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Results for “RNA interference (RNAi)”

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PubMed2006

Effects of siRNAs in combination with Gleevec on K-562 cell proliferation and Bcr-Abl expression.

RNA interference (RNAi) is the repression of gene expression through a cellular mechanism of transcript-specific mRNA degradation. RNAi has been observed in human cells and applied to the modulation of a variety of human transcripts. Our goals were to deliver small interfering RNA (siRNA) using a liposome-based method, and to show Bcr-Abl siRNA specificity against K-562 cells, alone or in combination with Gleevec. Both synthetic (syn) siRNA, consisting of homogeneous 21-nucleotide-long RNA duplexes specific for the Bcr-Abl fusion site, and recombinant (r)-generated Bcr-Abl siRNA were employed. siRNA was transfected into K-562 cells with greater than 90% efficiency using RNAiFect, as judged by fluorescence analysis. The Bcr-Abl transcript was inhibited using either siRNA preparation as measured by RT-PCR or real-time PCR. The IC(50) of Gleevec in the K-562 subline F(1) was lowered over 3-fold from 0.2 to 0.06 muM in cells transfected with either syn or rBcr-Abl siRNA. No effect was observed in cells after transfection with an irrelevant control siRNA. Therefore, K-562 cells transfected with RNAifect deliver Bcr-Abl siRNA efficiently and the Bcr-Abl siRNA decreased the IC(50) of Gleevec required to inhibit the high levels of Bcr-Abl protein found in K-562 cells.

Base Sequence↗
PubMed2005

MUC1 plays a role in tumor maintenance in aggressive thyroid carcinomas.

BACKGROUND: We recently identified MUC1 as a target driving selection for 1q21 amplification and validated it as an independent marker of aggressive behavior in thyroid cancer (TC). The aims of this study were to determine whether TC cell lines retain MUC1 expression patterns that are seen in primary tumors, assess the role of MUC1 in tumor maintenance, and develop a virally delivered anti-MUC1 RNA interference (RNAi) that is effective in decreasing MUC1 expression in vitro. METHODS: Fifteen TC cell lines were screened for MUC1 protein expression. Cell lines with varying MUC1 protein levels were treated with anti-MUC1 monoclonal antibody to assess cell viability. A recombinant retroviral short hairpin RNAi delivery system against MUC1 was developed. Efficacy and optimal dosing of short hairpin RNA against MUC1 was determined. RESULTS: MUC1 expression patterns in TC cell lines were found to be similar to that seen in primary tumors. Treatment with anti-MUC1 antibody resulted in a significant decrease in cell viability in MUC1 over-expressing cell lines. MUC1-779 RNAi construct showed excellent infection efficiency and reproducible silencing. CONCLUSION: These data offer functional evidence that implicates MUC1 over-expression as a key molecular event in the pathogenesis of aggressive TC. Retrovirally delivered anti-MUC1 RNAi is effective in silencing MUC1 and merits further investigation to establish therapeutic efficacy and safety in anticipation of potential clinical application.

Antigens↗
PubMed2005

RNA interference induced by siRNAs modified with 4'-thioribonucleosides.

Short interfering RNAs (siRNAs) variously modified with 4'-thioribonucleosides against the photinus luciferase gene and the renilla luciferase gene were tested for their induction of the RNA interference (RNAi) activity in cultured NIH/3T3 cells. Results indicated that modifications with 4'-thioribonucleosides on siRNA against the photinus luciferase were as potent as natural siRNA. On the other hand, modifications with 4'-thioribonucleosides on natural siRNA against the renilla luciferase improved their RNAi activity. These results suggest that 4'-thioribonucleosides might be potentially useful in the development of novel and effective chemically modified siRNAs.

Animals↗
PubMed2004

RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia.

