RNA interference: listening to the sound of silence

Mutagenesis by an antisense oligonucleotide and its degradation product

The European Medicines Agency has expressed concern regarding (1) the potential for antisense oligonucleotide (ASO) therapeutics to induce sequence-specific mutation at genomic DNA and (2) the capability of ASO degradation products (nucleotide analogues) to incorporate into newly synthesized genomic DNA via DNA polymerase and cause mutation if base pairing occurs with reduced fidelity. Treating human lymphoblastoid cells with a biologically active antisense molecule induced sequence-specific mutation within genomic DNA over fourfold, in a system where RAD51 protein expression was induced. This finding has implications for ASO therapeutics with individuals with an induced DNA damage response, such as cancer patients. Furthermore, a phosphorothioate nucleotide analogue potently induced mutation at genomic DNA two orders of magnitude above control. This study shows that a biologically active ASO molecule can induce heritable sequence alterations, and if degraded, its respective analogue may incorporate into genomic DNA with mutagenic consequences.

Molecular dissection of Flock house virus protein B2 reveals that electrostatic interactions between N-terminal domains of B2 monomers are critical for dimerization

Flock house virus (FHV) encodes a suppressor protein B2 to overcome antiviral RNA silencing during infection. Biochemical analyses have shown that a homodimer of B2 binds to double-stranded RNA to inhibit dicer-mediated cleavage of dsRNA and incorporation of small interfering RNAs into the RNA-induced silencing complex. In this study, using FHV-Nicotiana benthamiana system, we identified that the charged amino acids at the N-terminus of B2 are critical for dimerization. Interestingly, B2 mutants defective in dimerization exhibited enhanced silencing suppressor activity, Furthermore, we found that the C-terminal charged amino acids are dispensable for B2 dimerization and viral RNA silencing suppression but are critical for transgene silencing suppression. Additional yeast two hybrid assays revealed that dimerization of B2 is not essential for interacting with the RNA silencing machinery. Taken together, our data provide evidence that both monomeric and dimeric B2 proteins function in different modes to suppress RNA silencing.

Functional genomics approaches in parasitic helminths

As research on parasitic helminths is moving into the post-genomic era, an enormous effort is directed towards deciphering gene function and to achieve gene annotation. The sequences that are available in public databases undoubtedly hold information that can be utilized for new interventions and control but the exploitation of these resources has until recently remained difficult. Only now, with the emergence of methods to genetically manipulate and transform parasitic worms will it be possible to gain a comprehensive understanding of the molecular mechanisms involved in nutrition, metabolism, developmental switches/maturation and interaction with the host immune system. This review focuses on functional genomics approaches in parasitic helminths that are currently used, to highlight potential applications of these technologies in the areas of cell biology, systems biology and immunobiology of parasitic helminths.

Pulmonary delivery of therapeutic siRNA

Small interfering RNA (siRNA) has a huge potential for the treatment or prevention of various lung diseases. Once the RNA molecules have successfully entered the target cells, they could inhibit the expression of specific gene sequence through RNA interference (RNAi) mechanism and generate therapeutic effects. The biggest obstacle to translating siRNA therapy from the laboratories into the clinics is delivery. An ideal delivery agent should protect the siRNA from enzymatic degradation, facilitate cellular uptake and promote endosomal escape inside the cells, with negligible toxicity. Lung targeting could be achieved by systemic delivery or pulmonary delivery. The latter route of administration could potentially enhance siRNA retention in the lungs and reduce systemic toxic effects. However the presence of mucus, the mucociliary clearance actions and the high degree branching of the airways present major barriers to targeted pulmonary delivery. The delivery systems need to be designed carefully in order to maximize the siRNA deposition to the diseased area of the airways. In most of the pulmonary siRNA therapy studies in vivo, siRNA was delivered either intratracheally or intranasally. Very limited work was done on the formulation of siRNA for inhalation which is believed to be the direction for future development. This review focuses on the latest development of pulmonary delivery of siRNA for the treatment of various lung diseases.

RNAi knockdown of PIK3CA preferentially inhibits invasion of mutant PIK3CA cells

AIM: To explore the effects of siRNA silencing of PIK3CA on proliferation, migration and invasion of gastric cancer cells and to investigate the underlying mechanisms.

METHODS: The mutation of PIK3CA in exons 9 and 20 of gastric cancer cell lines HGC-27, SGC-7901, BGC-823, MGC-803 and MKN-45 was screened by polymerase chain reaction (PCR) followed by sequencing. BGC-823 cells harboring no mutations in either of the exons, and HGC-27 cells containing PIK3CA mutations were employed in the current study. siRNA targeting PIK3CA was chemically synthesized and was transfected into these two cell lines in vitro. mRNA and protein expression of PIK3CA were detected by real-time PCR and Western blotting, respectively. We also measured phosphorylation of a serine/threonine protein kinase (Akt) using Western blotting. The proliferation, migration and invasion of these cells were examined separately by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), wound healing and Transwell chambers assay.

RESULTS: The siRNA directed against PIK3CA effectively led to inhibition of both endogenous mRNA and protein expression of PIK3CA, and thus significantly down-regulated phosphorylation of Akt (P < 0.05). Furthermore, simultaneous silencing of PIK3CA resulted in an obvious reduction in tumor cell proliferation activity, migration and invasion potential (P < 0.01). Intriguing, mutant HGC-27 cells exhibited stronger invasion ability than that shown by wild-type BGC-823 cells. Knockdown of PIK3CA in mutant HGC-27 cells contributed to a reduction in cell invasion to a greater extent than in non-mutant BGC-823 cells.

CONCLUSION: siRNA mediated targeting of PIK3CA may specifically knockdown the expression of PIK3CA in gastric cancer cells, providing a potential implication for therapy of gastric cancer.

