siRNA干扰HSV1 gD糖蛋白基因的研究

以HSV1 gD糖蛋白基因为靶点,设计合成5对siRNA,并构建pEGFP-N1-gD融合表达质粒,脂质体法共转染Vero细胞,利用绿色荧光蛋白(EGFP)报告基因的特征,流式细胞仪筛选特异沉默gD表达的siRNA。然后有效siRNA转染Vero细胞并感染HSV1,通过空斑减数实验,Real-time PCR和子代病毒滴度评价其对HSV-1感染的作用。结果显示siRNA能有效抑制gD-EGFP融合蛋白和感染细胞内gD糖蛋白的表达,但对HSV-1的感染性无明显抑制作用,故选择gD作为siRNA抗病毒靶点还需进一步的论证。     

The apparent uptake of fluorescently labeled siRNAs by electroporated cells depends on the fluorochrome

Transfection of mammalian cells with preformed small interfering RNAs (siRNAs) permits a transient and often specific reduction of gene expression. It is possible to rapidly examine the uptake of siRNAs by transfection with fluorescently labeled siRNAs. We examined the apparent uptake of such siRNAs by several leukemic cell lines after electroporation. We show that Cy3 and Cy5-labeled siRNAs cause a significant amount of cell fluorescence, as judged by flow cytometry. In contrast, several fluorescein-labeled siRNAs could not be detected. Nevertheless, such fluoresceinated siRNAs efficiently suppressed a leukemic target gene, demonstrating that siRNA uptake must have taken place. Therefore, for cell electroporation, fluorescein-labeled siRNAs may lead to false negative results and should not be used to examine electroporation-mediated siRNA uptake.     

Cellular delivery of siRNA mediated by fusion-active virosomes

RNA interference is expected to have considerable potential for the development of novel specific therapeutic strategies. However, successful application of RNA interference in vivo will depend on the availability of efficient delivery systems for the introduction of small-interfering RNA (siRNA) into the appropriate target cells. This paper focuses on the use of reconstituted viral envelopes ("virosomes"), derived from influenza virus, as a carrier system for cellular delivery of siRNA. Complexed to cationic lipid, siRNA molecules could be efficiently encapsulated in influenza virosomes. Delivery to cultured cells was assessed on the basis of flow cytometry analysis using fluorescently labeled siRNA. Virosome-encapsulated siRNA directed against Green Fluorescent Protein (GFP) inhibited GFP fluorescence in cells transfected with a plasmid encoding GFP or in cells constitutively expressing GFP. Delivery of siRNA was dependent on the low-pH-induced membrane fusion activity of the virosomal hemagglutinin, supporting the notion that virosomes introduce their encapsulated siRNA into the cell cytosol through fusion of the virosomal membrane with the limiting membrane of cellular endosomes, after internalization of the virosomes by receptor-mediated endocytosis. It is concluded that virosomes represent a promising carrier system for cellular delivery of siRNA in vitro as well as in vivo.     

Cellular Delivery of siRNA Mediated by Fusion-Active Virosomes

RNA interference is expected to have considerable potential for the development of novel specific therapeutic strategies. However, successful application of RNA interference in vivo will depend on the availability of efficient delivery systems for the introduction of small-interfering RNA (siRNA) into the appropriate target cells. This paper focuses on the use of reconstituted viral envelopes (“virosomes”), derived from influenza virus, as a carrier system for cellular delivery of siRNA. Complexed to cationic lipid, siRNA molecules could be efficiently encapsulated in influenza virosomes. Delivery to cultured cells was assessed on the basis of flow cytometry analysis using fluorescently labeled siRNA. Virosome-encapsulated siRNA directed against Green Fluorescent Protein (GFP) inhibited GFP fluorescence in cells transfected with a plasmid encoding GFP or in cells constitutively expressing GFP. Delivery of siRNA was dependent on the low-pH-induced membrane fusion activity of the virosomal hemagglutinin, supporting the notion that virosomes introduce their encapsulated siRNA into the cell cytosol through fusion of the virosomal membrane with the limiting membrane of cellular endosomes, after internalization of the virosomes by receptor-mediated endocytosis. It is concluded that virosomes represent a promising carrier system for cellular delivery of siRNA in vitro as well as in vivo.     

