201
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Chiu Y, Ouyang P. Loss of Pnn expression attenuates expression levels of SR family splicing factors and modulates alternative pre-mRNA splicing in vivo. Biochem Biophys Res Commun 2006; 341:663-71. [PMID: 16430868 DOI: 10.1016/j.bbrc.2005.12.218] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 12/31/2005] [Indexed: 10/25/2022]
Abstract
SR and SR-related proteins have been implicated as trans-acting factors that play an important role in splice selection and are involved at specific stages of spliceosome formation. A well-established property of SR protein splicing factors is their ability to influence selection of alternative splice sites in a concentration-dependent manner. Identification of molecules that regulate SR family protein expression is therefore of vital importance in RNA biology. Here we report that depletion of Pnn expression, a SR-related protein with functions involved in pre-mRNA splicing and mRNA export, induces reduced expression of a subset of cellular proteins, especially that of SR family proteins, including SC35, SRm300, SRp55, and SRp40, but not that of other nuclear proteins, such as p53, Mdm2, and ki67. Knocking down Pnn expression was achieved in vitro by siRNA transfection. Expression levels of SR and SR-related proteins in Pnn-depleted cells as compared to those in control cells were evaluated by immunofluorescent staining and Western blot with specific antibodies. In addition, we also demonstrate that loss of Pnn expression could modulate splice site selection of model reporter gene in vivo. Our finding is significant in terms of regulation of SR protein cellular concentration because it reveals that Pnn may play a general role in the control of the cellular amount of family SR proteins through down-regulation of its own expression, thereby providing us with a better understanding of the cellular mechanism by which Pnn fulfills its biological function.
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Affiliation(s)
- Yali Chiu
- Epithelial Biology Laboratory, Department of Anatomy, Chang Gung University Medical College, Taoyuan 333, Taiwan, ROC
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202
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Sang N, Zhang J, Marcheselli V, Bazan NG, Chen C. Postsynaptically synthesized prostaglandin E2 (PGE2) modulates hippocampal synaptic transmission via a presynaptic PGE2 EP2 receptor. J Neurosci 2006; 25:9858-70. [PMID: 16251433 PMCID: PMC6725559 DOI: 10.1523/jneurosci.2392-05.2005] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Increasing evidence suggests that cyclooxygenase-2 (COX-2) is involved in synaptic transmission and plasticity, and prostaglandin E2 (PGE2) is a key molecule in COX-2-meduated synaptic modification. However, the precise mechanisms, in particular, which subtypes of PGE2 receptors (EPs) mediate the PGE2-induced synaptic response, are not clear. Recently, we demonstrated that EPs are expressed heterogeneously in the hippocampus, and EP2/4 are mainly expressed in presynaptic terminals. Here, we report that PGE2 increased synaptic stimulus-evoked amplitudes of EPSPs in hippocampal slices and frequency of miniature EPSCs (mEPSCs) in hippocampal neurons in culture. These actions were mimicked by an EP2 agonist and attenuated by protein kinase A inhibitors. Decrease of EP2 expression through silencing the EP2 gene eliminated PGE2-induced increase of the frequency of mEPSCs. COX-2 and microsomal PGE synthase-1 (mPGES-1) and mPGES-2 are present in postsynaptic dendritic spines, because they are colocalized with PSD-95 (postsynaptic density-95), a postsynaptic marker. In addition, the frequency of mEPSCs was enhanced in neurons pretreated with interleukin-1beta or lipopolysaccharide, which elevated expression of COX-2 and mPGES-1 and produced PGE2, and this enhancement was inhibited by a COX-2 inhibitor that inhibited production of PGE2. Our results suggest that PGE2 synthesized by postsynaptically localized COX-2 functions as a retrograde messenger in hippocampal synaptic signaling via a presynaptic EP2 receptor.
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Affiliation(s)
- Nan Sang
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA
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203
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Abstract
Small interfering RNAs (siRNAs) are as effective as long double-stranded RNAs (dsRNAs) at targeting and silencing genes by RNA interference (RNAi). siRNAs are widely used for assessing gene function in cultured mammalian cells or early developing vertebrate embryos. They are also promising reagents for developing gene-specific therapeutics. The specific inhibition of viral replication is particularly well suited to RNAi, as several stages of the viral life cycle and many viral and cellular genes can be targeted. The future success of this approach will depend on the recent advances in siRNA-based clinical trials.
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Affiliation(s)
- N Miyano-Kurosaki
- Department of Life and Environmental Sciences and High Technology Research Center, Chiba Institute of Technology, 2-17-1 Narashino, Tsudanuma, 275-0016 Chiba, Japan
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204
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Erdmann V, Barciszewski J, Brosius J. Antiviral Applications of RNAi. Handb Exp Pharmacol 2006:105-16. [PMID: 16594613 PMCID: PMC7122589 DOI: 10.1007/3-540-27262-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
RNA interference is a natural mechanism by which small interfering (si)RNA operates to specifically and potently down-regulate the expression of a target gene. This down-regulation has been thought to predominantly function at the level of the messenger (m)RNA, post-transcriptional gene silencing (PTGS). Recently, the discovery that siRNAs can function to suppress a gene's expression at the level of transcription, i.e., transcriptional gene silencing (TGS), has created a major paradigm shift in mammalian RNAi. These recent findings significantly broaden the role RNA, specifically siRNAs and potentially microRNAs, plays in the regulation of gene expression as well as the breadth of potential siRNA target sites. Indeed, the specificity and simplicity of design makes the use of siRNAs to target and suppress virtually any gene or gene promoter of interest a realized technology. Furthermore, since siRNAs are a small nucleic acid reagent, they are unlikely to elicit an immune response, making them a theoretically good future therapeutic. This review will focus on the development, delivery, and potential therapeutic use of antiviral siRNAs in treating viral infections as well as emerging viral threats.
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Affiliation(s)
- Volker Erdmann
- Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Scienes, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jürgen Brosius
- Institute of Experimental Pathology, Molecular Neurobiology (ZMBE), University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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205
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Kasim V, Taira K, Miyagishi M. Screening of siRNA target sequences by using fragmentized DNA. J Gene Med 2006; 8:782-91. [PMID: 16532512 DOI: 10.1002/jgm.900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) has become a powerful tool in silencing target genes in various organisms. In mammals, RNAi can be induced by using short interfering RNA (siRNA). The efficacy of inducing RNAi in mammalian cells by using siRNA depends very much on the selection of the target sequences. METHODS We developed an siRNA target sequence selection system by first constructing parallel-type siRNA expression vector libraries carrying siRNA expression fragments originating from fragmentized target genes, and then using a group selection system. For a model system, we constructed parallel-type siRNA expression vector libraries against DsRed and GFP reporter genes. RESULTS We carried out the first screening of groups containing more than 100 random siRNA expression plasmids in total for each target gene, and successfully obtained target sequences with very strong efficacy. Furthermore, we also obtained some clones that express dsRNAs of various lengths that might induce cytotoxicity. CONCLUSIONS This system should allow us to perform screening for powerful target sequences, by including all possible target sequences for any gene, even without knowing the whole sequence of the target gene in advance. At the same time, target sequences that should be avoided due to cytotoxicity can be identified.
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Affiliation(s)
- Vivi Kasim
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Tokyo 113-8656, Japan
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206
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Iyer RP, Padmanabhan S, Coughlin JE. Microwave-assisted functionalization of solid supports for rapid loading of nucleosides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2006; Chapter 3:Unit3.13. [PMID: 18428955 DOI: 10.1002/0471142700.nc0313s23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Ultra-fast and efficient functionalization of solid supports such as controlled-pore glass (CPG), amino methyl polystyrene, and Tentagel has been achieved using microwave-assisted procedures. Both amino- and carboxy-terminated supports are easily prepared within minutes, in a reproducible manner, using microwave-assisted methodologies. The resulting functionalized supports are efficiently coupled to nucleosides using dimethylformamide as a solvent in conjunction with a specially designed reactor and workstation called LOTUS. Using these improved protocols, CPG with loadings of 75 to 85 micromol/g can be prepared on a large scale within 3 to 4 days starting from native CPG, as opposed to traditional methods that require 10 to 15 days to achieve the same objective. In addition, the methods described here can potentially be employed for rapid functionalization of other solid matrices such as beads, slides, and pins for applications in microarrays or combinatorial chemistry.
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207
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Takasaki S, Konagaya A. Comparative analyses for selecting effective siRNA sequences. CHEM-BIO INFORMATICS JOURNAL 2006. [DOI: 10.1273/cbij.6.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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208
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Abstract
Engineered biological systems have been used to manipulate information, construct materials, process chemicals, produce energy, provide food, and help maintain or enhance human health and our environment. Unfortunately, our ability to quickly and reliably engineer biological systems that behave as expected remains quite limited. Foundational technologies that make routine the engineering of biology are needed. Vibrant, open research communities and strategic leadership are necessary to ensure that the development and application of biological technologies remains overwhelmingly constructive.
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Affiliation(s)
- Drew Endy
- Division of Biological Engineering, Massachusetts Institute of Technology, Room 68-580, Koch Biology Building, 31 Ames Street, Cambridge, Massachusetts 02139, USA.
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209
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Carmona S, Ely A, Crowther C, Moolla N, Salazar FH, Marion PL, Ferry N, Weinberg MS, Arbuthnot P. Effective inhibition of HBV replication in vivo by anti-HBx short hairpin RNAs. Mol Ther 2005; 13:411-21. [PMID: 16337206 DOI: 10.1016/j.ymthe.2005.10.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 10/08/2005] [Accepted: 10/27/2005] [Indexed: 01/29/2023] Open
Abstract
Exploiting the RNA interference pathway has shown promise for developing novel and effective treatment of hepatitis B virus (HBV) infection. To advance this approach, we analyzed the antiviral efficacy of a panel of 10 Pol III U6 promoter-encoded short hairpin RNAs (shRNAs) that target conserved sequences of the oncogenic HBx open reading frame. To facilitate intracellular processing, the shRNAs included mismatches in the 25-bp stem region and a terminal loop of miRNA-23. Two shRNAs (shRNA 5 and shRNA 6) showed knockdown of HBV markers by 80-100% in transfected hepatocytes and also in a murine hydrodynamic injection model of HBV replication. Intracellular processing of hairpin RNA with the intended strand bias correlated with antiviral efficacy. Moreover, markers of HBV replication were inhibited without inducing genes associated with the nonspecific interferon response. To assess the antiviral efficacy of the shRNAs in a context that is similar to natural HBV infection, shRNA-encoding cassettes were tested against the virus in a HBV transgenic murine model. When delivered using recombinant adenovirus vectors, U6 shRNA 5 and U6 shRNA 6 mediated significant HBV knockdown. Collectively, these observations indicate that U6 shRNA 5 and U6 shRNA 6 are promising candidates for therapy of chronic HBV infection.