Systemic RNA-interference in the honeybee Apis mellifera: tissue dependent uptake of fluorescent siRNA after intra-abdominal application observed by laser-scanning microscopy

RNA interference has been successfully used in adult honeybees, but there are only few reports about abdominal application of dsRNA/siRNA which have reached more distant tissues than the fat body. We studied systemic RNAi in honeybees by injecting fluorescent siRNA of the ubiquitously expressed honeybee homologue of the Glycerol-3-Phosphate Dehydrogenase (amGpdh) into the abdomens of adult bees and followed them by laser scanning microscopy and qPCR. The fat body was the sole tissue emitting fluorescence and showing a decreased gene expression, whereas the siRNA had apparently not reached the other tissues. Therefore, we conclude that certain genes in other tissues than the fat body cannot be easily reached by injecting siRNA into the body cavity. In particular, the lack of amGpdh knock down in ovaries after amGpdh dsRNA injection, supports that in some cases it may be particularly difficult to interfere with gene expression in ovaries by intra-abdominal injection. In these cases alternative inhibition techniques may be required to achieve an organismic non-lethal disruption of transcription.

Col V siRNA engineered tenocytes for tendon tissue engineering

The presence of uniformly small collagen fibrils in tendon repair is believed to play a major role in suboptimal tendon healing. Collagen V is significantly elevated in healing tendons and plays an important role in fibrillogenesis. The objective of this study was to investigate the effect of a particular chain of collagen V on the fibrillogenesis of Sprague-Dawley rat tenocytes, as well as the efficacy of Col V siRNA engineered tenocytes for tendon tissue engineering. RNA interference gene therapy and a scaffold free tissue engineered tendon model were employed. The results showed that scaffold free tissue engineered tendon had tissue-specific tendon structure. Down regulation of collagen V α1 or α2 chains by siRNAs (Col5α1 siRNA, Col5α2 siRNA) had different effects on collagen I and decorin gene expressions. Col5α1 siRNA treated tenocytes had smaller collagen fibrils with abnormal morphology; while those Col5α2 siRNA treated tenocytes had the same morphology as normal tenocytes. Furthermore, it was found that tendons formed by coculture of Col5α1 siRNA treated tenocytes with normal tenocytes at a proper ratio had larger collagen fibrils and relative normal contour. Conclusively, it was demonstrated that Col V siRNA engineered tenocytes improved tendon tissue regeneration. And an optimal level of collagen V is vital in regulating collagen fibrillogenesis. This may provide a basis for future development of novel cellular- and molecular biology-based therapeutics for tendon diseases.

Self-assembled multifunctional nanoplexes for gene inhibitory therapy

Aim: To enhance the stability of siRNA while improving their therapeutic properties and visualization at the target site, a novel nanoplex system was developed. Materials & Methods: The designed nanoplex system involved functionalizing siRNA with near-infrared quantum dots and loading them into histidylated glycol chitosan (GC-His). Results: Colocalization studies revealed a twofold increase in siRNA uptake after encapsulation with GC-His and nanoparticles were localized in cytoplasm, suggesting that histidine promoted their dissociation from the endosomal membranes. Furthermore, as opposed to siRNAs treated with commercial transfection reagent, siRNAs loaded within GC-His showed a marked reduction (64%) of MDM2 protein expression 24 h after transfection. Conclusion: These findings concur that GC-His/siRNA-quantum dot nanoplexes are promising multifunctional vehicles for gene inhibitory therapy.

MicroRNA-27a regulates basal transcription by targeting the p44 subunit of general transcription factor IIH

General transcription factor IIH (TFIIH) is a complex RNA polymerase II basal transcription factor comprising 10 different polypeptides that display activities involved in transcription and DNA repair processes. Although biochemical studies have uncovered TFIIH importance, little is known about how the mRNAs that code for TFIIH subunits are regulated. Here it is shown that mRNAs encoding seven of the TFIIH subunits (p34, p44, p52, p62, XPB, CDK7, and p8) are regulated at the posttranscriptional level in a Dicer-dependent manner. Indeed, abolition of the miRNA pathway induces abnormal accumulation, stabilization, and translational activation of these seven mRNAs. Herein, miR-27a was identified as a key regulator of p44 mRNA. Moreover, miR-27a was shown to destabilize the p44 subunit of the TFIIH complex during the G2-M phase, thereby modulating the transcriptional shutdown observed during this transition. This work is unique in providing a demonstration of global transcriptional regulation through the action of a single miRNA.

Molecular targeting of CSN5 in human hepatocellular carcinoma: a mechanism of therapeutic response

Development of targeted therapy for hepatocellular carcinoma (HCC) remains a major challenge. We have recently identified an elevated expression of the fifth subunit of COP9 signalosome (CSN5) in early HCC as compared to dysplastic stage. In the present study, we explored the possibility of CSN5 being a potential therapeutic target for HCC. Our results show that CSN5 knockdown by small interfering (si) RNA caused a strong induction of apoptosis and inhibition of cell cycle progression in HCC cells in vitro. The downregulation of CSN5 was sufficient to interfere with CSN function as evidenced by the accumulation of neddylated Cullin1 and changes in the protein levels of CSN controlled substrates SKP2, p53, p27 and NF-kB, albeit to a different degree depending on the HCC cell line, which could account for the CSN5 knockdown phenotype. The transcriptomic analysis of CSN5 knockdown signature showed that the anti-proliferative effect was driven by a common subset of molecular alterations including downregulation of CDK6 and ITGB1, which were functionally interconnected with key oncogenic regulators MYC and TGFβ1 involved in the control of proliferation, apoptotic cell death and HCC progression. Consistent with microarray analysis, western blotting revealed that CSN5 depletion increased phosphorylation of Smad 2/3, key mediators of TGFβ1 signaling, decreased the protein levels of ITGB1, CDK6, and cyclin D1 and caused reduced expression of anti-apoptotic Bcl-2 while elevating the levels of pro-apoptotic Bak. A chemically modified variant of CSN5 siRNA was then selected for in vivo application based on the growth inhibitory effect and minimal induction of unwanted immune response. Systemic delivery of the CSN5 3/8 variant by stable-nucleic-acid-lipid-particles (SNALP) significantly suppressed the tumor growth in Huh7-luc⁺ orthotopic xenograft model. Taken together, these results indicate that CSN5 plays a pivotal role in HCC pathogenesis and maybe an attractive molecular target for systemic HCC therapy.