The dominant polyglutamine expansion diseases, which include spinocerebellar ataxia type 1 (SCA1) and Huntington disease, are progressive, untreatable, neurodegenerative disorders. In inducible mouse models of SCA1 and Huntington disease, repression of mutant allele expression improves disease phenotypes. Thus, therapies designed to inhibit expression of the mutant gene would be beneficial. Here we evaluate the ability of RNA interference (RNAi) to inhibit polyglutamine-induced neurodegeneration caused by mutant ataxin-1 in a mouse model of SCA1. Upon intracerebellar injection, recombinant adeno-associated virus (AAV) vectors expressing short hairpin RNAs profoundly improved motor coordination, restored cerebellar morphology and resolved characteristic ataxin-1 inclusions in Purkinje cells of SCA1 mice. Our data demonstrate in vivo the potential use of RNAi as therapy for dominant neurodegenerative disease.

Adenoviridae↗
PubMedDate not supplied

[Regulation of the expression of repeated sequences and RNA interference].

Living organisms have to fight against the invasion of many parasites. Among them are viruses and transposable elements that are able to integrate in the genome of their host. After integration, they can replicate and propagate. The defence mechanisms against these invaders are still largely unknown but are widely studied in plants as well as in fungi and animals, particularly Caenorhabditis elegans and Drosophila melanogaster. The compilation of recent data allows us to draw a general scheme for these mechanisms. In particular, it seems that the propagation of viruses, transposable elements and repeated sequences is controlled by mechanisms repressing the expression of these sequences at both transcriptional and post-transcriptional levels. Post-transcriptional regulation of repeated sequences and transposable elements is related to RNA interference (RNAi), an evolutionary conserved silencing process induced by the presence of double-stranded RNAs (dsRNAs). Many genes and molecular intermediates have now been identified, revealing the different steps of the mechanism underlying this process. Finally, different results suggest that these post-transcriptional silencing processes are involved in the development of organisms. DICER is a nuclease responsible for the processing of dsRNA into short RNA molecules (siRNAs) considered as the interfering agent. siRNAs interact with the transcript of the targeted gene and this interaction induces degradation of the transcript. DICER is also involved in the processing of small temporal RNAs (stRNA) involved in the timing of development. stRNAs have the same structure as siRNAs. They regulate their target genes by interacting with elements present in their 3'UTR and blocking translation. RNAi appears to be an universal regulatory mechanism that was still unknown a few years ago. It is now largely used in large scale inactivation of genes to determine their function, and some recent studies indicate that it might be used in human therapy.

Animals↗
PubMed2005

shRNA-targeted hTERT suppress cell proliferation of bladder cancer by inhibiting telomerase activity.

RNA interference (RNAi) has demonstrated profound prospect in human gene research. hTERT, the rate-limiting component of telomerase activity, is highly expressed in bladder cancer cells. Here, we investigated the anti-proliferation effects of small hairpin interfering RNA (shRNA)-targeted hTERT gene on bladder cancer in vitro and in vivo. The results showed that ph2-shRNA, the most-effective vector carrying shRNA-targeted hTERT, could significantly inhibit the cell proliferation by down-regulating hTERT expression, decreasing telomerase activity, decreasing cell number of S phase, increasing the cell number of G0/G1 phase in T24 cells and xenograft tumor tissues, and attenuate the tumor growth of xenograft mice model compared with controls. Our results demonstrate that hTERT-directed shRNAs are potent inhibitors of bladder cancer.

Animals↗
PubMed2005

Chemical modification of gene silencing oligonucleotides for drug discovery and development.

Gene silencing, the specific inhibition of unwanted gene expression by blocking mRNA activity, has long appeared to be an ideal strategy to leverage new genomic knowledge for drug discovery and development. But effective delivery has continuously been a limiting factor. In the past two decades, valuable progress has been made through the development of various chemically modified single-stranded antisense oligonucleotides, with improved properties such as enhanced stability, higher affinity and lower toxicity. Although short interfering RNA (siRNA) can provide better specificity and stronger efficacy by means of RNA interference (RNAi), in vivo delivery of siRNA often relies on plasmids or vectors, both of which present therapeutic safety risks. This review presents a brief history of gene silencing from PS-ODN through siRNA, introduces DNP-RNA--a more potent and easily delivered gene silencing platform--and compares its performance with that of siRNA and other AS-oligonucleotides.

