No abstract available.
RNA, Small Interfering

Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.
High-Throughput Screening Assays ; RNA Interference ; RNA, Small Interfering

OBJECTIVETo construct Dishevelled 2 (Dvl2)-targeted siRNA plasmids and to identify the effective recombinant plasmids in transciently-transfected RAW264.7 cells.

METHODSThe interfering sequences of Dvl2 were designed according to the sequence of Dvl2 of GenBank. Five paires of oligonucleotides were synthesized and inserted into plasmid pMAGic 4.0 to generate siRNA expression vectors, which were identified by flora PCR and sequence analysis. The recombinant plasmids siRNA-Dvl2 was transciently transfected into RAW264.7 cells by Lipofectamine 2000, which was confirmed under a fluorescence microscope and the interfering efficiency was detected by real-time RT-PCR.

RESULTSFive Dvl2 siRNA frames were successfully inserted into the plasmid vector pMAGic 4.0, and the flora PCR and sequence analysis confirmed the correct construction. Three of the five siRNA vectors suppressed the expression of Dvl2 mRNA, in which the siRNA-Dvl2-3 was the most efficient.

CONCLUSIONThe Dvl2-targeted recombinant siRNA plasmids can be constructed successfully to inhibit Dvl2 mRNA expression in transciently-transfected RAW264.7 cells, which can be used to pack virus particles and to construct siRNA-Dvl2 stably-transfected RAW264.7 cells in further research.

RNA interference (RNAi), a highly conserved evolutionary process of post-transcriptional gene silencing, can be triggered by small interfering RNAs (siRNAs) that mediate sequence-specific mRNA degradation. The article summarized some aspects of the mechanism of RNAi, siRNA design and delivery of siRNAs to mammalian somatic cells. And some hurdles in practice were also discussed.
Animals ; Humans ; RNA Interference ; RNA, Small Interfering ; genetics ; Transfection

Nuclear protein-1 (NUPR1) is a small nuclear protein that is responsive to various stress stimuli. Although NUPR1 has been associated with cancer development, its expression and roles in cholangiocarcinoma have not yet been described. In the present study, we found that NUPR1 was over-expressed in human cholangiocarcinoma tissues, using immunohistochemistry. The role of NUPR1 in cholangiocarcinoma was examined by its specific siRNA. NUPR1 siRNA decreased proliferation, migration and invasion of human cholangiocarcinoma cell lines (HuCCT1 and SNU1196 cells). From these results, we conclude that NUPR1 is over-expressed in cholangiocarcinoma and regulates the proliferation and motility of cancer cells.
Cell Line ; Cholangiocarcinoma ; Humans ; Immunohistochemistry ; Nuclear Proteins ; RNA, Small Interfering

Transglutaminase 2 (TGase 2) plays a key role in p53 regulation, depleting p53 tumor suppressor through autophagy in renal cell carcinoma. We found that microtubule-associated protein 1A/1B-light chain 3 (LC3), a hallmark of autophagy, were tightly associated with the level of TGase 2 in cancer cells. TGase 2 overexpression increased LC3 levels, and TGase 2 knockdown decreased LC3 levels in cancer cells. Transcript abundance of LC3 was inversely correlated with level of wild type p53. TGase 2 knockdown using siRNA, or TGase 2 inhibition using GK921 significantly reduced autophagy through reduction of LC3 transcription, which was followed by restoration of p53 levels in cancer cells. TGase 2 overexpression promoted the autophagy process by LC3 induction, which was correlated with p53 depletion in cancer cells. Rapamycin-resistant cancer cells also showed higher expression of LC3 compared to the rapamycin-sensitive cancer cells, which was tightly correlated with TGase 2 levels. TGase 2 knockdown or TGase 2 inhibition sensitized rapamycin-resistant cancer cells to drug treatment. In summary, TGase 2 induces drug resistance by potentiating autophagy through LC3 induction via p53 regulation in cancer.
Autophagy* ; Carcinoma, Renal Cell ; Drug Resistance ; RNA, Small Interfering

Previous observations suggest that Bis, a Bcl-2-binding protein, may play a role the neuronal and glial differentiation in vivo. To examine this further, we investigated Bis expression during the in vitro differentiation of P19 embryonic carcinoma cells induced by retinoic acid (RA). Western blotting and RT-PCR assays showed that Bis expression was temporarily decreased during the free floating stage and then began to increase on day 6 after the induction of differentiation. Double immunostaining indicated that Bis-expressing cells do not express several markers of differentiation, including NeuN, MAP-2 and Tuj-1. However, some of the Bis-expressing cells also were stained with GFAP-antibodies, indicating that Bis is involved glial differentiation. Using an shRNA strategy, we developed bis-knock down P19 cells and compared them with control P19 cells for the expression of NeuroD, Mash-1 and GFAP during RA-induced differentiation. Among these, only GFAP induction was significantly attenuated in P19-dnbis cells and the population showing GFAP immunoreactivity was also decreased. It is noteworthy that distribution of mature neurons and migrating neurons was disorganized, and the close association of migrating neuroblasts with astrocytes was not observed in P19-dnbis cells. These results suggest that Bis is involved in the migration-inducing activity of glial cells.
Astrocytes ; Blotting, Western ; Neuroglia ; Neurons ; RNA, Small Interfering ; Tretinoin

Humans ; Neoplasms ; genetics ; immunology ; therapy ; RNA Interference ; RNA, Small Interfering ; RNA-Induced Silencing Complex

RNA interference (RNAi) is a post-transcriptional gene silencing process by targeting mRNA for degradation in a sequence-specific manner. This powerful platform has enormous potential in functional genomics and medical research. As a tool to knock out expression of specific genes in a variety of organisms, RNAi was used to investigate gene function in a high throughput fashion. Highly conserved in evolution RNAi appears to have evolved as a cellular defense mechanism in plants and animals to suppress viral infection, transposon jumping and endogenous aberrant genes. Exploiting the natural mechanism, the researchers can shut down disease-causing genes and develop novel therapeutics against infection, tumor and other disease.
Gene Expression Regulation ; Gene Silencing ; Genomics ; RNA Interference ; RNA, Small Interfering ; RNA-Induced Silencing Complex

The small RNAs include siRNA and miRNA. SiRNA is the splicing product of exogenous dsRNA by which to keep genome stability, while miRNA are processed from endogenous genome and work as a post-transcriptional regulator for gene expression. The small RNAs act in two ways: mediate degradation of of target RNA and inhibit translation of protein. The former requires the accurate complementation between small RNA and target RNA, while the latter requires only partial complementation. Which mechanism used depends on complementation degree, but not their origins. The RNAi as a technique for down-regulating target gene expression has been widely used in functional genomic studies and hematologic studies, especially for translocation-related fusion gene, apoptosis-related gene and MDR gene in leukemia. The results show that RNAi technique not only is the powerful tool for study mechanism but also has therapeutic potentials in clinic. Some studies reveal that changes of miRNA expression exist in many hematological malignancies and relate to known oncogenes, which indicates the miRNA is involved in pathogenesis of these diseases. This article reviews the discovery and effect of RNAi and small RNAs, as well as the similarities and differences between siRNA and miRNA, and focuses on the research of small RNAs in hematological malignancies.
Hematologic Neoplasms ; genetics ; Humans ; MicroRNAs ; genetics ; RNA ; genetics ; RNA Interference ; RNA, Small Interfering ; genetics