Advances in mRNA silencing and transgene expression: a gateway to functional genomics in schistosomes

The completion of the WHO Schistosoma Genome Project in 2008, although not fully annotated, provides a golden opportunity to actively pursue fundamental research on the parasites genome. This analysis will aid identification of targets for drugs, vaccines and markers for diagnostic tools as well as for studying the biological basis of drug resistance, infectivity and pathology. For the validation of drug and vaccine targets, the genomic sequence data is only of use if functional analyses can be conducted (in the parasite itself). Until recently, gene manipulation approaches had not been seriously addressed. This situation is now changing and rapid advances have been made in gene silencing and transgenesis of schistosomes.

RNAi-mediated knockdown of cyclooxygenase2 inhibits the growth, invasion and migration of SaOS2 human osteosarcoma cells: a case control study

Background

Cyclooxygenase2 (COX-2), one isoform of cyclooxygenase proinflammatory enzymes, is responsible for tumor development, invasion and metastasis. Due to its role and frequent overexpression in a variety of human malignancies, including osteosarcoma, COX-2 has received considerable attention. However, the function of COX-2 in the pathogenesis of cancer is not well understood. We examined the role of COX-2 in osteosarcoma.

Methods

We employed lentivirus mediated-RNA interference technology to knockdown endogenous gene COX-2 expression in human osteosarcoma cells (SaOS2) and analyzed the phenotypical changes. The effect of COX-2 treatment on the proliferation, cell cycle, invasion and migration of the SaOS2 cells were assessed using the MTT, flow cytometry, invasion and migration assays, respectively. COX-2, vascular endothelial growth factor (VEGF), epidermal growth factor (EGF), basic fibroblast growth factor (bFGF) mRNA and protein expression were detected by RT-PCR and western blotting.

Results

Our results indicate that a decrease of COX-2 expression in human osteosarcoma cells significantly inhibited the growth, decreased the invasion and migration ability of SaOS2 cells. In addition, it also reduced VEGF, EGF and bFGF mRNA and protein expression.

Conclusions

The COX-2 signaling pathway may provide a novel therapeutic target for the treatment of human osteosarcoma.

Direct transfer of synthetic double-stranded RNA into protoplasts of Arabidopsis thaliana

Double-stranded (ds) RNA interference (RNAi) is widely used as a reverse genetic approach for functional analysis of plant genes. Constitutive or transient RNAi effects in plants have been achieved via generating stable transformants expressing dsRNAs or artificial microRNAs (amiRNAs) in planta or by viral-induced gene silencing (VIGS). Although these tools provide outstanding resources for functional genomics, they require generation of vectors expressing dsRNAs or amiRNAs against targeted genes, transformation and propagation of transformed plants, or maintenance of multiple VIGS lines and thus impose time, labor, and space requirements. As we showed recently, these limitations can be circumvented by inducing RNAi effects in protoplasts via transfecting them with in vitro-synthesized dsRNAs. In this chapter we detail the procedure for transient gene silencing in protoplasts using synthetic dsRNAs and provide examples of approaches for subsequent functional analyses.

Inhibition of viral hemorrhagic septicemia virus replication using a short hairpin RNA targeting the G gene

RNA interference (RNAi), a mechanism for post-transcriptional silencing of homologous genes by double-stranded RNA (dsRNA), has emerged as an antiviral strategy in animals. In this study, the epithelioma papulosum cyprini (EPC) cell line, in combination with a fugu-U6-promoter-driven shRNA construct designed against G gene, was used to investigate whether short hairpin RNA (shRNA) could inhibit viral hemorrhagic septicemia virus (VHSV) proliferation by sequence-specific RNAi. The results showed that transfection with a shRNA-producing construct (shRNA-VG594) resulted in a sequence-specific knockdown of G gene mRNA in EPC cells. There were no significant differences in IFN-induced Mx1 gene expression among cells transfected with each shRNA vector including shRNA-VG594, -VG594sc (two nucleotides mismatch) and -EGFP (non-specific control), suggesting that knockdown of G gene expression was not due to an IFN response but instead by sequence-specific RNAi. Transfection of EPC cells with shRNA-VG594 conferred resistance to VHSV, and this anti-VHSV effect was not observed when using a two-nucleotide-mismatched shRNA-VG594sc or a shRNA targeting EGFP. Furthermore, shRNA-VG594 expressed in EPC cells did not confer protection against infectious hematopoietic necrosis virus (IHNV), suggesting sequence-specific RNAi-dependent suppression of viral replication.

Small molecule-mediated inhibition of translation by targeting a native RNA G-quadruplex

Herein, we show that a naturally occurring RNA G-quadruplex element within the 5' UTR of the human NRAS proto-oncogene is a target for a small molecule that inhibits translation in vitro. The present study provides a first demonstration that natural 5' UTR mRNA G-quadruplexes have potential as molecular targets for small molecules that modulate translation.

Natural and artificial mutants as valuable resources for functional genomics and molecular breeding

With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs) is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.

Cricket paralysis virus antagonizes Argonaute 2 to modulate antiviral defense in Drosophila

Insect viruses have evolved strategies to control the host RNAi antiviral defense mechanism. In nature, Drosophila melanogaster C virus (DCV) infection causes low mortality and persistent infection, whereas the closely related cricket paralysis virus (CrPV) causes a lethal infection. We show that these viruses use different strategies to modulate the host RNAi defense machinery. The DCV RNAi suppressor (DCV-1A) binds to long double-stranded RNA and prevents processing by Dicer2. In contrast, the CrPV suppressor (CrPV-1A) interacts with the endonuclease Argonaute 2 (Ago2) and inhibits its activity without affecting the microRNA (miRNA)-Ago1-mediated silencing. We examined the link between viral RNAi suppressors and the outcome of infection using recombinant Sindbis viruses encoding either CrPV-1A or DCV-1A. Flies infected with Sindbis virus expressing CrPV-1A showed a marked increase in virus production, spread and mortality. In contrast, Sindbis pathogenesis was only modestly increased by expression of DCV- 1A. We conclude that RNAi suppressors function as virulence factors in insects and can target the Drosophila RNAi pathway at different points.