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Affiliation(s)
- Sergio Carmona
- Hepatitis B Virus Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Wits, South Africa
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210
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Li YC, Kong LH, Cheng BZ, Li KS. Construction of influenza virus siRNA expression vectors and their inhibitory effects on multiplication of influenza virus. Avian Dis 2005; 49:562-73. [PMID: 16405000 DOI: 10.1637/7365-041205r2.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three plasmid constructs were prepared that express small interfering RNAs (siRNAs) targeted to sequences encoding the ribonucleoprotein member, nucleoprotein (NP) and/or PA, of influenza virus genome. The antiviral properties of siRNAs against the H5N1 strain of influenza virus were studied by evaluating their capacity to silence expression of target genes as well as their effect on influenza virus-induced apoptosis in Madin-Darby canine kidney cells, chicken embryo fibroblast cells, and embryonated chicken eggs in a transient replication model. The results demonstrated that all three siRNAs expressing plasmids efficiently transcribed the short hairpin RNAs and inhibited expression of the NP or PA proteins measured by northern blot and western blot analyses, respectively, in the transfected cells. We also found that the integrated siRNA expression plasmid pEGFP/NP+PA, which we constructed for the first time to synchronously target NP and PA segments of the influenza virus genome, could more efficiently inhibit synthesis of influenza virus detected by cytopathogenic effects, hemagglutinin, and plaque-forming unit assays in the transfected cells. Furthermore, the integrated siRNA expression plasmid pEGFP/NP+PA could remarkably interrupt the cellular apoptotic course caused by influenza virus, which protected infected cells from apoptotic damage. In contrast, a control siRNA expression plasmid, pEGFP/HK, could neither inhibit the protein expression and production of influenza virus nor interrupt the cell apoptotic course mediated by influenza virus. These results demonstrate that RNA interference (RNAi) can be used to inhibit protein expression and replication of influenza virus and that RNAi treatment holds potential as a new approach to prevent avian influenza.
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Affiliation(s)
- Yao-Chen Li
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou Guangdong 515031, China
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211
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Yang F, Zhang Y, Cao YL, Wang SH, Liu L. Establishment and utilization of a tetracycline-controlled inducible RNA interfering system to repress gene expression in chronic myelogenous leukemia cells. Acta Biochim Biophys Sin (Shanghai) 2005; 37:851-6. [PMID: 16331330 DOI: 10.1111/j.1745-7270.2005.00112.x] [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: 11/29/2022] Open
Abstract
RNA interference (RNAi), a posttranscriptional gene silencing process mediated by small double-stranded RNA specifically complementary to the targeted transcript, has been used extensively in the development of novel therapeutic approaches against various human diseases including chronic myelogenous leukemia (CML). Here, we report the successful construction of a tetracycline-controlled siRNA in CML cell line K562. A K562 cell line stably expressing the reverse tetracycline-controlled transactivator (rtTA) was constructed. A tetracycline responsive element (TRE) was integrated into the RNA polymerase III promoter region of pBS/U6 that was used to drive specific siRNA to target the novel cytokine receptor-like factor 3 (CRLF3) gene. The results show that rtTA was able to recognize the TRE to prevent siRNA-mediated exogenous and endogenous CRLF3 gene repressions. Moreover, CRLF3-siRNA mediated gene repression could be induced in a dose-dependent manner in the presence of doxycycline. Thus, the inducible siRNAi system in K562 cells might be useful for the study of RNAi-mediated therapeutic approaches against CML.
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MESH Headings
- Base Sequence
- Gene Expression Regulation
- Gene Targeting
- Genetic Vectors
- Humans
- K562 Cells
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA Interference
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Small Nuclear
- Receptors, Cytokine/genetics
- Response Elements
- Tetracyclines/pharmacology
- Trans-Activators
- Transfection
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Affiliation(s)
- Fan Yang
- Department of Microbiology and Etiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
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212
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Ge G, Wong GW, Luo B. Prediction of siRNA knockdown efficiency using artificial neural network models. Biochem Biophys Res Commun 2005; 336:723-8. [PMID: 16153609 DOI: 10.1016/j.bbrc.2005.08.147] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 08/03/2005] [Indexed: 11/29/2022]
Abstract
Selective knockdown of gene expression by short interference RNAs (siRNAs) has allowed rapid validation of gene functions and made possible a high throughput, genome scale approach to interrogate gene function. However, randomly designed siRNAs display different knockdown efficiencies of target genes. Hence, various prediction algorithms based on siRNA functionality have recently been constructed to increase the likelihood of selecting effective siRNAs, thereby reducing the experimental cost. Toward this end, we have trained three Back-propagation and Bayesian neural network models, previously not used in this context, to predict the knockdown efficiencies of 180 experimentally verified siRNAs on their corresponding target genes. Using our input coding based primarily on RNA structure thermodynamic parameters and cross-validation method, we showed that our neural network models outperformed most other methods and are comparable to the best predicting algorithm thus far published. Furthermore, our neural network models correctly classified 74% of all siRNAs into different efficiency categories; with a correlation coefficient of 0.43 and receiver operating characteristic curve score of 0.78, thus highlighting the potential utility of this method to complement other existing siRNA classification and prediction schemes.
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Affiliation(s)
- Guangtao Ge
- Department of Computer Science, Tufts University, 161 College Avenue, Medford, MA 02155, USA.
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213
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Hemmrich K, Kröncke KD, Suschek CV, Kolb-Bachofen V. What sense lies in antisense inhibition of inducible nitric oxide synthase expression? Nitric Oxide 2005; 12:183-99. [PMID: 15894496 DOI: 10.1016/j.niox.2005.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2004] [Revised: 03/10/2005] [Accepted: 04/04/2005] [Indexed: 01/21/2023]
Abstract
The impact of nitric oxide (NO) synthesized after activation by proinflammatory cytokines and/or bacterial products by an inducible NO synthase (iNOS) is still contradictory. Expression of iNOS in inflammatory reactions is often found predominantly in cells of epithelial origin, and in these cases NO may serve as a protective agent limiting pathogen spreading, downregulating local inflammatory reactions by inducing production of Th2-like responses in a classical feedback circle, or limiting tissue damage during stress conditions. However, an abundant amount of data on chronic human disorders with predominant proinflammatory Th1-like reactions points to a destructive role of iNOS activity calling for a specific inhibition. Various methods to inhibit iNOS have been established to elucidate a protective versus a destructive role of NO during various stresses. In this review, we focus on antisense (AS)-mediated gene knock-down as a relatively new method to inhibit NO production and summarize the techniques applied and their successes. At least in theory, it provides a specific, rapid, and potentially high-throughput method for inhibiting gene expression and function. We here discuss the opportunities of iNOS-directed AS-ODN, and extensively deal with limitations and experimental problems.
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Affiliation(s)
- Karsten Hemmrich
- Research Group Immunobiology, MED-Heinrich-Heine-University of Düsseldorf, Gebäude 23.12, Postfach 10 10 07, D-40001 Düsseldorf, Germany.
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214
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Coma S, Noe V, Lavarino C, Adán J, Rivas M, López-Matas M, Pagan R, Mitjans F, Vilaró S, Piulats J, Ciudad CJ. Use of siRNAs and antisense oligonucleotides against survivin RNA to inhibit steps leading to tumor angiogenesis. Oligonucleotides 2005; 14:100-13. [PMID: 15294074 DOI: 10.1089/1545457041526290] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The antiapoptotic protein survivin is an attractive target in cancer therapy because it is expressed differently in tumors and normal tissues and it is potentially required for cancer cells to remain viable. Given that survivin is also overexpressed in endothelial cells (ECs) of newly formed blood vessels found in tumors, its RNA targeting might compromise EC viability and interfere with tumor angiogenesis. We used two antisense strategies against survivin expression, antisense oligonucleotides (aODN) and small interfering RNA (siRNA), to study in ECs the contribution of survivin in various steps leading to tumor angiogenesis. A 21-mer phosphorothioate aODN and two siRNA oligonucleotides against survivin mRNA were designed to downregulate survivin expression. Survivin targeting caused (1) a strong growth-inhibitory effect, (2) a 4-fold increase in apoptosis, (3) an accumulation of cells in the S phase and a decrease in G2/M phase, (4) a dose-dependent inhibition of EC migration on Vitronectin, and (5) a decrease in capillary formation. Control oligonucleotides, an unrelated oligonucleotide, and one with four mismatches, had no significant effect. All these results show that survivin is a suitable target in cancer therapy because its inhibition in EC causes both a proapoptotic effect and an interruption of tumor angiogenesis. The two strategies used, classic aODN and siRNA technology, were very effective. Moreover, the latter can be used in the low nanomolar range, thus increasing the sensitivity of the treatment.
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Affiliation(s)
- Sílvia Coma
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Barcelona, Spain
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215
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Liao H, Wang JH. Biomembrane-permeable and Ribonuclease-resistant siRNA with enhanced activity. Oligonucleotides 2005; 15:196-205. [PMID: 16201907 DOI: 10.1089/oli.2005.15.196] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Small interfering RNAs (siRNA) could be the ideal inhibitor of specific gene expression if they could be delivered efficiently to their targets. Although siRNAs cannot by themselves cross cell membranes, they can enter cells with the help of transfection reagents via facilitated transport. Inside cells, however, they can still be hydrolyzed by cytoplasmic RNases before reaching their target. Here we show that poly-2'- O-(2,4-dinitrophenyl)-siRNA (DNP-siRNA) can by itself diffuse into mammalian cells and stay in the cells for several days, with no detectable degradation. Using the DNP-RNA targeting to the insulin-like growth factor receptor (IGF-IR) as an example, we demonstrate that the efficacy of this DNP-siRNA for inhibiting the growth of three different types of tumor cells is several-fold higher than that of the corresponding native siRNA. Similar results were obtained from Western blotting assay. As expected, the control siRNAs with mismatched, scrambled, and reverse sequences are all inactive. These results illustrate that both the biomembrane permeability and intracellular stability of siRNA can be greatly improved by DNP derivatization without loss of its sequence specificity.