Animals↗
PubMed2005

Neuromuscular function in plant parasitic nematodes: a target for novel control strategies?

Over the last decade the need for new strategies and compounds to control parasitic helminths has become increasingly urgent. The neuromuscular systems of these worms have been espoused as potential sources of target molecules for new drugs which may address this need. One facet of helminth neuromuscular biology which has garnered considerable research interest is that of neuropeptidergic neurotransmission, particularly regarding parasites of humans and animals, as well as free-living nematode model species. This research interest has been piqued by the fact that neuropeptides have been demonstrated to be fundamentally important to nematode biology and thus may be of utility in this search for new drug targets. This review focuses on the neuropeptide biology of plant parasitic nematodes, a subject which has been comparatively neglected despite the fact that the search for alternative control measures also extends to these economically important parasites. We focus on the FMRFamide-like peptide (FLP) neuropeptides and the complexity and distribution of this peptide family in plant parasitic nematodes. Possible roles for FLPs in plant parasitic nematode behaviour, as elucidated by a combination of molecular imaging techniques and RNA interference (RNAi), are discussed. We propose that disruption of FLP neurosignalling in plant parasitic nematodes represents a novel form of pest control and speculate as to how this may be achieved.

Animals↗
PubMed2006

Mutation of siRNA results in thermodynamically unstable duplex which influences knockdown of dmrt1 by RNA interference.

MicroRNAs (miRNAs) constitute a growing class of non-coding RNAs that are thought to regulate gene expression by translational repression and mRNA degradation. We report here that short interfering RNA (siRNA) mutation significantly changed kinetics of the folding and unfolding of secondary structures and decreased Tm value of the duplex melting. The mutant duplex was more unstable thermodynamically than the normal structure. Furthermore negative effects of the mutation on RNA interference (RNAi) was observed in both mouse dmrt1 transfected COS-7 and Sertoli cells in which endogenous dmrt1 was expressed. However, interference efficiency of mutational and normal duplex in Sertoli cells was not significant in comparison with those in dmrt1 transfected COS-7 cells, suggesting complex regulatory mechanisms in RNAi in endogenous dmrt1 expression. Abundance of intronic miRNA structures observed in the dmrt1 gene may also contribute to the precise regulation cascade in the dmrt1 expression. These findings help in further understanding RNA silence in vertebrate development and drug design for target gene.

Animals↗
PubMed2003

Efficiency and specificity of RNA interference generated by intra- and intermolecular double stranded RNA in Trypanosoma brucei.

In many eukaryotes, double-stranded (ds) RNA leads to specific degradation of RNA of cognate sequence, a process termed RNA interference (RNAi). Here we used the protozoan Trypanosoma brucei as a model to investigate efficiency and specificity of RNAi generated by expression of long dsRNA of PFRA and PFRC genes, which code for flagellar proteins required for cell motility. Consequences of RNAi were monitored at all three levels: target RNA expression, protein expression and phenotype observation, using population or individual cell analysis. Expression of PFRA dsRNA from an inverted repeat was extremely efficient, knocking down PFRA RNA and PFRA protein, and producing a severe paralysis phenotype. Silencing by expression of PFRA dsRNA using a dual facing promoter system was also very efficient, producing a clear phenotype, although low amounts of PFRA RNA and PFRA protein were detected. Expression via the dual facing promoters of PAR2 dsRNA (83% overall identity with PFRA, including nine blocks of >20 nt total identity) did not produce significant reduction of total amounts of PFRA RNA or PFRA protein. However, individual cell analysis by immunofluorescence revealed that 10-60% cells (depending on subclones) exhibited lower PFRA amounts in their flagellum, producing a reduced-motility phenotype.

Animals↗
PubMed2006

Moment analysis for kinetics of gene silencing by RNA interference.