RNA interference with 2',4'-bridged nucleic acid analogues

In this study, a number of 2',4'-BNA- and 2',4'-BNA(NC)-modified siRNAs were designed and synthesized. Their thermal stability, nuclease resistance and gene silencing properties against cultured mammalian cells were evaluated and compared with those of natural siRNAs. The 2',4'-BNA- and 2',4'-BNA(NC)-modified siRNAs (named siBNA and siBNA(NC), respectively) showed very high T(m) values, were remarkably stable in serum sample and showed promising RNAi properties equal to those exhibited by natural siRNAs. Thermally stable siBNAs composed of slightly modified sense and antisense strands were capable of suppressing gene expression equal to that of natural siRNA. A number of modifications on the sense strand by 2',4'-BNA or 2',4'-BNA(NC), either consecutively or separated by natural RNA nucleotides, is tolerable in RNAi machinery. Modifications at the Argonauate (Ago2) cleavage site of the sense strand (9-11th positions from the 5'-end of the sense strand) produced variable results depending on siRNA composition. Mostly, modification at the 10th position diminished siRNA activity. In moderately modified siRNAs, modification at the 11th position displayed usual RNAi activity, while modification at the 9th position showed variable results depending on siRNA composition.

High GC content: critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana

Plants like Arabidopsis thaliana are convenient model systems to study fundamental questions related to regulation of the stress transcriptome in response to stress challenges. Microarray results of the Arabidopsis transcriptome indicate that several genes could be upregulated during multiple stresses. High-salinity, drought, and low temperature are three common environmental stress factors that seriously influence plant growth and development worldwide. Recently, microRNAs (miRNAs) have emerged as a class of gene expression regulators that have also been linked to stress responses. However, the relationship between miRNA expression and stress responses is just beginning to be explored. Here we have computationally analyzed 123 non redundant miRNA sequences reported for Arabidopsis thaliana, including 17 miRNA sequences which were reported to be stress regulated in literature. A significant increase in the GC content of stress regulated miRNA sequences was observed which further extends the view that miRNAs act as ubiquitous regulators under stress conditions. GC content may also be considered as a critical parameter for predicting stress regulated miRNAs in plants like Arabidopsis thaliana.

Effect of siRNA targeting HIF-1alpha combined L-ascorbate on biological behavior of hypoxic MiaPaCa2 cells

The aim of the study was to observe the effect of small interference RNA (siRNA) targeting hypoxia-inducible factor 1alpha (HIF-1alpha) combined L-ascorbate on proliferation, migration, and apoptosis of hypoxic MiaPaCa2 human pancreatic cancer cells. A cassette encoding siRNA targeting HIF-1alpha mediated by recombinant adeno-associated virus (rAAV) was constructed, giving rAAV-siHIF. rAAV-siHIF and L-ascorbate, which were used alone or in combination, were delivered to exponentially growing MiaPaCa2 cells under hypoxic conditions. Then, we observed the expression of HIF-1alpha mRNA and protein, the proliferation, apoptosis, and migration of MiaPaCa2 cells by real-time PCR, Western blot, MTT, TUNEL, and Transwell assay, respectively. Under hypoxic conditions, rAAV-siHIF inhibited the expression of HIF-1alpha mRNA in MiaPaCa2 cells but L-ascorbate did not. However, rAAV-siHIF and L-ascorbate both inhibited the expression of HIF-1alpha protein and the proliferation and migration of MiaPaCa2 cells and induced MiaPaCa2 cell apoptosis. The effect in the combined group was more efficient than that seen when rAAV-siHIF or L-ascorbate was used separately. rAAV-siHIF and L-ascorbate both affect biological behavior of hypoxic MiaPaCa2 cells through modulating HIF-1alpha protein expression and rAAV-siHIF and L-ascorbate have synergy under hypoxic conditions.

Silent chromatin at the middle and ends: lessons from yeasts

Eukaryotic centromeres and telomeres are specialized chromosomal regions that share one common characteristic: their underlying DNA sequences are assembled into heritably repressed chromatin. Silent chromatin in budding and fission yeast is composed of fundamentally divergent proteins tat assemble very different chromatin structures. However, the ultimate behaviour of silent chromatin and the pathways that assemble it seem strikingly similar among Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe) and other eukaryotes. Thus, studies in both yeasts have been instrumental in dissecting the mechanisms that establish and maintain silent chromatin in eukaryotes, contributing substantially to our understanding of epigenetic processes. In this review, we discuss current models for the generation of heterochromatic domains at centromeres and telomeres in the two yeast species.

Silencing epidermal growth factor receptor by RNA interference in glioma

Glioblastoma multiforme (GBM) can arise de novo or progress from a lower to higher grade and can possess a series of genetic alterations and dynamic progressions, which have been correlated with the molecular pathology of GBM. Epidermal growth factor receptor (EGFR) has been shown to be overexpressed in a variety of tumors and is one of the important mediators responsible for the development of high-grade gliomas, especially in primary glioblastomas. Most recently, RNA interference (RNAi), in which double-stranded RNA (dsRNA) induces sequence-specific degradation of the targeting messenger RNA (mRNA), has been extensively developed and studied. RNAi is able to silence the targeted gene expression more efficiently and specifically. In the present study, we silence the EGFR expression using two separate short interfering RNAs (siRNAs) targeting the extracellular ligand-binding domain and intracellular tyrosine kinase domain, respectively. We demonstrate that suppression of EGFR expression, by using either antisense or siRNA approaches, inhibits U251 glioblastoma cell growth in vitro and in vivo, and siRNA seems to be more effective than the antisense approach.