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MESH Headings
- 2,4-Dinitrophenol/chemistry
- Base Sequence
- Biological Transport
- Blotting, Western
- Cell Culture Techniques
- Cell Line, Tumor
- Cell Membrane Permeability/drug effects
- Cell Proliferation/drug effects
- Diffusion
- Humans
- Hydrolysis/drug effects
- In Situ Hybridization
- Lipid Metabolism
- Lipids
- Molecular Sequence Data
- Mutation
- Oligonucleotides, Antisense/chemistry
- Polymers/chemistry
- RNA, Double-Stranded/pharmacology
- RNA, Small Interfering/chemical synthesis
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Small Interfering/pharmacology
- Receptors, Somatomedin/metabolism
- Ribonucleases/metabolism
- Time Factors
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Affiliation(s)
- Hongtao Liao
- Bioenergetics Laboratory, Natural Sciences Complex, University at Buffalo, Buffalo, NY 14260-3000, USA
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216
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Choi I, Cho BR, Kim D, Miyagawa S, Kubo T, Kim JY, Park CG, Hwang WS, Lee JS, Ahn C. Choice of the adequate detection time for the accurate evaluation of the efficiency of siRNA-induced gene silencing. J Biotechnol 2005; 120:251-61. [PMID: 16095743 DOI: 10.1016/j.jbiotec.2005.06.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 06/15/2005] [Accepted: 06/20/2005] [Indexed: 11/25/2022]
Abstract
RNA interference (RNAi) mediated by small interfering RNA (siRNA) has become a popular tool of examining the function of various genes. However, many studies have failed to identify any inhibitory effect of the siRNAs on the expression of the target gene, even though the siRNA being tested had been designed sequence-specifically. In order to determine if this failure is due to the incorrect choice of observation time rather than that of the target site of the gene of interest, this study examined the RNAi efficiency of a vector-driven siRNA targeting two different reporter proteins, EGFP and d2EGFP, whose targeted sequences were identical but the half-lives within the cells differed remarkably from each other (>24h versus 2h), during the time course after transfection. The EGFP expression levels in both cells were reduced in time-dependent manner but the reduction patterns were quite different from each other. The RNAi efficiency varied among the different observation time points and the time required for the maximum RNAi efficiency was proportional to the half-life of the target protein. Stable knocked down cell lines for EGFP expression were then established and the reduced EGFP expression levels in these cell lines were retained for a long period. These results suggest that the choice of an adequate observation time or the establishment of stable knocked down cells by antibiotic selection might be required for making an accurate evaluation of the RNAi effect on the target protein possessing a long half-life.
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Affiliation(s)
- Inho Choi
- Laboratory of Immunology, Transplantation Research Institute and Clinical Research Institute, Seoul National University Hospital, Seoul 110-744, Republic of Korea
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217
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Bradley SP, Rastellini C, da Costa MA, Kowalik TF, Bloomenthal AB, Brown M, Cicalese L, Basadonna GP, Uknis ME. Gene silencing in the endocrine pancreas mediated by short-interfering RNA. Pancreas 2005; 31:373-9. [PMID: 16258373 DOI: 10.1097/01.mpa.0000179730.69081.64] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES RNA interference as mediated by short-interfering RNA (siRNA) offers a nonviral means to silence genes in tissue; however, few data exist about gene therapy using siRNA in pancreas tissue. To determine if siRNA treatment could silence an endogenous gene in pancreatic islets, we developed a murine model using the endocrine pancreas. METHODS The insulin 2 (Ins2) gene was targeted with siRNA, and quantitative RT-PCR, fluorescent microscopy, and FACS were used to measure transcript levels and siRNA cellular uptake and transfection efficiency. Isolated pancreatic islets were transfected with siRNA in vitro using a liposomal delivery method in a dose titration (50-400 nM) or pooled from BALB/c mice having received siRNA (100 microg) via hydrodynamic tail vein injection. RESULTS The Ins2 transcript level was significantly reduced by 55% in vitro with FACS data showing a transfection efficiency over 45% with the 400 nM concentration. In vivo delivery of siRNA to pancreatic islets revealed a 33% reduction in Ins2 mRNA levels, although siRNA was able to be detected in 19% of isolated islet cells. CONCLUSION We have successfully used RNA interference to silence an endogenous tissue-specific gene (Ins2) in pancreatic islets when transfected in vitro or administered in vivo.
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Affiliation(s)
- Sean P Bradley
- Department of Surgery, Division of Transplantation, University of Massachusetts Medical School, Worcester, MA 01605, USA
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218
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Li L, Lin X, Staver M, Shoemaker A, Semizarov D, Fesik SW, Shen Y. Evaluating hypoxia-inducible factor-1alpha as a cancer therapeutic target via inducible RNA interference in vivo. Cancer Res 2005; 65:7249-58. [PMID: 16103076 DOI: 10.1158/0008-5472.can-04-4426] [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: 02/07/2023]
Abstract
Validating potential targets is an important step in the drug discovery process. In this study, we tested the feasibility of using inducible RNA interference (RNAi) in vivo to obtain an unbiased evaluation on the efficacy of inhibiting hypoxia-inducible factor-1alpha (HIF-1alpha) in established tumors. We showed that HIF-1alpha inhibition resulted in transient tumor stasis or tumor regression, and inhibiting HIF-1alpha in early-stage tumors was found to be more efficacious than inhibiting HIF-1alpha in more established tumors. A differential requirement of HIF-1alpha for tumor growth was also observed among different tumor types. Examination of tumors resistant to HIF-1alpha inhibition suggested that the resistance might result from a less hypoxic tumor environment and the level of HIF-1alpha expression in tumors may be a useful marker for predicting tumor response to HIF-1 inhibition. This study shows that inducible RNAi is a versatile tool for evaluating cancer targets in vivo. In addition to broad implications on in vivo validation of cancer targets, results from this study will also be instructive for practical applications of HIF-1-based cancer therapeutics.
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Affiliation(s)
- Leiming Li
- Cancer Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, USA
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219
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Cengel KA, McKenna WG. Molecular targets for altering radiosensitivity: lessons from Ras as a pre-clinical and clinical model. Crit Rev Oncol Hematol 2005; 55:103-16. [PMID: 16006139 DOI: 10.1016/j.critrevonc.2005.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Revised: 01/01/2005] [Accepted: 02/03/2005] [Indexed: 11/19/2022] Open
Abstract
Ras activation has been correlated with malignant and metastatic cancer phenotypes and poor prognosis for cancer patients. In the preclinical setting, Ras activation by mutation or EGFR amplification results in increased clonogenic cell survival and decreased tumor growth delay following irradiation. Activation of the Ras pathway has also been associated with increased risk of local failure and decreased overall survival in patients receiving radiotherapy. Prenyltransferase inhibitors target the post-translational processing of Ras and have been shown to increase the radiosensitivity of human cancer cell lines. In the clinical setting, these inhibitors have been used with concurrent radiotherapy in a small number of phase I clinical trials with acceptable toxicity. Therefore, inhibiting Ras activation represents a promising molecular approach for radiosensitization in cancer therapy.
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Affiliation(s)
- Keith A Cengel
- Department of Radiation Oncology, University of Pennsylvania, 3400 Spruce Street, 2 Donner, Philadelphia, PA 19104, USA
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220
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Berger EM, Dubrovsky EB, Appleby L, Dubrovskaya V. Inhibition of micro-RNA-induced RNA silencing by 2'-o-methyl oligonucleotides in Drosophila S2 cells. In Vitro Cell Dev Biol Anim 2005; 41:12-8. [PMID: 15926855 DOI: 10.1290/040902.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
More than 90 different micro-ribonucleic acid (miRNA) encoding genes have been identified in Drosophila, yet the function of only two of these, bantam and DmiR-14, has been elucidated. In an effort to develop a general strategy for the analysis of miRNA function in Drosophila, two procedures were developed, in a Schneider line 2 cell culture system, which may be adapted to that end. First, we show that endogenous miRNAs can partially inhibit the expression of a transiently transfected reporter gene that has been modified to contain sequences complementary to that miRNA in the 3' UTR of a target messenger RNA (mRNA). Inhibition occurs by RNA interference (RNAi), which involves mRNA degradation. Second, we demonstrate that this miRNA-induced RNAi can be partially rescued with 2'-O-methyl oligonucleotides that contain sequences complementary to the cognate miRNA. We discuss how these techniques may be used, in vivo, both for localizing the tissue distribution of endogenous miRNAs during Drosophila development and identifying phenotypes associated with a loss of miRNA function.
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Affiliation(s)
- Edward M Berger
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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221
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Chen F, Guo Q, Yang Y, Song H, Wen T. Inhibition of AF116909 gene expression enhances the differentiation of neural stem cells. Neurol Res 2005; 27:557-61. [PMID: 15978185 DOI: 10.1179/016164105x25162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
OBJECTIVES Neural stem cells (NSCs) are self-renewed, pluripotent cells that can differentiate into neurons, astrocytes and oligodendrocytes. Such multipotency that allows production of specific types of nerve cells for basic research and therapeutic purposes depends on how these cells are directed in their differentiation. Here, we investigate the function of the AF116909 gene in the differentiation of NSC. METHODS NSC culture was isolated from the striatum corpora of embryonic brain tissues in a 14-day pregnant rat. A constructed RNAi (RNA-mediated interference) vector was transfected to knock down the expression of this gene. Afterwards, RT-PCT was applied to examine the presence of endogenous AF116909 mRNA and the effect of RNA interference. RESULTS After the knockdown of this gene, we detected that the differentiation rate of cells was enhanced to 80% on the 11th day in comparison with 12% in the control cells transfected with the expression vector alone. DISCUSSION These findings suggest that AF116909 functions in inhibiting the differentiation of NSCs, and AF116909 gene-targeting by RNAi provides a useful method to study the differentiation mechanisms of NSCs.