siRNA cell arrays for high-content screening microscopy

RNA interference (RNAi) is a recent advance that provides the possibility to reduce the expression of specific target genes in cultured mammalian cells with potential applications on a genome-wide scale. However, to achieve this, robust methodologies that allow automated and efficient delivery of small interfering RNAs (siRNAs) into living cultured cells and reliable quality control of siRNA function must be in place. Here we describe the production of cell arrays for reverse transfection of tissue culture cells with siRNA and plasmid DNA suitable for subsequent high-content screening microscopy applications. All the necessary transfection components are mixed prior to the robotic spotting on noncoated chambered coverglass tissue culture dishes, which are ideally suited for time-lapse microscopy applications in living cells. The addition of fibronectin to the spotting solution improves cell adherence. After cell seeding, no further cell culture manipulations, such as medium changes or the addition of 7 serum, are needed. Adaptation of the cell density improves autofocus performance for high-quality data acquisition and cell recognition. The co-transfection of a nonspecific fluorescently labeled DNA oligomer with the specific siRNA helps to mark each successfully transfected cell and cell cluster. We demonstrate such an siRNA cell array in a microscope-based functional assay in living cells to determine the effect of various siRNA oligonucleotides against endogenous targets on cellular secretion.     

Effect of siRNA nuclease stability on the in vitro and in vivo kinetics of siRNA-mediated gene silencing

Small interfering RNA (siRNA) molecules achieve sequence-specific gene silencing through the RNA interference (RNAi) mechanism. Here, live-cell and live-animal bioluminescent imaging (BLI) is used to directly compare luciferase knockdown by unmodified and nuclease-stabilized siRNAs in rapidly (HeLa) and slowly (CCD-1074Sk) dividing cells to reveal the impact of cell division and siRNA nuclease stability on the kinetics of siRNA-mediated gene silencing. Luciferase knockdown using unmodified siRNAs lasts approximately 1 week in HeLa cells and up to 1 month in CCD-1074Sk cells. There is a slight increase in the duration of luciferase knockdown by nuclease-stabilized siRNAs relative to unmodified siRNAs after cationic lipid transfection, but this difference is not observed after electroporation. In BALB/cJ mice, a fourfold increase in maximum luciferase knockdown is observed after hydrodynamic injection (HDI) of nuclease-stabilized siRNAs relative to unmodified siRNAs, yet the overall kinetics of the recovery after knockdown are nearly identical. By using a mathematical model of siRNA-mediated gene silencing, the trends observed in the experimental data can be duplicated by changing model parameters that affect the stability of the siRNAs before they reach the cytosolic compartment. Based on these findings, we hypothesize that the stabilization advantages of nuclease-stabilized siRNAs originate primarily from effects prior to and during internalization before the siRNAs can interact with the intracellular RNAi machinery.     

Gene expression silencing with 'specific' small interfering RNA goes beyond specificity - a study of key parameters to take into account in the onset of small interfering RNA off-target effects

RNA-mediated gene silencing (RNA interference) is a powerful way to knock down gene expression and has revolutionized the fields of cellular and molecular biology. Indeed, the transfection of cultured cells with small interfering RNAs (siRNAs) is currently considered to be the best and easiest approach to loss-of-function experiments. However, several recent studies underscore the off-target and potential cytotoxic effects of siRNAs, which can lead to the silencing of unintended mRNAs. In this study, we used a low-density microarray to assess gene expression modifications in response to five different siRNAs in various cell types and transfection conditions. We found major differences in off-target signature according to: (a) siRNA sequence; (b) cell type; (c) duration of transfection; and (d) post-transfection time before analysis. These results contribute to a better understanding of important parameters that could impact on siRNA side effects in knockdown experiments.     

Role of caspase‐9 in the effector caspases and genome expressions,and growth of bovine skeletal myoblasts

Caspase‐9 has been reported as the key regulator of apoptosis, however, its role in skeletal myoblast development and molecular involvements during cell growth still remains unknown. The current study aimed to present the key role of caspase‐9 in the expressions of apoptotic caspases and genome, and cell viability during myoblast growth using RNA interference mediated silencing. Three small interference RNA sequences (siRNAs) targeting caspase‐9 gene was designed and ligated into pSilencer plasmid vector to construct shRNA expression constructs. Cells were transfected with the constructs for 48 h. Results indicated that all three siRNAs could silence the caspase‐9 mRNA expression significantly. Particularly, the mRNA expression level of caspase‐9 in the cells transfected by shRNA1, shRNA2 and shRNA3 constructs were reduced by 37.85%, 68.20% and 58.14%, respectively. Suppression of caspase‐9 led to the significant increases in the mRNA and protein expressions of effector caspase‐3, whereas the reduction in mRNA and protein expressions of caspase‐7. The microarray results showed that the suppression of caspase‐9 resulted in significant upregulations of cell proliferation‐, adhesion‐, growth‐, development‐ and division‐regulating genes, whereas the reduction in the expressions of cell death program‐ and stress response‐regulating genes. Furthermore, cell viability was significantly increased following the transfection. These data suggest that caspase‐9 could play an important role in the control of cell growth, and knockdown of caspase‐9 may have genuine potential in the treatment of skeletal muscle atrophy.     