The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes

Genetic studies and large-scale sequencing experiments have revealed that the PIWI subfamily proteins and PIWI-interacting RNAs (piRNAs) play an important role in germ line development and transposon control. Biochemical studies in vitro have greatly contributed to the understanding of small interfering RNA (siRNA) and microRNA (miRNA) pathways. However, in vitro analyses of the piRNA pathway have been thus far quite challenging, because their expression is largely restricted to the germ line. Here we report that Bombyx mori ovary-derived cultured cell line, BmN4, endogenously expresses two PIWI subfamily proteins, silkworm Piwi (Siwi) and Ago3 (BmAgo3), and piRNAs associated with them. Siwi-bound piRNAs have a strong bias for uridine at their 5' end and BmAgo3-bound piRNAs are enriched for adenine at position 10. In addition, Siwi preferentially binds antisense piRNAs, whereas BmAgo3 binds sense piRNAs. Moreover, we identified many pairs in which Siwi-bound antisense and BmAgo3-bound sense piRNAs are overlapped by precisely 10 nt at their 5' ends. These signatures are known to be important for secondary piRNA biogenesis in other organisms. Taken together, BmN4 is a unique cell line in which both primary and secondary steps of piRNA biogenesis pathways are active. This cell line would provide useful tools for analysis of piRNA biogenesis and function.

Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus

Rice stripe virus (RSV) is a single-stranded (ss) RNA virus belonging to the genus Tenuivirus. RSV is present in many East Asian countries and causes severe diseases in rice fields, especially in China. In this study, we analyzed six proteins encoded by the virus for their abilities to suppress RNA silencing in plant using a green fluorescent protein (GFP)-based transient expression assay. Our results indicate that NS3 encoded by RSV RNA3, but not other five RSV encoded proteins, can strongly suppress local GFP silencing in agroinfiltrated Nicotiana benthamiana leaves. NS3 can reverse the GFP silencing, it can also prevent long distance spread of silencing signals which have been reported to be necessary for inducing systemic silencing in host plants. The NS3 protein can significantly reduce the levels of small interfering RNAs (siRNAs) in silencing cells, and was found to bind 21-nucleotide ss-siRNA, siRNA duplex and long ssRNA but not long double-stranded (ds)-RNA. Both N and C terminal of the NS3 protein are critical for silencing suppression, and mutation of the putative nuclear localization signal decreases its local silencing suppression efficiency and blocks its systemic silencing suppression. The NS3-GFP fusion protein and NS3 were shown to accumulate predominantly in nuclei of onion, tobacco and rice cells through transient expression assay or immunocytochemistry and electron microscopy. In addition, transgenic rice and tobacco plants expressing the NS3 did not show any apparent alteration in plant growth and morphology, although NS3 was proven to be a pathogenicity determinant in the PVX heterogenous system. Taken together, our results demonstrate that RSV NS3 is a suppressor of RNA silencing in planta, possibly through sequestering siRNA molecules generated in cells that are undergoing gene silencing.

Knockdown of survivin expression by siRNAs enhances chemosensitivity of prostate cancer cells and attenuates its tumorigenicity

Survivin, a member of inhibitor of apoptosis family protein, has become an attractive therapeutic target in cancer due to its selective expression in tumor cells and its important roles for tumor cell viability. Here, we show that vector-based small interfering RNAs (siRNAs) silenced survivin expression in prostate cancer cells, resulting in significantly reduced cell proliferation and enhanced apoptosis, and increased the sensitivity of prostate cancer cells (PC-3) to the apoptosis- inducing agent, platinol. Furthermore, PC-3 cells transfected with the siRNA-expressing vector showed lower tumor formation in nude mice xenografts in vivo. These results demonstrated that inhibition of survivin expression by siRNA attenuated the malignant phenotypes of prostate cancer cells, and may provide a novel approach for gene therapy of androgen-independent prostate cancer.

The mechanisms on apoptosis by inhibiting VEGF expression in human breast cancer cells

This study investigated apoptotic mechanisms of down-expression vascular endothelial growth factor (VEGF) by short interfering RNA (siRNA) in human breast cancer MCF-7 cells. Human breast cancer cells were evaluated for the expression of VEGF and VEGF receptor 2 (VEGFR-2). siRNA targeting VEGF mRNA were chemically synthesized and transfected into cells with Lipofectamine2000. In vitro assessments were then made of the ability of anti-VEGF siRNA to knock down expression of VEGF and the subsequent effect this decreased expression had on breast cancer cell apoptosis. Growth curve construction and nude mice experimentation in vivo were performed to assess the effects of VEGF silencing on tumor growth. Those cells transfected with siRNA targeting VEGF showed a 65% knockdown in VEGF expression and a marked increase in cell apoptosis. The expression of Bcl-2 protein in MCF-7 cells was decreased, the level of Bax protein was kept the same, cytochrome c was released from mitochondria into cytosol, and the cleaved Caspase-3 protein rose after siRNA transfection. The siRNA targeting human VEGF could induce apoptosis in MCF-7 cells and the mechanism of apoptosis is possibly related with changing Bcl-2/Bax expression ratio, releasing cytochrome c from mitochondria into cytosol, and up-regulation of Caspase-3 protein, but also could suppress the growth of breast cancer cells in vivo. VEGF might be a potential therapeutic target for human breast cancer.

Downregulation of SS18-SSX1 expression by small interfering RNA inhibits growth and induces apoptosis in human synovial sarcoma cell line HS-SY-II in vitro

Substantial evidence indicates that the characteristic SS18-SSX fusion gene may play an important role in synovial sarcoma development and progression. For obtaining better insights into the genetic alterations and molecular mechanisms involved in synovial sarcomas and for developing novel therapeutic strategies for this disease, we first examined the efficiency of small interfering RNAs (siRNAs) targeting the SS18-SSX1 fusion gene in knocking down its expression in the human synovial sarcoma cell line HS-SY-II, and then evaluated the effects of downregulation of this gene on apoptosis, apoptosis-related gene expression, growth regulatory proteins, and the growth of tumor cells in vitro. We observed a marked decrease (by more than 87.6%) in SS18-SSX1 expression levels in cells transfected with a plasmid expressing hairpin siRNA for this gene, which was accompanied by (i) reduction in protein levels of cyclin D1 and cyclin A, (ii) reduction in antiapoptotic protein Bcl-2 and activation of caspase 3/apoptosis, and (iii) growth inhibition of HS-SY-II cells in vitro. Our results demonstrate that siRNA targeting of SS18-SSX1 may have therapeutic potential in the treatment of synovial sarcomas.