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Affiliation(s)
- Fuxue Chen
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, P R China.
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222
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Detwiller KY, Fernando NT, Segal NH, Ryeom SW, D'Amore PA, Yoon SS. Analysis of hypoxia-related gene expression in sarcomas and effect of hypoxia on RNA interference of vascular endothelial cell growth factor A. Cancer Res 2005; 65:5881-9. [PMID: 15994966 DOI: 10.1158/0008-5472.can-04-4078] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vascular endothelial cell growth factor A (VEGF-A) and hypoxia play important roles in tumor angiogenesis. VEGF-A gene expression is up-regulated in tumors under hypoxic conditions, yet it is unclear how such up-regulation will affect the efficacy of RNA interference strategies targeting VEGF-A. Four potential short interfering RNA (siRNA) sequences for the VEGF-A gene were cloned into expression plasmids and transfected into HT1080 human fibrosarcoma cells. Stable transfection of these plasmids decreased VEGF-A mRNA levels and protein secretion by up to 99%. Our analysis of >100 hypoxia-related genes using oligonucleotide microarrays of 38 human sarcoma samples and 14 normal tissues identified distinctly different patterns of expression between sarcomas and normal tissues as assessed by hierarchical clustering analysis. Numerous hypoxia-related genes were significantly up-regulated in sarcomas including hypoxia-inducible factor 1alpha (HIF-1alpha). Exposure of wild-type HT1080 cells to 1% hypoxia resulted in HIF-1alpha up-regulation and a 74% increase in VEGF-A secretion as compared with secretion under normoxic conditions. Surprisingly, stable cell lines expressing VEGF-A siRNAs silenced VEGF-A expression equally well in hypoxia and normoxia. S.c. injection of cells with VEGF-A siRNAs into athymic nude mice led to slower-growing tumors, decreased blood vessel density, and greater apoptosis when compared with controls. Immunofluorescence analysis of tumor sections revealed areas of HIF-1alpha nuclear expression, suggesting areas of hypoxia, in both control tumors and VEGF-suppressed tumors. We conclude that hypoxia plays an important role in human sarcomas but hypoxic up-regulation of VEGF-A expression does not attenuate the efficacy of VEGF-A RNA interference.
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Affiliation(s)
- Kara Y Detwiller
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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223
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Chen B, Bixby JL. A novel substrate of receptor tyrosine phosphatase PTPRO is required for nerve growth factor-induced process outgrowth. J Neurosci 2005; 25:880-8. [PMID: 15673668 PMCID: PMC6725615 DOI: 10.1523/jneurosci.4365-04.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The receptor protein tyrosine phosphatase PTPRO may be involved in axon guidance both as a ligand and as a neuronal receptor. We have begun to characterize signaling by PTPRO as a receptor by screening for proteins interacting with the intracellular domain of PTPRO. In a yeast-two hybrid screen, we identified a novel class of protein, which we named neuronal pentraxin with chromo domain (NPCD), as a PTPRO-interacting protein. We have shown recently that NPCD has multiple cytoplasmic isoforms as a result of alternative splicing and that these proteins are present in many neurons, mainly associated with the inner side of the plasma membrane. Through additional two-hybrid experiments, cotransfection and reciprocal coprecipitation, glutathione S-transferase pulldown, and immunoprecipitation in vivo, we confirm that NPCD isoforms interact with the catalytic phosphatase domain of PTPRO. We also find that at least one NPCD isoform is tyrosine phosphorylated in vivo and can serve as a substrate for PTPRO in vitro. Analysis of PTPRO knock-out mice demonstrates that normal localization of NPCD at the plasma membrane requires PTPRO expression, suggesting a physiological role for the NPCD/PTPRO interaction. NPCD is likely to be relevant to axon growth and/or guidance, because RNA interference mediated knock-down of NPCD expression in pheochromocytoma cells inhibits NGF-induced neuronal process outgrowth without affecting NGF-dependent survival or initial NGF signaling.
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Affiliation(s)
- Bo Chen
- Department of Molecular and Cellular Pharmacology, The Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, Florida 33136, USA
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224
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Li MJ, Kim J, Li S, Zaia J, Yee JK, Anderson J, Akkina R, Rossi JJ. Long-term inhibition of HIV-1 infection in primary hematopoietic cells by lentiviral vector delivery of a triple combination of anti-HIV shRNA, anti-CCR5 ribozyme, and a nucleolar-localizing TAR decoy. Mol Ther 2005; 12:900-9. [PMID: 16115802 DOI: 10.1016/j.ymthe.2005.07.524] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Revised: 07/11/2005] [Accepted: 07/11/2005] [Indexed: 11/15/2022] Open
Abstract
Combinatorial therapies for the treatment of HIV-1 infection have proven to be effective in reducing patient viral loads and slowing the progression to AIDS. We have developed a series of RNA-based inhibitors for use in a gene therapy-based treatment for HIV-1 infection. The transcriptional units have been inserted into the backbone of a replication-defective lentiviral vector capable of transducing a wide array of cell types, including CD34+ hematopoietic progenitor cells. The combinatorial therapeutic RNA vector harbors a U6 Pol III promoter-driven short hairpin RNA (shRNA) targeting the rev and tat mRNAs of HIV-1, a U6 transcribed nucleolar-localizing TAR RNA decoy, and a VA1-derived Pol III cassette that expresses an anti-CCR5 ribozyme. Each of these therapeutic RNAs targets a different gene product and blocks HIV infection by a distinct mechanism. Our results demonstrate that the combinatorial vector suppresses HIV replication long term in a more-than-additive fashion relative to the single shRNA or double shRNA/ribozyme or decoy combinations. Our data demonstrate the validity and efficacy of a combinatorial RNA-based gene therapy for the treatment of HIV-1 infection.
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Affiliation(s)
- Ming-Jie Li
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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225
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Ahn J, Jun ES, Lee HS, Yoon SY, Kim D, Joo CH, Kim YK, Lee H. A small interfering RNA targeting coxsackievirus B3 protects permissive HeLa cells from viral challenge. J Virol 2005; 79:8620-4. [PMID: 15956603 PMCID: PMC1143761 DOI: 10.1128/jvi.79.13.8620-8624.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the ability of small interfering RNAs (siRNAs) to disrupt infection by coxsackievirus B3 (CVB3). The incorporation of siRNAs dramatically decreased cell death in permissive HeLa cells in parallel with a reduction in viral replication. Three of four siRNAs had potent anti-CVB3 activity. The present study thus demonstrates that the antiviral effect is due to the downregulation of viral replication. In addition, an effective CVB3-specific siRNA had similar antiviral effects in other related enteroviruses possessing sequence homology in the targeted region. Because the CVB3-specific siRNA is effective against other enteroviruses, siRNAs have potential for a universal anti-enterovirus strategy.
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Affiliation(s)
- Jeonghyun Ahn
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Korea
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226
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Zheng JN, Ma TX, Cao JY, Sun XQ, Chen JC, Li W, Wen RM, Sun YF, Pei DS. Knockdown of Ki-67 by small interfering RNA leads to inhibition of proliferation and induction of apoptosis in human renal carcinoma cells. Life Sci 2005; 78:724-9. [PMID: 16111722 DOI: 10.1016/j.lfs.2005.05.064] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Accepted: 05/13/2005] [Indexed: 10/25/2022]
Abstract
To investigate the effect of small-interfering RNA (siRNA) targeted against Ki-67, which is an attractive molecular target for cancer therapy, on inhibiting Ki-67 expression and cell proliferation in human renal carcinoma cells (HRCCs), siRNAs were used to inhibit the expression of Ki-67 in HRCCs. Ki-67 mRNA levels were detected by RT-PCR and in situ hybridization analysis. Ki-67 protein levels were detected by Western blot and immunocytochemistry analysis. TUNEL assay was used to measure the apoptosis of carcinoma cells. Results of RT-PCR and in situ hybridization demonstrated reduction of Ki-67 mRNA expression in Ki-67 siRNAs treated 786-0 cells. Similar reduction in Ki-67 protein measured by Western blot and immunocytochemistry was observed in cells transfected with Ki-67 siRNA. Ki-67-siRNA treatment of HRCCs resulted in specific inhibition of proliferation and increased apoptotic cell death. From these findings we conclude that inhibition of Ki-67 expression by siRNA may be a reasonable approach in renal cancer therapy.
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Affiliation(s)
- Jun-Nian Zheng
- Laboratory of Urology, Affiliated Hospital of Xuzhou Medical College, Xuzhou 221002, China
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227
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Anderson J, Akkina R. CXCR4 and CCR5 shRNA transgenic CD34+ cell derived macrophages are functionally normal and resist HIV-1 infection. Retrovirology 2005; 2:53. [PMID: 16109172 PMCID: PMC1199620 DOI: 10.1186/1742-4690-2-53] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 08/18/2005] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Stable simultaneous knock down of the HIV-1 coreceptors CCR5 and CXCR4 is a promising strategy to protect cells from both R5 macrophage tropic and X4 T cell tropic as well as dual tropic viral infections. The potency of shRNAs in targeted gene silencing qualifies them as powerful tools for long term HIV gene therapy. Our previous work with a bispecific lentiviral vector containing CXCR4 and CCR5 shRNAs showed efficacy in down regulating both coreceptors and conferring viral resistance to both X4 and R5-tropic strains of HIV-1 in cultured cell lines. To extend these results to a stem cell gene therapy setting, here we show transduction of primary CD34+ hematopoietic progenitor cells to derive normal end stage cells that are resistant to HIV-1 infection. RESULTS The bispecific XHR lentiviral vector harboring CXCR4 and CCR5 shRNA expression cassettes was efficient in transducing CD34+ cells. The transduced cells gave rise to morphologically normal transgenic macrophages when cultured in cytokine media. There was a marked down regulation of both coreceptors in the stably transduced macrophages which showed resistance to both R5 and X4 HIV-1 strains upon in vitro challenge. Since off target effects by some shRNAs may have adverse effects on transgenic cells, the stably transduced macrophages were further analyzed to determine if they are phenotypically and functionally normal. FACS evaluation showed normal levels of the characteristic surface markers CD14, CD4, MHC class II, and B7.1. Phagocytic functions were also normal. The transgenic macrophages demonstrated normal abilities in up-regulating the costimulatory molecule B7.1 upon LPS stimulation. Furthermore, IL-1 and TNFalpha cytokine secretion in response to LPS stimulation was also normal. Thus, the transgenic macrophages appear to be phenotypically and functionally normal. CONCLUSION These studies have demonstrated for the first time that a bispecific lentiviral vector could be used to stably deliver shRNAs targeted to both CCR5 and CXCR4 coreceptors into CD34+ hematopoietic progenitor cells and derive transgenic macrophages. Transgenic macrophages with down regulated coreceptors were resistant to both R5 and X4 tropic HIV-1 infections. The differentiated cells were also phenotypically and functionally normal indicating no adverse effects of shRNAs on lineage specific differentiation of stem cells. It is now possible to construct gene therapeutic lentiviral vectors incorporating multiple shRNAs targeted to cellular molecules that aid in HIV-1 infection. Use of these vectors in a stem cell setting shows great promise for sustained HIV/AIDS gene therapy.