长链非编码RNA-H19 在妇科恶性肿瘤细胞的糖代谢中的作用

目的:检测长链非编码RNA-H19在常见的妇科恶性肿瘤中的表达,并探讨其在肿瘤细胞糖代谢过程中发挥的可能作用。方法:以ARK2子宫内膜癌细胞株和OVCAR-3上皮性卵巢癌细胞株作为实验对象;利用脂质体转染技术,将特异性靶向小干扰RNA序列转染进细胞;利用TRIzol法提取样品的总RNA,并通过逆转录和实时定量PCR技术检测样品中目的基因的表达;利用荧光标记的非放射性2-NBDG评估肿瘤细胞的葡萄糖摄取能力;采用方差齐性检验和t检验进行统计学分析。结果:H19在ARK2和OVCAR-3细胞中的表达均较高。在ARK2和OVCAR-3细胞中,si H19抑制H19表达的效率分别为34.02%和30.30%。是否添加Insulin对于转染si Con的肿瘤细胞的糖摄取能力无明显影响,但是si H19转染后的ARK2和OVCAR-3细胞,在经Insulin处理后糖摄取能力均明显增强。结论:ARK2和OVCAR-3这两种细胞是研究H19在妇科恶性肿瘤中机制的较为理想的实验对象,ARK2和OVCAR-3细胞本身存在胰岛素抵抗,外源性抑制H19表达后,细胞的胰岛素抵抗有所改善,H19或成为我们改善妇科恶性肿瘤患者机体葡萄糖代谢的标记物。     

A method for evaluating the host range of bacteriophages using phages fluorescently labeled with 5-ethynyl-2′-deoxyuridine (EdU)

The evaluation of bacteriophage (phage) host range is a significant issue in understanding phage and prokaryotic community interactions. However, in conventional methods, such as plaque assay, target host strains must be isolated, although almost all environmental prokaryotes are recalcitrant to cultivation. Here, we introduce a novel phage host range evaluation method using fluorescently labeled phages (the FLP method), which consists of the following four steps: (i) Fluorescently labeled phages are added to a microbial consortium, and host cells are infected and fluorescently labeled. (ii) Fluorescent cells are sorted by fluorescence-activated cell sorting. (iii) 16S rRNA gene sequences retrieved from sorted cells are analyzed, and specific oligonucleotide probes for fluorescence in situ hybridization (FISH) are designed. (iv) Cells labeled with both fluorescently labeled phage and FISH probe are identified as host cells. To verify the feasibility of this method, we used T4 phage and Escherichia coli as a model. We first used nucleic acid stain reagents for phage labeling; however, the reagents also stained non-host cells. Next, we employed the Click-iT EdU (5-ethynyl-2'-deoxyuridine) assay kit from Invitrogen for phage labeling. Using EdU-labeled T4 phage, we could specifically detect E. coli cells in a complex microbial consortium from municipal sewage. We also confirmed that FISH could be applied to the infected E. coli cells. These results suggest that this FLP method using the EdU assay kit is a useful method for evaluating phage host range and may have a potential application for various types of phages, even if their prokaryotic hosts are currently unculturable.     

抗结缔组织生长因子特异性小干扰RNA的设计、合成及筛选

目的 设计和合成针对抗肝纤维化关键基因抗结缔组织生长因子（connective tissue growth factor,CTGF）的特异性小干扰RNA（siRNA）,并筛选高效的CTGF siRNA抗肝纤维化序列.方法 参照siRNA设计原则,应用RNA在线设计软件,设计3段RNA干扰候选序列,分别转染正常干细胞株（L-02）,以转染非特异性siRNA（与CTGF mRNA无同源性）作为对照,应用Western 印迹检测L-02细胞CTGF蛋白质表达.结果 与对照相比,转染siRNA的L-02细胞CTGF蛋白表达明显下调,且siCTGF-1、siCTGF-2、siCTGF-3各片段干扰率分别为44.91 %、93.99 %、81.34%,其中以siCTGF-2干扰率最高,效果最明显.转染非特异性siRNA的L-02细胞CTGF蛋白表达无明显变化（P＜0.05）.结论 不同的CTGF siRNA对L-02细胞CTGF表达水平具有不同的干扰效能,成功合成能高效阻抑CTGF表达的CTGF siRNA,为进一步探索更特异、更有效的抗肝纤维化基因治疗这一新途径打下坚实基础.     