Effect of small interference RNA targeting HIF-1alpha mediated by rAAV combined L: -ascorbate on pancreatic tumors in athymic mice

To study the effect of recombinant adeno-associated virus (rAAV) vector bearing small inference RNA (siRNA) targeting hypoxia inducible factor 1alpha (HIF-1alpha) combined L: -ascorbate on pancreatic tumors in athymic mice primarily. A cassette encoding siRNA targeting HIF-1alpha mediated by rAAV was constructed, giving rAAV-siHIF. In vitro, rAAV-hrGFP, rAAV-siHIF and L: -ascorbate which were used alone or in combination were delivered to exponentially growing MiaPaCa2 cells. Then, we examined the expression of HIF-1alpha mRNA and protein, the secretion of VEGF in MiaPaCa2 cells under hypoxic condition with Real-time PCR, Western Blot, ELISA, respectively. In vivo, MiaPaCa2 cells were inoculated subcutaneously on the back of nude mice. Nude mice with xenograft tumor were randomly divided into equal groups and were injected with rAAV-hrGFP or rAAV-siHIF or were fed with L: -ascorbate. Then, we measured the size of tumor every 3 days and drew a tumor growth curve. After 30 days, all mice were sacrificed and the tumors were dissected. At last, we examined the expression of HIF-1alpha, VEGF and CD34 by immunohistochemistry and counted micro-vessel density (MVD). In vitro, we found that rAAV-siHIF could inhibit the expression of HIF-1alpha mRNA and protein in MiaPaCa2 human pancreatic cancer cells but L: -ascorbate could only restrain the expression of HIF-1alpha protein. Moreover, rAAV-siHIF and L: -ascorbate could all inhibit the secretion of vascular VEGF. In vivo, we found that rAAV-siHIF could inhibit the growth of nude mice xenograft tumor and the expression of HIF-1alpha and VEGF and MVD while L: -ascorbate can only inhibit the growth of xenograft tumor in the early and middle stage. These results suggest that rAAV-siHIF and L: -ascorbate can inhibit the growth of nude mice xenograft tumor and HIF-1alpha could be a target of pancreatic cancer genetic and pharmacological therapy.

Blocked autophagy sensitizes resistant carcinoma cells to radiation therapy

Autophagy or "self eating" is frequently activated in tumor cells treated with chemotherapy or irradiation. Whether autophagy represents a survival mechanism or rather contributes to cell death remains controversial. To address this issue, the role of autophagy in radiosensitive and radioresistant human cancer cell lines in response to gamma-irradiation was examined. We found irradiation-induced accumulation of autophagosomes accompanied by strong mRNA induction of the autophagy-related genes beclin 1, atg3, atg4b, atg4c, atg5, and atg12 in each cell line. Transduction of specific target-siRNAs led to down-regulation of these genes for up to 8 days as shown by reverse transcription-PCR and Western blot analysis. Blockade of each autophagy-related gene was associated with strongly diminished accumulation of autophagosomes after irradiation. As shown by clonogenic survival, the majority of inhibited autophagy-related genes, each alone or combined, resulted in sensitization of resistant carcinoma cells to radiation, whereas untreated resistant cells but not sensitive cells survived better when autophagy was inhibited. Similarly, radiosensitization or the opposite was observed in different sensitive carcinoma cells and upon inhibition of different autophagy genes. Mutant p53 had no effect on accumulation of autophagosomes but slightly increased clonogenic survival, as expected, because mutated p53 protects cells by conferring resistance to apoptosis. In our system, short-time inhibition of autophagy along with radiotherapy lead to enhanced cytotoxicity of radiotherapy in resistant cancer cells.

Gene silencing by RNAi in mammalian cells

This unit provides information how to use short interfering RNA (siRNA) for sequence specific gene silencing in mammalian cells. Several ways for siRNA generation and optimisation, as well as recommendations for cell transfection are presented.

Overview of RNA interference and related processes

The history of RNA interference (RNAi) has unfolded rapidly since 1997 with a series of discoveries from plants, fungi, and animals. Initially, the interest was directed towards development of gene silencing technology that could be applied in research, medical therapy, and crop improvement. However, as the underlying mechanism was revealed, it became apparent that RNAi manifests a novel system of genetic regulation that was only hinted at by previous data. This overview unit gives a brief history of the field, describes the natural role of RNAi and related processes, identifies strategies for RNAi and cosuppression in plants and animals, and describes methods for detection and characterization of siRNA and miRNA.

Therapeutic applications of aptamers

Aptamers constitute a new class of oligonucleotides that have gained therapeutic importance. With the approval of the first aptamer drug, pegaptanib, interest in this class of oligonucleotides, often referred to as 'chemical antibodies', has increased. This article discusses aptamers in relation to other oligonucleotide molecules such as antisense nucleotides, short inhibitory sequences, ribozymes and so on. The development of pegaptanib is looked at from the point of view of the challenges faced in converting aptamers into therapeutic molecules. Cases of other aptamers, which show promise as drugs, are discussed in slightly greater detail. Comparison with antibodies and small molecules, which have hitherto held monopoly in this area, is also made.

Silencing of the major family of NBS-LRR-encoding genes in lettuce results in the loss of multiple resistance specificities

The RGC2 gene cluster in lettuce (Lactuca sativa) is one of the largest known families of genes encoding nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins. One of its members, RGC2B, encodes Dm3 which determines resistance to downy mildew caused by the oomycete Bremia lactucae carrying the cognate avirulence gene, Avr3. We developed an efficient strategy for analysis of this large family of low expressed genes using post-transcriptional gene silencing (PTGS). We transformed lettuce cv. Diana (carrying Dm3) using chimeric gene constructs designed to simultaneously silence RGC2B and the GUS reporter gene via the production of interfering hairpin RNA (ihpRNA). Transient assays of GUS expression in leaves accurately predicted silencing of both genes and were subsequently used to assay silencing in transgenic T(1) plants and their offspring. Levels of mRNA were reduced not only for RGC2B but also for all seven diverse RGC2 family members tested. We then used the same strategy to show that the resistance specificity encoded by the genetically defined Dm18 locus in lettuce cv. Mariska is the result of two resistance specificities, only one of which was silenced by ihpRNA derived from RGC2B. Analysis of progeny from crosses between transgenic, silenced tester stocks and lettuce accessions carrying other resistance genes previously mapped to the RGC2 locus indicated that two additional resistance specificities to B. lactucae, Dm14 and Dm16, as well as resistance to lettuce root aphid (Pemphigus bursarius L.), Ra, are encoded by RGC2 family members.

Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants

Viroids, small non-coding pathogenic RNAs, are able to induce RNA silencing, a phenomenon that has been associated with the pathogenesis and evolution of these small RNAs. It has been recently suggested that viroids may resist this plant defense mechanism. However, the simultaneous degradation of non-replicating full-length viroid RNA, and the resistance of mature forms of viroids to RNA silencing, have not been experimentally demonstrated. Transgenic Nicotiana benthamiana plants expressing a dimeric form of Hop stunt viroid (HSVd) that have the capability to cleave and circularize this viroid RNA were used to address this question. A reporter construct, consisting of a full-length HSVd RNA fused to GFP-mRNA, was agroinfiltrated in these plants and its expression was suppressed. Interestingly, both circular and linear HSVd molecules were stable and able to traffic through grafts in these restrictive conditions, indicating that the mature forms of HSVd are able, in some way, to resist the RNA-silencing mechanism. The observation that a full-length HSVd RNA fused to GFP-mRNA, but not circular and/or linear viroid forms, was fully susceptible to RNA degradation strongly suggests that structures adopted by the free mature monomer protect the pathogenesis-associated forms of the viroid from RNA silencing.

Silencing of the type 1 insulin-like growth factor receptor increases the sensitivity to apoptosis and inhibits invasion in human lung adenocarcinoma A549 cells

The type 1 insulin-like growth factor receptor (IGF-1R), which is over-expressed or activated in many human cancers, including lung cancer, mediates cancer cell proliferation and metastasis. Several studies indicate that blocking IGF-1R expression can inhibit tumor cell proliferation and metastasis. In this study, inhibition of the endogenous IGF-1R by recombinant adenoviruses encoding short hairpin RNAs against IGF-1R was found to significantly suppress IGF-1R expression, arrest the cell cycle, enhance the apoptotic response, and inhibit proliferation, adhesion, invasion and migration in A549 cells. Moreover, silencing IGF-1R decreases the expression of invasive-related genes including matrix metalloproteinase-2 (MMP-2), MMP-9, and urokinase-plasminogen activator (u-PA), and the phosphorylation of Akt and ERK1/2. These results suggest that the silencing of IGF-1R has the potential to be an effective cancer gene therapy strategy for human lung cancer.

The RNAi pathway initiated by Dicer-2 in Drosophila

Injection or expression of double-stranded RNA (dsRNA) in Drosophila serves as a trigger that causes cells to specifically cleave homologous mRNA transcripts. Our approach is to identify essential components of the RNA interference (RNAi) mechanism by isolating and characterizing mutations that cause the RNAi response to be abnormal. These studies have thus far led to the identification of seven genetic loci that encode proteins acting at various steps in the RNAi process. We have molecularly identified several of these proteins. Two are members of the Dicer family. Dicer-1 and Dicer-2 are required for short interfering RNA (siRNA)-directed mRNA cleavage by facilitating distinct steps in the assembly of the RNA-induced silencing complex (RISC). AGO2 is a RISC component that both carries out transcript cleavage and facilitates RISC maturation. Other factors appear to function as regulators of RISC assembly rather than as core factors for RNAi.

DNA methylation as a therapeutic target in cancer

Targeting DNA methylation for cancer therapy has had a rocky history. The first reports on DNA methylation changes in cancer described global loss of methylation, which has been suggested to drive tumorigenesis through activation of oncogenic proteins or induction of chromosomal instability. In this context, reducing DNA methylation was viewed as a tumor-promoting event rather than a promising cancer therapy. The idea of inhibiting DNA methylation therapeutically emerged from subsequent studies showing that, in parallel to global decreases in methylation, several genes (including many critical to the tumor phenotype) displayed gains of methylation in their promoters during tumorigenesis, a process associated with epigenetic silencing of expression and loss of protein function. This led to revival of interest in drugs discovered decades ago to be potent inhibitors of DNA methyltransferases. These drugs have now been approved for clinical use in the United States in the treatment of myelodysplastic syndrome, thus opening the floodgate for a whole new approach to cancer therapy--epigenetic therapy.

Gene Suppression Technologies in High-Throughput Analysis: Front- and Back-side Applications

Our understanding of gene function and gene interactions has changed dramatically with the development of high-throughput systems. It now seems clear that any given gene interacts with a number of different partners, and in a number of different molecular pathways. Traditionally, gene function has been studied using animal knockout systems or naturally occurring mutants. RNA-based gene suppression systems for example, RNA interference or ribozymes, offer a number of advantages over the traditional systems, including ease of use, high specificity, and efficacy in nearly any biological system, and the ability to perform large-scale screens. Since their advent in the mid-1990s, DNA microarrays have been the choice for genome-wide expression analysis. The synergistic effect from the combined use of RNA-based gene suppression and molecular profiling is providing researchers with vast amounts of data. As a result, we are rapidly gaining an understanding of gene interactions and function. This review will focus primarily on gene inactivation systems that have been proven worthy of use in molecular pathway analysis when combined with microarray analysis.

The future of genomic nursing research

PURPOSE

To look toward the future of genomics research and identify genomic-based resources and opportunities for nurse scientists to incorporate genomic concepts into their programs of research.

ORGANIZING FRAMEWORK

Five research themes for the future, developed by the National Institute of Nursing Research in collaboration with nurse scientists, are the framework for this article: (a) changing lifestyle behaviors for better health; (b) managing the effects of chronic illness to improve health and quality of life; (c) identifying effective strategies to reduce health disparities; (d) harnessing advanced technologies to serve human needs; and (e) enhancing end-of-life experiences for patients and their families.