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Affiliation(s)
- Joseph Anderson
- Dept. Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Ramesh Akkina
- Dept. Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
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228
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Zhu L, Somlo G, Zhou B, Shao J, Bedell V, Slovak ML, Liu X, Luo J, Yen Y. Fibroblast growth factor receptor 3 inhibition by short hairpin RNAs leads to apoptosis in multiple myeloma. Mol Cancer Ther 2005; 4:787-98. [PMID: 15897243 DOI: 10.1158/1535-7163.mct-04-0330] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The presence of t(4;14)(p16.3;q32.3) in multiple myeloma cells results in dysregulated expression of the fibroblast growth factor receptor 3 (FGFR3). FGFR3 acts as an oncogene to promote multiple myeloma cell proliferation and antiapoptosis. These encourage the clinical development of FGFR3-specific inhibitors. Three short hairpin RNAs (shRNA) targeting different sites of FGFR3 were selected and subsequently transfected into KMS-11, OPM-2, and NCI-H929 human myeloma cell lines, all of which are characterized by t(4;14) and FGFR3 over expression. The combination of these three shRNAs can effectively inhibit FGFR3 expression in all three cell lines. Sequential immunocytochemistry/fluorescence in situ hybridization was employed to validate that the shRNAs specifically inhibited FGFR3 expression in OPM-2 cells. Decreased expression of B-cell chronic lymphocytic leukemia/lymphoma 2 (BCL2) and myeloid cell leukemia sequence 1 (MCL1) proteins and increased staining of Annexin V-positive cells showed that inhibition of FGFR3 induces apoptosis. After confirming down-regulation of FGFR3 by real-time PCR, HU-133 plus 2.0 array was employed to compare the gene expression profile of shRNA-treated sample with that of the control. Besides the down-regulation of FGFR3, expression of the antiapoptotic genes CFLAR, BCL2, MCL1, and some members of NF-kappaB family decreased, whereas expression of the proapoptotic genes CYC, BID, CASP2, and CASP6 increased. Microarray results also revealed changes in genes previously implicated in multiple myeloma pathogenesis (RAS, RAF, IL-6R, and VEGF), as well as others (TLR4, KLF4, and GADD45A) not previously linked to multiple myeloma. Our observations indicate that shRNAs can specifically and effectively inhibit FGFR3 expression. This targeted approach may be worth testing in multiple myeloma patients with t(4;14) and FGFR3 overexpression in the future.
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MESH Headings
- Apoptosis
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 4/genetics
- Gene Expression Profiling
- Humans
- Kruppel-Like Factor 4
- Multiple Myeloma/metabolism
- Multiple Myeloma/pathology
- Myeloid Cell Leukemia Sequence 1 Protein
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oligonucleotide Array Sequence Analysis
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- RNA Interference
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/pharmacology
- Receptor, Fibroblast Growth Factor, Type 3
- Receptors, Fibroblast Growth Factor/antagonists & inhibitors
- Receptors, Fibroblast Growth Factor/genetics
- Receptors, Fibroblast Growth Factor/metabolism
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- Lijun Zhu
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA
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229
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Hiroi N, Funahashi A, Kitano H. Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA. Cancer Gene Ther 2005; 13:7-12. [PMID: 16082382 DOI: 10.1038/sj.cgt.7700869] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One of the distinguishing features of malignant tumor cells is the ability to proliferate in an anchorage-independent manner; methods that effectively suppress this phenotype may be applicable to the therapeutic inhibition of the malignancy of cancers. Interfering RNA is a potentially powerful tool for cancer therapy because of its specificity of target selection and remarkably high efficiency in target mRNA suppression. We studied the use of two knockdown strategies, antisense oligo DNA (AS-ODN) and small interfering RNA (siRNA), and showed how the anchorage-independent proliferation of malignant cells could be blocked efficiently. Anchorage-independent proliferation of rat fibroblasts transformed with v-src was suppressed with only a single 1-microM dose of AS-ODN; similar suppression using siRNA required treatment with 1 nM siRNA every 12 h. With our experimental system, the molecular stability of AS-ODN allowed the use of a simple treatment regimen to control the amount of the target molecule, providing that the treatment dose was sufficiently high. In comparison, siRNA treatment was effective at lower doses, but more frequent treatment was necessary to achieve the same suppression of proliferation.
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Affiliation(s)
- N Hiroi
- ERATO-SORST, Kitano Symbiotic Systems Project, Japan Science and Technology Agency, Shibuya-ku, Tokyo.
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230
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Li Z, Xiong Y, Peng Y, Pan J, Chen Y, Wu X, Hussain S, Tien P, Guo D. Specific inhibition of HIV-1 replication by short hairpin RNAs targeting human cyclin T1 without inducing apoptosis. FEBS Lett 2005; 579:3100-6. [PMID: 15913611 DOI: 10.1016/j.febslet.2005.04.074] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 04/10/2005] [Accepted: 04/17/2005] [Indexed: 11/20/2022]
Abstract
RNA interference (RNAi), a sequence-specific RNA degradation mechanism mediated by small interfering RNA (siRNA), can be used not only as a research tool but also as a therapeutic strategy for viral infection. We demonstrated that intracellular expression of short hairpin RNA (shRNA) targeting human cyclin T1 (hCycT1), a cellular factor essential for transcription of messenger and genomic RNAs from the long terminal repeat promoter of provirus of human immunodeficiency virus type 1 (HIV-1), could effectively suppress the replication of HIV-1. We also showed that downregulation of hCycT1 did not cause apoptotic cell death, therefore, targeting cellular factor hCycT1 by shRNAs may provide an attractive approach for genetic therapy of HIV-1 infection in the future.
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Affiliation(s)
- Zhaoyang Li
- The Modern Virology Research Centre and State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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231
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Takada T, Nemoto KI, Yamashita A, Kato M, Kondo Y, Torii R. Efficient gene silencing and cell differentiation using siRNA in mouse and monkey ES cells. Biochem Biophys Res Commun 2005; 331:1039-44. [PMID: 15882982 DOI: 10.1016/j.bbrc.2005.04.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Indexed: 11/17/2022]
Abstract
Small interfering RNA (siRNA) has been widely used for suppressing gene expression in various organisms. Here, we describe efficient methods to suppress target genes (EGFP or Oct4) using siRNA in mouse and monkey ES cells, and differentiation. In mouse ES cells, FACS analysis revealed that EGFP expression was suppressed in 97% of transfected cells at 48 h after transfection. In addition, cells expressed Hand1 and Cdx2, which are the marker genes of trophoblast lineage by the transient suppression of Oct4. In the case of monkey ES cells, highly efficient suppression was achieved in 98% of cells at 96 h post-transfection using the Sendai virus (hemagglutinating virus of Japan, HVJ) envelope as a carrier of siRNA. These efficient transfection methods using synthetic siRNA should contribute to evaluate specific gene function in ES cells and can be used to differentiate ES cells into desired cell lineages.
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Affiliation(s)
- Tatsuyuki Takada
- Research Center for Animal Life Science, Shiga University of Medical Science, Ohtsu, Shiga 520-2192, Japan.
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232
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Wen T, Li H, Song H, Chen F, Zhao C, Lu W, Bao K, Jin Y. Down-regulation of specific gene expression by double-strand RNA induces neural stem cell differentiation in vitro. Mol Cell Biochem 2005; 275:215-21. [PMID: 16335801 DOI: 10.1007/s11010-005-2049-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the postgenomic era the elucidation of the physiological function of genes has become the rate-limiting step in the quest to understand the development and function of living organisms. Double-stranded RNA (dsRNA) interferes with gene expression in various species, a phenomenon known as RNA interference (RNAi). We show here that RNAi is also effective in modifying gene expression in neural stem cell differentiation. The progenitor cells were obtained from E14 mouse embryonic forebrain and maintained using N-2 medium containing basic fibroblast growth factor (bFGF), epidermal growth factor (EGF) and B27.A gene (NM017084.1) was previously discovered and validated to express obviously differently between differentiated and undifferentiated neural stem cells in our laboratory. Here we report a long double-stranded RNA to knock out or knock down this gene. The results demonstrated that following RNAi inhibition of expression of the NM017084.1 gene, the differentiation of neural stem cells is accelerated. Thus the NM017084.1 gene may play a pivotal role in the process of differentiation of neural stem cells.
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Affiliation(s)
- Tieqiao Wen
- Laboratory of Neural Molecular Biology, School of Life Sciences, Shanghai University, Shanghai, PR China.
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233
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Tang W, Samuels V, Whitley N, Bloom N, DeLaGarza T, Newton RJ. Post-transcriptional gene silencing induced by short interfering RNAs in cultured transgenic plant cells. GENOMICS PROTEOMICS & BIOINFORMATICS 2005; 2:97-108. [PMID: 15629049 PMCID: PMC5172445 DOI: 10.1016/s1672-0229(04)02015-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Short interfering RNA (siRNA) is widely used for studying post-transcriptional gene silencing and holds great promise as a tool for both identifying function of novel genes and validating drug targets. Two siRNA fragments (siRNA-a and -b), which were designed against different specific areas of coding region of the same target green fluorescent protein (GFP) gene, were used to silence GFP expression in cultured gfp transgenic cells of rice (Oryza sativa L.; OS), cotton (Gossypium hirsutum L.; GH), Fraser fir [Abies fraseri (Pursh) Poir; AF], and Virginia pine (Pinus virginiana Mill.; PV). Differential gene silencing was observed in the bombarded transgenic cells between two siRNAs, and these results were consistent with the inactivation of GFP confirmed by laser scanning microscopy, Northern blot, and siRNA analysis in tested transgenic cell cultures. These data suggest that siRNA-mediated gene inactivation can be the siRNA specific in different plant species. These results indicate that siRNA is a highly specific tool for targeted gene knockdown and for establishing siRNA-mediated gene silencing, which could be a reliable approach for large-scale screening of gene function and drug target validation.