RNA interference (RNAi) was quantitatively evaluated from a kinetic viewpoint. A simple kinetic evaluation based on moment analysis was proposed, assuming suppression and recovery phases of gene expression. We defined the area under the curve of the inhibitory effect (AUC(IE)) as an index of the total intensity of RNAi and the mean response time of the inhibitory effect (MRT(IE)) as an index of its duration. The proposed kinetic analysis helps to understand the RNAi effect in a quantitative and time-dependent manner, which will be beneficial for designing RNAi-based gene silencing for both experimental and therapeutic purposes.

Animals↗
PubMed2005

An antiviral role for the RNA interference machinery in Caenorhabditis elegans.

RNA interference (RNAi) is a sequence-specific gene-silencing mechanism triggered by exogenous dsRNA. In plants an RNAi-like mechanism defends against viruses, but the hypothesis that animals possess a similar natural antiviral mechanism related to RNAi remains relatively untested. To test whether genes needed for RNAi defend animal cells against virus infection, we infected wild-type and RNAi-defective cells of the nematode C. elegans with vesicular stomatitis virus engineered to encode a GFP fusion protein. We show that upon infection, cells lacking components of the RNAi apparatus produce more GFP and infective particles than wild-type cells. Furthermore, we show that mutant cells with enhanced RNAi produce less GFP. Our observation that multiple genes required for RNAi are also required for resistance to vesicular stomatitis virus suggests that the RNAi machinery functions in resistance to viruses in nature.

Animals↗
PubMed2006

Targeted suppression of E-cadherin gene expression in bovine preimplantation embryo by RNA interference technology using double-stranded RNA.

RNA interference (RNAi) has become acknowledged as an effective and useful tool to study gene function in diverse groups of cells. We aimed to suppress the expression of the E-cadherin gene during in vitro development of bovine preimplantation embryos using RNAi approach. In this experiment the effect of microinjection of E-cadherin and Oct-4 (as control) double-stranded (ds) RNA on the mRNA and protein expression level of the target E-cadherin gene was investigated. For this, a 496 bp long bovine E-cadherin and 341 bp long Oct-4 dsRNA sample were prepared using in vitro transcription. In vitro produced bovine zygotes were categorized into four treatment groups including those injected with E-cadherin dsRNA, Oct-4 dsRNA, RNase-free water, and uninjected controls. While the injection of E-cadherin dsRNA resulted in the reduction of E-cadherin mRNA and protein levels at the morula and blastocyst stage, the transcript and protein product remained unaffected in the Oct-4 dsRNA, water injected and uninjected control groups. The relative abundance of E-cadherin mRNA in the E-cadherin dsRNA injected morula stage embryos was reduced by 80% compared to the control group (P < 0.05). The Western blot analysis also showed a significant decrease in the E-cadherin protein (119 kDa) in E-cadherin dsRNA injected embryos compared to the other three groups. Microinjection of E-cadherin dsRNA has resulted only 22% blastocyst rate compared to 38%-40% in water injected and uninjected controls. In conclusion, our results indicated the suppression of E-cadherin mRNA and protein has resulted in lower blastocyst rate and the RNAi technology is a promising approach to study the function of genes in early bovine embryogenesis.

Animals↗
PubMed2006

Thermodynamics of RNA-RNA binding.

BACKGROUND: Reliable prediction of RNA-RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA-mRNA binding and antisense interactions. The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to 'open' the binding site and (2) the energy gained from hybridization. METHODS: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. RESULTS: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target. AVAILABILITY: RNAup will be distributed as part of the Vienna RNA Package, www.tbi.univie.ac.at/~ivo/RNA/

Algorithms↗
PubMed2006

RNA interference techniques to study epithelial cell adhesion and polarity.

Polarized epithelial cells are characterized by distinct plasma membrane domains and asymmetrical distribution of cell surface proteins and lipids. In vertebrates, tight junctions act as a fence between the apical and basolateral domains. Although many of the key components of the polarity machinery have been identified, their functions in cell polarization and junction formation remain to be determined. With the rapid improvement of the RNA interference (RNAi) technique, it is now possible to silence the expression of these polarity proteins in mammalian cells and to systematically analyze their distinct roles in orchestrating the polarization program. Here we describe approaches to achieve specific gene suppression in MDCK cells, a well-established cell culture model of canine kidney cells. We discuss the potential challenges and problems associated with the RNAi technique and describe basic protocols for suppressing gene expression using a vector-based short hairpin RNA (shRNA) expression system coupled with nucleofection.