CONCLUSIONS

Nurse scientists around the world are increasingly integrating genomics into their programs of research. Emerging international genomic initiatives, discoveries, and resources will provide rich opportunities for nurse scientists, as members of interdisciplinary teams, to address important biological, behavioral, social, and ethical questions. This evolving genomic nursing science will be necessary in practice, education, and policy in a time when rapid genomic discoveries are occurring.

ERK1 and ERK2 mitogen-activated protein kinases affect Ras-dependent cell signaling differentially

Background

The mitogen-activated protein (MAP) kinases p44^ERK1 and p42^ERK2 are crucial components of the regulatory machinery underlying normal and malignant cell proliferation. A currently accepted model maintains that ERK1 and ERK2 are regulated similarly and contribute to intracellular signaling by phosphorylating a largely common subset of substrates, both in the cytosol and in the nucleus.

Results

Here, we show that ablation of ERK1 in mouse embryo fibroblasts and NIH 3T3 cells by gene targeting and RNA interference results in an enhancement of ERK2-dependent signaling and in a significant growth advantage. By contrast, knockdown of ERK2 almost completely abolishes normal and Ras-dependent cell proliferation. Ectopic expression of ERK1 but not of ERK2 in NIH 3T3 cells inhibits oncogenic Ras-mediated proliferation and colony formation. These phenotypes are independent of the kinase activity of ERK1, as expression of a catalytically inactive form of ERK1 is equally effective. Finally, ectopic expression of ERK1 but not ERK2 is sufficient to attenuate Ras-dependent tumor formation in nude mice.

Conclusion

These results reveal an unexpected interplay between ERK1 and ERK2 in transducing Ras-dependent cell signaling and proliferation. Whereas ERK2 seems to have a positive role in controlling normal and Ras-dependent cell proliferation, ERK1 probably affects the overall signaling output of the cell by antagonizing ERK2 activity.

Selection and validation of optimal siRNA target sites for RNAi-mediated gene silencing

RNA interference (RNAi)-mediated gene silencing has become a valuable tool for functional studies, reverse genomics, and drug discoveries. One major challenge of using RNAi is to identify the most effective short interfering RNAs (siRNAs) sites of a given gene. Although several published bioinformatic prediction models have proven useful, the process to select and validate optimal siRNA sites for a given gene remains empirical and laborious. Here, we developed a fluorescence-based selection system using a retroviral vector backbone, namely pSOS, which was based on the premise that candidate siRNAs would knockdown the chimeric transcript between GFP and target gene. The expression of siRNA was driven by the opposing convergent H1 and U6 promoters. This configuration simplifies the cloning of duplex siRNA oligonucleotide cassettes. We demonstrated that GFP signal reduction was closely correlated with siRNA knockdown efficiency of human beta-catenin, as well as with the inhibition of beta-catenin/Tcf4 signaling activity. The pSOS should not only facilitate the selection and validation of candidate siRNA sites, but also provide efficient delivery tools of siRNAs via viral vectors in mammalian cells. Thus, the pSOS system represents an efficient and user-friendly strategy to select and validate siRNA target sites.

Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes

The soybean cyst nematode (SCN; Heterodera glycines) is a devastating obligate parasite of Glycine max (soybean) causing one billion dollars in losses to the US economy per year and over ten billion dollars in losses worldwide. While much is understood about the pathology of H. glycines, its genome sequence is not well characterized or fully sequenced. We sought to create bioinformatic tools to mine the H. glycines nucleotide database. One way is to use a comparative genomics approach by anchoring our analysis with an organism, like the free-living nematode Caenorhabditis elegans. Unlike H. glycines, the C. elegans genome is fully sequenced and is well characterized with a number of lethal genes identified through experimental methods. We compared an EST database of H. glycines with the C. elegans genome. Our goal was identifying genes that may be essential for H. glycines survival and would serve as an automated pipeline for RNAi studies to both study and control H. glycines. Our analysis yielded a total of nearly 8334 conserved genes between H. glycines and C. elegans. Of these, 1508 have lethal phenotypes/phenocopies in C. elegans. RNAi of a conserved ribosomal gene from H. glycines (Hg-rps-23) yielded dead and dying worms as shown by positive Sytox fluorescence. Endogenous Hg-rps-23 exhibited typical RNA silencing as shown by RT-PCR. However, an unrelated gene Hg-unc-87 did not exhibit RNA silencing in the Hg-rps-23 dsRNA-treated worms, demonstrating the specificity of the silencing.

Reduced expression of Rho guanine nucleotide dissociation inhibitor-α modulates the cytotoxic effect of busulfan in HEK293 cells

High-dose busulfan is an important component in many conditioning protocols for hematopoietic stem cell or bone marrow transplantation. Treatment with busulfan results in the inhibition of cell cycle progression and apoptosis of tumor cells. As Rho GTPases are involved in cell cycle regulation, we investigated the influence of modified Rho guanine nucleotide dissociation inhibitor-alpha (GDI), a physiological inhibitor of Rho GTPases, on busulfan activity in cancer cells. RhoGDIalpha has been shown to be overexpressed in multiple types of tumors such as ovarian and breast cancer. To investigate the role of RhoGDIalpha, we established a RhoGDIalpha knockdown by the transient transfection of HEK293 cells with specific small interfering RNA resulting in strongly reduced RhoGDIalpha mRNA and protein expression. Other members of the RhoGDI family such as RhoGDIbeta and RhoGDIgamma were not affected. In RhoGDIalpha knockdown cells, cell cycle regulation was not altered by the downregulation of RhoGDIalpha; however, the rate of apoptotic cells increased when compared with the control small interfering RNA-transfected cells. In addition, treatment of cells with busulfan resulted in a further increased apoptotic rate, as determined by fluorescence-activated cell sorter analysis and caspase-3 activation. Such a sensitization of RhoGDIalpha small interfering RNA transfected cells was also found upon treatment with doxorubicin and taxol. In summary, we could demonstrate that the expression of RhoGDIalpha influences the sensitivity of cells toward busulfan-induced cytotoxicity.