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Affiliation(s)
- Wei Tang
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA.
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234
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Oleinikov AV, Zhao J, Gray MD. RNA interference by mixtures of siRNAs prepared using custom oligonucleotide arrays. Nucleic Acids Res 2005; 33:e92. [PMID: 15942024 PMCID: PMC1143701 DOI: 10.1093/nar/gni091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNA interference (RNAi) is a process in which double-strand RNA (dsRNA) directs the specific degradation of a corresponding target mRNA. The mediators of this process are small dsRNAs, of approximately 21 bp in length, called small interfering RNAs (siRNAs). siRNAs, which can be prepared in vitro in a number of ways and then transfected into cells, can direct the degradation of corresponding mRNAs inside these cells. Hence, siRNAs represent a powerful tool for studying gene functions, as well as having the potential of being highly specific pharmaceutical agents. Some limitations in using this technology exist because the preparation of siRNA in vitro and screening for siRNAs efficient in RNAi can be expensive and time-consuming processes. Here, we demonstrate that custom oligonucleotide arrays can be efficiently used for the preparation of defined mixtures of siRNAs for the silencing of exogenous and endogenous genes. The method is fast, inexpensive, does not require siRNA optimization and has a number of advantages over methods utilizing enzymatic preparation of siRNAs by digestion of longer dsRNAs, as well as methods based on chemical synthesis of individual siRNAs or their DNA templates.
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235
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de los Santos T, Wu Q, de Avila Botton S, Grubman MJ. Short hairpin RNA targeted to the highly conserved 2B nonstructural protein coding region inhibits replication of multiple serotypes of foot-and-mouth disease virus. Virology 2005; 335:222-31. [PMID: 15840521 DOI: 10.1016/j.virol.2005.03.001] [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: 12/14/2004] [Revised: 01/06/2005] [Accepted: 03/02/2005] [Indexed: 11/28/2022]
Abstract
Foot-and-mouth disease virus (FMDV) is one of the most contagious agents of animals. Recent disease outbreaks in FMD-free countries have prompted the development of new control strategies that could improve the levels of protection against this virus. We have delivered a plasmid expressing a short hairpin RNA (shRNA) directed against a highly conserved sequence in the 2B nonstructural protein coding region of FMDV RNA to porcine cells. After virus infection, these cells showed a significant reduction in the synthesis of viral RNA and proteins, as well as a decrease in virus yield when compared to control cells. The antiviral effect was sequence specific and not attributable to induction of the interferon pathway. Since FMDV is an antigenically variable virus, we examined the effectiveness of this strategy against multiple serotypes and found that expressed 2B shRNA resulted in efficient silencing of at least 4 FMDV serotypes. Thus, RNA interference may be a potential alternative control strategy to limit the spread of this highly contagious virus in livestock.
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Affiliation(s)
- Teresa de los Santos
- U.S. Department of Agriculture, Plum Island Animal Disease Center, North Atlantic Area, Agricultural Research Service, PO Box 848, Greenport, NY 11944, USA
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236
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Lakka SS, Gondi CS, Dinh DH, Olivero WC, Gujrati M, Rao VH, Sioka C, Rao JS. Specific Interference of Urokinase-type Plasminogen Activator Receptor and Matrix Metalloproteinase-9 Gene Expression Induced by Double-stranded RNA Results in Decreased Invasion, Tumor Growth, and Angiogenesis in Gliomas. J Biol Chem 2005; 280:21882-92. [PMID: 15824107 DOI: 10.1074/jbc.m408520200] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have previously demonstrated the effectiveness of adenovirus-mediated expression of antisense urokinase-type plasminogen activator receptor (uPAR) and matrix metalloproteinase-9 (MMP-9) in inhibiting tumor invasion in vitro and ex vivo. However, the therapeutic effect of the adenovirus-mediated antisense approach was shown to be transient and required potentially toxic, high viral doses. In contrast, RNA interference (RNAi)-mediated gene targeting may be superior to the traditional antisense approach, because the target mRNA is completely degraded and the molar ratio of siRNA required to degrade the target mRNA is very low. Here, we have examined the siRNA-mediated target RNA degradation of uPAR and MMP-9 in human glioma cell lines. Using RNAi directed toward uPAR and MMP-9, we achieved specific inhibition of uPAR and MMP-9. This bicistronic construct (pUM) inhibited the formation of capillary-like structures in both in vitro and in vivo models of angiogenesis. We demonstrated that blocking the expression of these genes results in significant inhibition of glioma tumor invasion in Matrigel and spheroid invasion assay models. RNAi for uPAR and MMP-9 inhibited cell proliferation, and significantly reduced the levels of phosphorylated forms of MAPK, ERK, and AKT signaling pathway molecules when compared with parental and empty vector/scrambled vector-transfected SNB19 cells. Furthermore, using RNAi to simultaneously target two proteases resulted in total regression of pre-established intracerebral tumor growth. Our results provide evidence that the use of hairpin siRNA expression vectors for uPAR and MMP-9 may provide an effective tool for cancer therapy.
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MESH Headings
- Animals
- Brain Neoplasms/blood supply
- Brain Neoplasms/metabolism
- Brain Neoplasms/pathology
- Cell Line, Transformed
- Cell Line, Tumor
- Cell Proliferation
- Collagen/pharmacology
- Down-Regulation
- Drug Combinations
- Extracellular Signal-Regulated MAP Kinases/metabolism
- Female
- Gene Expression Regulation, Enzymologic
- Gene Silencing
- Genetic Vectors
- Glioblastoma/metabolism
- Glioma/blood supply
- Glioma/metabolism
- Glioma/therapy
- Green Fluorescent Proteins/chemistry
- Green Fluorescent Proteins/metabolism
- Humans
- Immunohistochemistry
- Laminin/pharmacology
- MAP Kinase Signaling System
- Male
- Matrix Metalloproteinase 9/metabolism
- Mice
- Mice, Nude
- Models, Biological
- Models, Genetic
- Neoplasm Invasiveness
- Neovascularization, Pathologic
- Nucleic Acid Conformation
- Phosphorylation
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- Proteoglycans/pharmacology
- RNA Interference
- RNA, Double-Stranded/genetics
- RNA, Small Interfering/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Urokinase Plasminogen Activator
- Time Factors
- Transfection
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Affiliation(s)
- Sajani S Lakka
- Departments of Biomedical and Therapeutic Sciences (Program of Cancer Biology), College of Medicine, University of Illinois, Peoria, IL 61656, USA
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237
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Li H, Fu X, Chen Y, Hong Y, Tan Y, Cao H, Wu M, Wang H. Use of adenovirus-delivered siRNA to target oncoprotein p28GANK in hepatocellular carcinoma. Gastroenterology 2005; 128:2029-41. [PMID: 15940635 DOI: 10.1053/j.gastro.2005.03.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIMS RNA interference (RNAi) is a powerful tool to silence gene expression. The adenoviral vector expressing small interfering RNA (siRNA) is highly effective in mammalian cells. However, its potential use as a therapeutic tool to target an oncogene specifically remains to be seen. We applied the adenovirus-delivered siRNA (AdSiRNA) to inhibit a hepatocellular carcinoma (HCC) oncogene, p28GANK, in HCC cell lines and investigated its antitumor effects. METHODS The T7-RNA polymerase system was used to screen the specific target site. Double-strand oligonucleotide for transcription of short hairpin RNA was constructed into the adenoviral vector. Four HCC cell lines were infected with the RNAi-containing adenovirus. The RNAi effects on HCC were studied in cultured cells as well as in animal models. RESULTS p28GANK expression was suppressed by up to 80% in HCC cells. Depletion of p28GANK inhibited HCC cell growth and tumorigenesis, enhanced dephosphorylation of RB1, and decreased transcription activity of E2F-1 in HuH-7 cells. Furthermore, depletion of p28GANK induced caspase-8- and caspase-9-mediated apoptosis of HCC cells. Finally, targeting p28GANK by adenovirus injection inhibited the growth of established tumors in nude mice. CONCLUSIONS This study shows that the T7-system screening-based AdSiRNA can be used successfully to silence an oncogene. We proved the therapeutic potential of AdSiRNA on the treatment of HCC by targeting p28GANK. Our results indicate that p28GANK may serve as a novel therapeutic target for treating HCC.
