PMID: 15604463 DOI: 10.1152/jn.00161.2004] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genetic manipulation for “knockout” (KO) is a useful tool for characterizing a target gene. However, its shortcomings that need to be overcome hinder its easy and ready usage in ordinary laboratories. Here we describe a knockdown technique termed the RNA interference (RNAi)-induced gene silencing by local electroporation (RISLE). Small interfering RNA (siRNA) introduction by electroporation into a specific brain region results in a marked reduction in the expression levels of both the mRNA and protein of the target genes such as GluR2 and Cox-1 without affecting the expression levels of proteins other than that of the target protein or causing pathological changes in the target tissues. The effective electrical pulses are relatively weak, consisting of a strong short pulse and a weak long pulse applied in tandem. RISLE can knock down a gene at the target region, for example, the visual cortex and the CA1 region of the hippocampus, without affecting other regions. Moreover, the knockdown models constructed using this technique have physiological functions consistent with previous findings, that is, glutamate release from presynaptic sites, long-term potentiation (LTP), and long-term depression (LTD). These results suggest that this technique is applicable and characterized by spatial flexibility, temporal accessibility, and ease of establishment of knockdown models. The intactness of the tissue subjected to RISLE is due to the weak electrical pulses applied and the limited area of gene silencing. Thus RISLE may be applicable to disease therapy in the future.
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Affiliation(s)
- Yukio Akaneya
- Division of Neurophysiology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan.
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Bantounas I, Glover CPJ, Kelly S, Iseki S, Phylactou LA, Uney JB. Assessing adenoviral hammerhead ribozyme and small hairpin RNA cassettes in neurons: Inhibition of endogenous caspase-3 activity and protection from apoptotic cell death. J Neurosci Res 2005; 79:661-9. [PMID: 15657876 DOI: 10.1002/jnr.20389] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Antisense technology, including ribozyme and small interfering RNA, is being developed to mediate the down-regulation of specific intracellular genes. It was observed in this study that both antiluciferase ribozymes and short hairpin RNAs (shRNAs) could significantly reduce the activity of exogenously expressed luciferase in primary hippocampal neurons in a viral titer-dependent manner. shRNAs were more effective gene-silencing agents than ribozymes, although they exhibited some nonspecific gene-silencing effects at high viral titers. We also attempted to increase ribozyme efficacy by using a woodchuck hepatitis posttranscriptional regulatory element (WPRE) in the ribozyme expression cassette. The results showed that adenoviral vectors encoding specific ribozymes could silence the cellular expression of luciferase and endogenous procaspase-3 significantly. Furthermore, the antiprocaspase-3 ribozyme was shown to inhibit staurosporine-mediated cell death. The addition of a WPRE did not, however, increase or decrease ribozyme activity. As far as we are aware, this is the first example of adenovirally mediated delivery of hammerhead ribozymes being used to manipulate gene expression in primary neurons. The results therefore suggest that hammerhead ribozymes may be useful tools for studying neuronal gene function and have potential as therapeutic agents to treat CNS diseases.
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Affiliation(s)
- Ioannis Bantounas
- The Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
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Godfray J, Fraser A, Page D, Barnard E, Estibeiro P. The use of nucleic acid tools for target validation in central nervous system therapy. DRUG DISCOVERY TODAY. TECHNOLOGIES 2004; 1:85-91. [PMID: 24981376 DOI: 10.1016/j.ddtec.2004.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The main challenge facing target validation today comes from the ongoing genomics revolution, which is generating an unprecedented number of potential targets. Existing technologies, such as mouse knockouts, are struggling to provide the throughput now required. Nucleic acid tools including antisense, RNA interference, ribozymes and aptamers offer a potentially higher throughput means of manipulating gene expression and thus validating targets in complex biological systems such as the central nervous system.
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Affiliation(s)
- Jenny Godfray
- ExpressOn BioSystems Ltd., The Logan Building, Roslin BioCentre, Roslin, Midlothian EH25 9TT, UK. http://www.expresson.co.uk
| | - Adrian Fraser
- ExpressOn BioSystems Ltd., The Logan Building, Roslin BioCentre, Roslin, Midlothian EH25 9TT, UK
| | - David Page
- ExpressOn BioSystems Ltd., The Logan Building, Roslin BioCentre, Roslin, Midlothian EH25 9TT, UK
| | - Eleanor Barnard
- ExpressOn BioSystems Ltd., The Logan Building, Roslin BioCentre, Roslin, Midlothian EH25 9TT, UK
| | - Peter Estibeiro
- ExpressOn BioSystems Ltd., The Logan Building, Roslin BioCentre, Roslin, Midlothian EH25 9TT, UK
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