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At least 613 records · Page 34Linked to original sources
PubMed2005

Biology calls the targets: combining RNAi and disease biology.

Target-based drug discovery starts with the identification of target genes and their respective protein products (associated with or controlling a disease-relevant phenotype) that, when inhibited or activated, ameliorate the associated disease. To identify disease-relevant genes, robust tools are needed to allow biology-driven target discovery and validation. Moreover, insight into the underlying biology of a disease is essential to model a disease in vitro. Key questions are: What are the disease hallmarks? What are, from a biological point of view, the best points for therapeutic intervention? How can scientists model these points in vitro? What is the desired target profile? The closer the cellular models resemble the disease situation, the better the target profile will be. The profile is the set of biological data needed to accept the target for drug discovery. In this review, a focused approach for target discovery and validation is presented. Arrayed adenoviral siRNA libraries and disease-based cellular models are used that generate high-quality and functionally validated targets.

Animals↗
PubMed2005

Exploring the sounds of silence: RNAi-mediated gene silencing for target identification and validation.

Drug development begins with the identification and early preclinical validation of novel biological targets, a process often called 'target identification and validation'. This process usually uses various approaches, such as observations from literature and findings from animal or clinical studies, together with cutting edge molecular techniques that include analyses of gene and protein expression, interaction and function. The publication of the human genome has increased research in gene and protein expression analysis that, in combination with RNA interference technology, promises the evaluation of novel functions for known genes, as well as hitherto unknown or unstudied genes with functions relevant to disease.

Drug Design↗
PubMed2002

RNAi and related mechanisms and their potential use for therapy.

Introduction of double-stranded RNAs into cells can suppress gene expression by mechanisms such as mRNA degradation or inhibition of translation. In mammalian cells, these two responses intersect, a feature that was recently used for the development of novel tools for stable and specific gene inactivation. These new tools were successfully applied to inhibit tumorigenicity and viral replication. Future development of appropriate in vivo delivery systems may make this technology useful for disease therapy.

Animals↗
PubMed2006

Nucleic acid structure and intracellular immunity: some recent ideas from the world of RNAi.

Cells face a constant struggle against unwanted instructions that arrive in the form of viruses and transposons. At the core of this battle are two issues: how can cellular machinery recognize certain informational molecules as 'unwanted' and how can the cell use this recognition to effectively silence malicious genetic activity. While defenses against some specific parasites may be triggered by individual nucleic acid or protein sequences, such sequence-specific mechanisms have the limitation of allowing the parasite to evade following relatively minor evolutionary change. A more general set of defense mechanisms is based on recognition of structural features that are intrinsic aspects of one or more parasitic lifestyle. Recognition of extended regions of double-stranded RNA (dsRNA) provides cells with one such defensive modality. Essentially absent during 'normal' gene expression, long stretches of dsRNA within a cell serve as a dramatic warning that a segment of information may be replicating as RNA. In addition to exemplifying many of the mechanistic issues in genome defense, the cellular response to dsRNA provides several examples of the logic by which organisms attempt to focus their limited immunity resources on the most immediate and dangerous targets.

Biophysical Phenomena↗
PubMedDate not supplied

RNAi silencing of exogenous and endogenous reporter genes using a macrocyclic octaamine as a "compact" siRNA carrier. Studies on the nonsilenced residual activity.

A macrocyclic octaamine 1 having a covalently linked lipid-bundle structure was introduced as a new type of siRNA carrier. Gel electrophoresis, DLS, and SPR results indicate that it strongly binds to a luciferase-targeting 21-mer (42P) siRNA with a ratio of 1/P congruent with 0.3 (1/N congruent with 2.4) to give remarkably compact 1-siRNA complexes with an average size of approximately 10 nm. The 1-mediated siRNA silencing of the exogenous luciferase gene occurs with a 90-95% efficiency. The overall suppression-[siRNA] profile with a 5-10% residual activity in the saturation region is commonly observed irrespective of the cell type (HeLa, HepG2, or HEK293), the order, or timing (stepwise or simultaneous) of supply of the siRNA and that of the luciferase-encoding plasmid, the level of mRNA transcribed, or the type of carriers (1 vs lipofectamine 2000). The silencing of the endogenous DsRed2 gene stably incorporated in the genome of HeLa cells also has a similar overall profile. These results suggest that (1) the cellular uptake of the plasmid and that of the siRNA are basically independent of each other and (2) the incomplete silencing is not due to insufficient siRNA delivery. Implication of item 2 is briefly discussed.

Cell Line↗
PubMed2005

Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.

A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.

Animals↗
PubMed2006

Identification of pathways regulating cell size and cell-cycle progression by RNAi.

Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity.

Active Transport, Cell Nucleus↗