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Affiliation(s)
- Honghai Li
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Shanghai, Peoples Republic of China
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238
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Iyer RP, Coughlin JE, Padmanabhan S. RAPID FUNCTIONALIZATION AND LOADING OF SOLID SUPPORTS. ORG PREP PROCED INT 2005; 37:205-212. [PMID: 16604159 PMCID: PMC1431690 DOI: 10.1080/00304940509354949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Radhakrishnan P Iyer
- Spring Bank Technologies, Inc., Suite S-7, 113 Cedar Street, Milford, MA 01757, USA
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239
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Hassan A, Tian Y, Zheng W, Ji H, Sandberg K, Verbalis JG. Small interfering RNA-mediated functional silencing of vasopressin V2receptors in the mouse kidney. Physiol Genomics 2005; 21:382-8. [PMID: 15784697 DOI: 10.1152/physiolgenomics.00147.2004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The antidiuretic effects of arginine vasopressin (AVP) on the kidney are mediated by V2subtype AVP receptors (V2R). To investigate the role of regulation of V2R in water and sodium homeostasis, we have developed a method for small interfering RNA (siRNA)-mediated inhibition of V2R expression in vivo. Three 21-nt siRNA sequences were chosen that specifically targeted the mouse V2R but shared no appreciable sequence homology to any other known mouse genes, including the vasopressin V1aand V1breceptors. Additionally, an siRNA sequence that shared no significant matches to any known mammalian gene sequences was chosen for use as a control. Chemically synthesized siRNA was complexed with the liposomal transfection reagent DOTAP. Each mouse (male C57BL/6) received 3.6 nmol (∼50 μg) of either the control (nonsilencing) or one of the V2R-targeting siRNAs via intravenous injection. Forty-eight hours after injection membranes were prepared from the inner medulla of the kidneys, and V2R expression was measured by a radioligand binding assay and Western immunoblotting. Treatment with one of the V2R-targeting siRNAs (R2) caused a 39.7 ± 8.7% reduction in V2R-specific binding compared with the control ( n = 11, P < 0.05) and a 37.0 ± 2.3% reduction in V2R protein expression as measured by Western immunoblotting ( n = 4, P < 0.001). Additionally, real-time PCR revealed that R2 siRNA treatment induced a 68.8 ± 2.2% reduction in V2R mRNA. However, this siRNA treatment did not alter the animals’ basal urine concentrating capacity under unstimulated conditions. In subsequent experiments, treatment with R2 siRNA was found to significantly attenuate the antidiuretic effects the V2R-specific AVP agonist 1-desamino-[8-d-arginine]vasopressin (dDAVP). Mice were infused with dDAVP (0.25 ng/h) for 3 days to produce maximal antidiuresis and then were injected with either the R2 siRNA or the nonsilencing control. On day 2 after treatment, urine osmolality was significantly decreased from 3,455 ± 72 in control animals ( n = 12) to 3,155 ± 129 mosmol/kgH2O in R2 siRNA-treated animals ( n = 12) ( P < 0.05); similarly, on day 2 24-h urine volume was significantly increased from 0.86 ± 0.07 ml/day to 1.11 ± 0.06 ml/day in R2 siRNA-treated animals ( P < 0.05). In summary we have demonstrated that RNA interference methodology can be used successfully in vivo to significantly reduce functional expression of the V2R in the mouse kidney.
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Affiliation(s)
- Ali Hassan
- Center for the Study of Sex Differences in Health, Aging and Disease, Georgetown University Medical Center, Washington, District of Columbia 20057, USA.
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240
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Lustigman S, Zhang J, Liu J, Oksov Y, Hashmi S. RNA interference targeting cathepsin L and Z-like cysteine proteases of Onchocerca volvulus confirmed their essential function during L3 molting. Mol Biochem Parasitol 2005; 138:165-70. [PMID: 15555728 DOI: 10.1016/j.molbiopara.2004.08.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Accepted: 08/02/2004] [Indexed: 11/17/2022]
Abstract
We describe the successful use of RNA interference (RNAi) to investigate gene function in the human filarial parasite Onchocerca volvulus third-stage larvae (L3). We targeted two specific gene products, the O. volvulus cathepsin L (Ov-CPL) and cathepsin Z-like (Ov-CPZ) cysteine proteases, which were proposed to function during O. volvulus L3 molting. We show that fluorescent-labeled Cy3-dsRNA corresponding to cpl or cpz regions encoding the mature enzymes can enter the larvae. The molting rate of larvae treated overnight with 0.5 mg ml(-1) cpl was reduced by 92% and 86% in comparison to normal control worms. It appeared that although the larvae started the molting process the last stage of molting, ecdysis was inhibited. The effect was gene specific, as larvae that did not molt in the presence of cpl or cpz dsRNA expressed the other cysteine protease, CPZ and CPL, respectively. This was confirmed by immunoelectron microscopy using antibodies directed against each enzyme. Our present study validate conclusively that both enzymes are essential for the molting of O. volvulus L3 to fourth-stage larvae. We also confirmed that the activity of the enzymes is specific to the changes that occur during the molting process on days 1-3, when the separation between the cuticles is in progress. The development of RNAi in O. volvulus L3 could further help study many of the abundant L3 and molting L3 genes identified through the filarial genome project, many of which, although have no attributed function, were identified as vaccine candidates or potential drug targets.
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Affiliation(s)
- Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY 10021, USA.
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241
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Bot I, Guo J, Van Eck M, Van Santbrink PJ, Groot PHE, Hildebrand RB, Seppen J, Van Berkel TJC, Biessen EAL. Lentiviral shRNA silencing of murine bone marrow cell CCR2 leads to persistent knockdown of CCR2 function in vivo. Blood 2005; 106:1147-53. [PMID: 15886324 DOI: 10.1182/blood-2004-12-4839] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major barrier in hematopoietic gene function studies is posed by the laborious and time-consuming generation of knockout mice with an appropriate genetic background. Here we present a novel lentivirus-based strategy for the in situ generation of hematopoietic knockdowns. A short hairpin RNA (shRNA) was designed targeting murine CC-chemokine receptor 2 (CCR2), which was able to specifically blunt CCR2 expression at the mRNA, protein, and functional levels in vitro. Reconstitution of irradiated recipient mice with autologous bone marrow that had been ex vivo transduced with shRNA lentivirus led to persistent down-regulation of CCR2 expression, which translated into a 70% reduction in CCR2-dependent recruitment of macrophages to an inflamed peritoneal cavity without noticeable side effects on related chemokine receptors or general inflammation status. These findings clearly demonstrate the potential of shRNA lentivirus-infected bone marrow transplantation as a rapid and effective method to generate hematopoietic knockdowns for leukocyte gene function studies.
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MESH Headings
- Animals
- Bone Marrow Cells
- Bone Marrow Transplantation
- Chemotaxis
- Down-Regulation
- Lentivirus/genetics
- Macrophages
- Methods
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Models, Animal
- RNA Interference
- RNA, Messenger/drug effects
- RNA, Small Interfering/chemical synthesis
- RNA, Small Interfering/genetics
- RNA, Small Interfering/pharmacology
- Receptors, CCR2
- Receptors, Chemokine/deficiency
- Receptors, Chemokine/drug effects
- Receptors, Chemokine/genetics
- Transduction, Genetic
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Affiliation(s)
- Ilze Bot
- Division of Biopharmaceutics, Leiden/Amsterdam Center for Drug Research, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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242
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Dodo H, Konan K, Viquez O. A genetic engineering strategy to eliminate peanut allergy. Curr Allergy Asthma Rep 2005; 5:67-73. [PMID: 15659267 DOI: 10.1007/s11882-005-0058-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peanut allergy is an IgE-mediated hypersensitivity reaction with an increasing prevalence worldwide. Despite its seriousness, to date, there is no cure. Genetic engineering strategies can provide a solution. The post-transcriptional gene silencing (PTGS) model can be used effectively to knock out the production of allergenic proteins in peanut by specific degradation of the endogenous target messenger RNA (mRNA). Ara h 2, the most potent peanut allergenic protein, was selected as a model to demonstrate the feasibility of this concept. Transgenic peanut plants were produced via microprojectile-mediated transformation of peanut embryos using a plasmid construct, which contains a fragment of the coding region of Ara h 2 linked to an enhanced CaMV 35S constitutive promoter. Molecular analyses, including polymerase chain reaction and Southern blots, confirmed the presence of the stable integration of the Ara h 2 transgene into the peanut genome. Northern hybridization showed the expression of the Ara h 2 transgene in all vegetative tissues of the mature transgenic peanut plants, indicating the stable expression of the truncated Ara h 2 transgene throughout the development of the plants. It is, therefore, reasonable to expect that the truncated Ara h 2 transgene transcripts will be synthesized in the seeds and will trigger the specific degradation of endogenous Ara h 2 mRNA. The next step will be to grow the transgenic peanut plants to full maturity for seed production and to determine the level of allergen Ara h 2.
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Affiliation(s)
- Hortense Dodo
- Food Biotechnology Laboratory, Department of Food & Animal Sciences, PO Box 1628, Alabama A&M University, Normal, AL 35762, USA.
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243
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Li Y, Kelly WG, Logsdon JM, Schurko AM, Harfe BD, Hill-Harfe KL, Kahn RA. Functional genomic analysis of the ADP-ribosylation factor family of GTPases: phylogeny among diverse eukaryotes and function in C. elegans. FASEB J 2005; 18:1834-50. [PMID: 15576487 DOI: 10.1096/fj.04-2273com] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ADP-ribosylation factor (Arf) and Arf-like (Arl) proteins are a family of highly conserved 21 kDa GTPases that emerged early in the evolution of eukaryotes. These proteins serve regulatory roles in vesicular traffic, lipid metabolism, microtubule dynamics, development, and likely other cellular processes. We found evidence for the presence of 6 Arf family members in the protist Giardia lamblia and 22 members in mammals. A phylogenetic analysis was performed to delineate the evolutionary relationships among Arf family members and to attempt to organize them by both their evolutionary origins and functions in cells and/or organisms. The approximately 100 protein sequences analyzed from animals, fungi, plants, and protists clustered into 11 groups, including Arfs, nine Arls, and Sar proteins. To begin functional analyses of the family in a metazoan model organism, we examined roles for all three C. elegans Arfs (Arf-1, Arf-3, and Arf-6) and three Arls (Arl-1, Arl-2, and Arl-3) by use of RNA-mediated interference (RNAi). Injection of double-stranded RNA (dsRNA) encoding Arf-1 or Arf-3 into N2 hermaphrodites produced embryonic lethality in their offspring and, later, sterility in the injected animals themselves. Injection of Arl-2 dsRNA resulted in a disorganized germline and sterility in early offspring, with later offspring exhibiting an early embryonic arrest. Thus, of the six Arf family members examined in C. elegans, at least three are required for embryogenesis. These data represent the first analysis of the role(s) of multiple members of this family in the development of a multicellular organism.
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Affiliation(s)
- Yawei Li
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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244
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Wagner A, Phillips L, Narayan RD, Moody JM, Geddes B. Gene silencing studies in the gymnosperm species Pinus radiata. PLANT CELL REPORTS 2005; 24:95-102. [PMID: 15662500 DOI: 10.1007/s00299-004-0911-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2004] [Revised: 12/04/2004] [Accepted: 12/06/2004] [Indexed: 05/20/2023]
Abstract
A biolistic transformation procedure was used to transform embryogenic Pinus radiata tissue with constructs containing the Zea mays UBI1 (ubiquitin)-promoter followed by the P. radiata CAD (cinnamyl alcohol dehydrogenase) cDNA in sense or anti-sense orientation or in the form of an inverted-repeat. The effect of the different constructs on silencing the endogenous CAD gene was monitored in embryogenic tissue and somatic seedlings of 28 P. radiata transclones. Quantitative CAD measurements demonstrated that the construct containing an inverted-repeat of the CAD cDNA was most efficient in triggering gene silencing in P. radiata. Northern hybridization experiments with silenced transclones revealed that reduced CAD activities were the result of reduced steady state levels of the targeted CAD mRNA. Monitoring of the activity of the UBI1-promoter in the P. radiata transclones and heat-shock experiments with transgenic somatic P. radiata seedlings indicated that gene silencing is positively correlated with the expression level of the transgene. The obtained data are also consistent with a role for the expression level of the endogenous CAD gene in gene silencing.