Efficient shRNA delivery into B and T lymphoma cells using lentiviral vector-mediated transfer

RNA interference is a powerful tool for the functional analysis of proteins by specific gene knockdown. In this study, we devised a rapid and efficient way to screen suitable siRNA sequences and subsequently employ them for specific gene knockdown in usually hard-to-transfect lymphoid cell lines, using a self-inactivating lentiviral vector. Two proteins with different half-lives were chosen, cyclin D1 and STAT3. A specific lacZ reporter fusion assay was used to identify highly effective siRNA sequences. Only siRNA molecules with more than 85% of knockdown efficiency were selected for the generation of lentiviral transfer vectors. Transduction rates of 75–99% were achieved in the lymphoma cell lines Granta 519 (mantle cell lymphoma), Karpas 299, and SUDHL-1 (anaplastic large T cell lymphoma), as demonstrated by green fluorescent protein expression in fluorescence-activated cell sorting analysis. The high level of transduction efficiency allows RNA interference studies to be performed on transduced cells without further manipulation, such as cell sorting or cloning. The LacZ reporter system together with the lentivirus technology is a very important tool in the hematology field, which enables experiments in lymphoid cells that were not possible before.

Electronic supplementary material

The online version of this article (doi:10.1007/s12308-008-0020-x) contains supplementary material, which is available to authorized users.     

siRNA-like double-stranded RNAs are specifically protected against degradation in human cell extract

RNA interference (RNAi) is a set of intracellular pathways in eukaryotes that controls both exogenous and endogenous gene expression. The power of RNAi to knock down (silence) any gene of interest by the introduction of synthetic small-interfering (si)RNAs has afforded powerful insight into biological function through reverse genetic approaches and has borne a new field of gene therapeutics. A number of questions are outstanding concerning the potency of siRNAs, necessitating an understanding of how short double-stranded RNAs are processed by the cell. Recent work suggests unmodified siRNAs are protected in the intracellular environment, although the mechanism of protection still remains unclear. We have developed a set of doubly-fluorophore labeled RNAs (more precisely, RNA/DNA chimeras) to probe in real-time the stability of siRNAs and related molecules by fluorescence resonance energy transfer (FRET). We find that these RNA probes are substrates for relevant cellular degradative processes, including the RNase H1 mediated degradation of an DNA/RNA hybrid and Dicer-mediated cleavage of a 24-nucleotide (per strand) double-stranded RNA. In addition, we find that 21- and 24-nucleotide double-stranded RNAs are relatively protected in human cytosolic cell extract, but less so in blood serum, whereas an 18-nucleotide double-stranded RNA is less protected in both fluids. These results suggest that RNAi effector RNAs are specifically protected in the cellular environment and may provide an explanation for recent results showing that unmodified siRNAs in cells persist intact for extended periods of time.     

SiRNA-VEGF对子宫内膜癌ishikawa细胞增殖及凋亡的影响

目的:研究针对VEGF的RNAi技术对人子宫内膜癌细胞系ishikawa细胞中VEGF的抑制作用及对细胞生长、增殖的影响。方法:设计并合成针对VEGF序列特异性siRNA及阴性对照siRNA,转染ishikawa细胞,分别于转染后12h、24h、48h、72h、7d后提取细胞RNA,应用实时荧光定量PCR检测其对VEGF mRNA表达水平的影响,MTT法检测细胞增殖的情况,于转染后48h收集细胞软琼脂培养检测细胞克隆形成能力。结果:转染针对siRNA-VEGF的ishikawa细胞,于转染后12h、24h、48h、72h VEGF mRNA表达水平明显下降、细胞增殖受到明显的抑制,与对照组相比差异有统计学意义(P<0.05),于转染后7天这种抑制作用消失(P>0.05)。转染后48h实验组细胞克隆形成率低于对照组(P<0.05)。结论:针对VEGF的RNAi技术可有效抑制子宫内膜癌细胞系ishikawa细胞中VEGF基因的表达,抑制细胞生长增殖及细胞集落形成能力,提示VEGF基因在子宫内膜癌的发生、发展中可能具有重要作用,为进一步利用RNAi技术抑制肿瘤生长、血管形成及局部侵袭和远处转移提供研究基础。     

Myostatin gene silencing by RNA interference in chicken embryo fibroblast cells

Myostatin (MSTN), a member of transforming growth factor-β (TGF-β) superfamily, is a negative regulator of the skeletal muscle growth, and suppresses the proliferation and differentiation of myoblast cells. Dysfunction of MSTN gene either by natural mutation or genetic manipulation (knockout or knockdown) has been reported to interrupt its proper function and to increase the muscle mass in many mammalian species. RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful tool for gene knockdown studies. In the present study transient silencing of MSTN gene in chicken embryo fibroblast cells was evaluated using five different shRNA expression constructs. We report here up to 68% silencing of myostatin mRNA using these shRNA constructs in transiently transfected fibroblasts (p<0.05). This was, however, associated with induction of interferon responsive genes (OAS1, IFN-β) (3.7-64 folds; p<0.05). Further work on stable expression of antimyostatin shRNA with minimum interferon induction will be of immense value to increase the muscle mass in the transgenic animals.