Adaptor Proteins, Signal Transducing↗
PubMed2005

Drosophila mitochondrial transcription factor B1 modulates mitochondrial translation but not transcription or DNA copy number in Schneider cells.

We report the cloning and molecular analysis of Drosophila mitochondrial transcription factor (d-mtTF) B1. An RNA interference (RNAi) construct was designed that reduces expression of d-mtTFB1 to 5% of its normal level in Schneider cells. In striking contrast with our previous study on d-mtTFB2, we found that RNAi knock-down of d-mtTFB1 does not change the abundance of specific mitochondrial RNA transcripts, nor does it affect the copy number of mitochondrial DNA. In a corollary manner, overexpression of d-mtTFB1 did not increase either the abundance of mitochondrial RNA transcripts or mitochondrial DNA copy number. Our data suggest that, unlike d-mtTFB2, d-mtTFB1 does not have a critical role in either transcription or regulation of the copy number of mitochondrial DNA. Instead, because we found that RNAi knockdown of d-mtTFB1 reduces mitochondrial protein synthesis, we propose that it serves its primary role in modulating translation. Our work represents the first study to document the role of mtTFB1 in vivo and establishes clearly functional differences between mtTFB1 and mtTFB2.

Amino Acid Sequence↗
PubMed2006

RNA interference as potential therapy for neurodegenerative disease: applications to inclusion-body myositis?

The discovery of RNA interference (RNAi) has led to powerful new approaches to silence targeted genes in a sequence-specific manner. The potential therapeutic application of RNAi to neurologic disease is highlighted by the recent success of several laboratories in suppressing the expression of neurodegenerative disease genes in transgenic mouse models. Here I discuss potential applications of RNAi to inclusion-body myositis (IBM) after first reviewing its application more generally to neurologic disease. The clearest application of RNAi to IBM is as a research tool to identify critical target genes that contribute to pathogenesis. Provided that proximal pathogenic targets are identified, RNAi could surface as a potential therapeutic strategy to modulate their expression.

Animals↗
PubMed2004

Long double-stranded RNA-mediated RNA interference as a tool to achieve site-specific silencing of hypothalamic neuropeptides.

RNA interference (RNAi) has become a popular tool to silence gene expression in a variety of in vitro and in vivo systems. However, it has met with limited success in inhibiting gene expression in adult mammals. Here we demonstrate that long double-stranded RNA (dsRNA) can be used to create a "site-specific", transient knockdown of genes in a fashion that is phenotypically akin to genetically manipulated organisms. Corticotropin-releasing factor (CRF) and arginine vasopressin (AVP) that regulate a variety of physiological processes including the hypothalamic-pituitary-adrenal axis (HPA axis), energy and water homeostasis were used as model systems. Stereotaxic injections of dsRNA against CRF and AVP in the PVN specifically abolished the expression of these genes in the PVN leaving expression in other loci intact. Control dsRNA did not affect CRF or AVP expression in any brain region, suggesting that dsRNA did not shut down global protein synthesis. ANOVA showed significant main effects of silencing of CRF on dampening of the stress-activated release of adrenocorticotrophin hormone (ACTH) (F(2,7)=4.87; p<0.047). Silencing of AVP resulted in increased water consumption, increased urine output and decreased urine osmolality as compared to control dsRNA-treated rats. Furthermore, dsRNA had no obvious deleterious effects on body weight or food consumption, variables considered essential in ruling out adverse physiologic effects in animal models. Thus, using long dsRNA, we were able to ascertain site-specific roles of CRF and AVP in adult rats without any developmental compensation and in a wild-type background.

Adrenocorticotropic Hormone↗