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MESH Headings
- Alcohol Oxidoreductases/genetics
- DNA, Complementary/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Enzymologic/genetics
- Gene Expression Regulation, Plant/genetics
- Gene Silencing/physiology
- Pinus/embryology
- Pinus/genetics
- Pinus/growth & development
- Plant Proteins/genetics
- Plant Shoots/embryology
- Plant Shoots/genetics
- Plant Shoots/growth & development
- Plants, Genetically Modified/embryology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- Promoter Regions, Genetic/genetics
- RNA, Messenger/metabolism
- Seeds/embryology
- Seeds/genetics
- Seeds/growth & development
- Transformation, Genetic/genetics
- Transgenes/genetics
- Ubiquitin C/genetics
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Affiliation(s)
- Armin Wagner
- Cellwall Biotechnology Centre (CBC), Forest Research, Private Bag 3020, Rotorua, New Zealand.
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245
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Bezanilla M, Perroud PF, Pan A, Klueh P, Quatrano RS. An RNAi system in Physcomitrella patens with an internal marker for silencing allows for rapid identification of loss of function phenotypes. PLANT BIOLOGY (STUTTGART, GERMANY) 2005; 7:251-7. [PMID: 15912444 DOI: 10.1055/s-2005-837597] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
RNAi is a powerful method for generating loss of function mutants, especially for targeting genes belonging to large gene families. We have recently shown that RNAi functions in the moss Physcomitrella patens. We obtained stable lines that show constitutive silencing of a nuclearly localized GFP:GUS fusion protein (NLS:GFP:GUS). However, lines that display silencing of the protein do not necessarily have reduced transcript levels. Therefore, a system has been developed that silences the NLS:GFP:GUS reporter construct at the same time as it silences a gene of interest. Gateway (Invitrogen) recombination cassettes were incorporated into these vectors to facilitate cloning of many different cDNA sequences. In addition, vectors were generated that contain genomic moss DNA sequence information to increase the production of stable moss lines. Transformation with these constructs results in strong silencing within 24 h and is stable for at least a month after transformation. FtsZ2-1, whose loss of function phenotype is known, was incorporated as a test case for analyzing phenotypes. One hundred per cent of regenerating colonies that have silenced GFP exhibit a loss of function FtsZ2-1 phenotype, validating the use of this system to assay phenotypes for plant genes of unknown function.
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Affiliation(s)
- M Bezanilla
- Department of Biology, Washington University, 1 Brookings Drive, Saint Louis, MO 63130, USA.
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246
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Logashenko EB, Vladimirova AV, Repkova MN, Venyaminova AG, Chernolovskaya EL, Vlassov VV. Silencing of MDR 1 gene in cancer cells by siRNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:861-6. [PMID: 15560073 DOI: 10.1081/ncn-200026032] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Inhibition of p-glycoprotein (PGP) expression and reverse of multidrug resistance (MDR) phenotype in KB-8-5 cells by synthetic 21-bp double-stranded oligoribonucleotides were investigated. siRNA constructs for the efficient down regulation of MDR1 that are active in nanomolar concentrations and cause reversal of MDR phenotype in cells were developed.
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Affiliation(s)
- E B Logashenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
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247
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Nishitsuji H, Ikeda T, Miyoshi H, Ohashi T, Kannagi M, Masuda T. Expression of small hairpin RNA by lentivirus-based vector confers efficient and stable gene-suppression of HIV-1 on human cells including primary non-dividing cells. Microbes Infect 2005; 6:76-85. [PMID: 14738896 DOI: 10.1016/j.micinf.2003.10.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
RNA interference (RNAi) is a sequence-specific RNA degradation process mediated by short double-stranded RNAs termed small interfering RNAs. Here, we describe the lentivirus-based vector small interfering RNA system expressing. As a pilot study, we generated constructs expressing small hairpin RNA (shRNA) specific for luciferase gene (shLuc) or green fluorescence protein (shGFP) under the control of human H1 RNA polymerase III promoter. The effect of the shRNA was evaluated against HIV-1 infection in a single-round or multiple-round infectious system using an HIV-1 molecular clone carrying the luc or GFP gene. In the single-round infectious system, cells transduced with shLuc by lentiviral vector significantly reduced (approximately 90% reduction) viral gene expression after challenge infection at a multiplicity of infection of 10. These transduced cells continued to resist against at least four sequentially repeated challenge infections. Importantly, this efficient antiviral activity persisted over 35 days in culture. In a multiple-round infectious system using a replication-competent HIV-1 molecular clone carrying the GFP gene, we also observed that a lentiviral vector expressing shGFP could inhibit HIV-1 replication for at least 1 week. The profound effect of lentiviral shRNA was also observed in human primary monocyte-derived macrophages. Thus, shRNA introduced through the lentiviral vector can be useful for efficient and stable gene suppression in human cells including primary non-dividing cells. Moreover, quantitative analysis of viral cDNA synthesis on challenge infection showed that viral genomic RNAs packaged in incoming virus core might not be targeted by shLuc. Instead, the degradation of transcripts from integrated proviral DNAs might be a major cause of the profound reduction in HIV-1 gene expression by shRNA in our system.
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Affiliation(s)
- Hironori Nishitsuji
- Department of Immunotherapeutics, Graduate School of Medicine and Dentistry, Tokyo Medical and Dental University, 1-5-45 Yushima, Tokyo 113-8519, Bunkyo-ku, Japan
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248
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Chen W, Liu M, Cheng G, Yan W, Fei L, Zheng Z. RNA silencing: A remarkable parallel to protein-based immune systems in vertebrates? FEBS Lett 2005; 579:2267-72. [PMID: 15848156 DOI: 10.1016/j.febslet.2005.03.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 03/24/2005] [Accepted: 03/25/2005] [Indexed: 12/26/2022]
Abstract
Sequence-specific gene silencing by double-strand RNA has been observed in many eukaryotes. Accumulating data suggest that it is the major antiviral defense mechanism in plants and invertebrates. The discovery that this cellular mechanism is also highly conserved though somewhat impaired in mammals has stimulated debate about the evolution of antiviral systems. Here we suggest that the existence of the interferon response as an evolutionary intermediate could account for both the relative decline of RNA silencing and the development of protein-based immune systems in vertebrates. In addition, we emphasize the opportunities presented by RNA silencing and the deeper understanding of vertebrate antiviral systems that is needed.
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Affiliation(s)
- Weizao Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, PR China
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249
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Bahramian MB, Zarbl H. GENE impedance: a natural process for control of gene expression and the origin of RNA interference. J Theor Biol 2005; 233:301-14. [PMID: 15652140 DOI: 10.1016/j.jtbi.2004.10.007] [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] [Received: 03/08/2004] [Revised: 09/21/2004] [Accepted: 10/07/2004] [Indexed: 10/26/2022]
Abstract
Gene expression is controlled by coordinated transcriptional and post-transcriptional mechanisms. Normally, expression of a gene switches on and off in response to specific physiological signals that are triggered by cellular demand for the gene products at a given time. Based on our previous studies and the scientific literature, we hypothesize that when a gene promoter switches to transcriptional repression mode, transcription of the gene ceases, and a small amount of double-stranded RNA (dsRNA) is synthesized by the RNA polymerase switching to the opposite DNA strand at the termination region of the gene. These dsRNA structures, which result from normal transcriptional repression, can then be processed into short interfering RNAs (siRNAs) within the nucleus. These molecules subsequently direct specific cleavage of the cognate mRNAs and interfere with their translation through sequence complementarily. We further hypothesize that cellular defense mechanisms invoked by invading genetic elements could be rooted in this fundamental regulatory pathway that we call "GENE impedance", or simply, GENEi. Here, we present a working model that illustrates how transcription-termination and transcription-arrest can contribute to the regulation of gene expression via GENEi. In our model RNAi is only one component of GENEi, which is a more generalized mechanism of gene regulation.
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250
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Sumitani M, Yamamoto DS, Lee JM, Hatakeyama M. Isolation of white gene orthologue of the sawfly, Athalia rosae (Hymenoptera) and its functional analysis using RNA interference. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2005; 35:231-240. [PMID: 15705502 DOI: 10.1016/j.ibmb.2004.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2004] [Revised: 12/03/2004] [Accepted: 12/06/2004] [Indexed: 05/24/2023]
Abstract
We isolated and characterized the white gene orthologue of the sawfly, Athalia rosae (Hymenoptera). The A. rosae white (Ar white) cDNA cloned was 2058-bp long encoding 685 amino acids in a single open reading frame (ORF). Comparison of the cDNA sequence with the genomic DNA sequence revealed that the ORF was derived from 11 exons. Ar white was a single copy gene as evidenced by genomic Southern blotting and its cytological localization on the metaphase chromosomes. The deduced amino acid sequence aligned well with known insect white orthologous gene products sharing conserved regions such as the ATP-binding motif and the six transmembrane-spanning segments. Expression of Ar white was detected at embryonic and pupal stages by Northern blotting. In situ hybridization detected the embryonic expression in a pair of the lateral tips of protocephalic placodes from where optic organs are formed. Ar white function was examined using double-stranded RNA (dsRNA)-mediated interference. The synthesized dsRNA targeting Ar white transcripts caused a decrease in the level of the original mRNAs, and resulted in the white phenocopy in the embryonic eye pigmentation when microinjected into eggs from wild-type females. The effects occurred in a dose-dependent manner.
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Affiliation(s)
- Megumi Sumitani
- Division of Bioscience, Graduate School of Science and Technology, Kobe University, Nada, Kobe 657-8501, Japan
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