Genomewide view of gene silencing by small interfering RNAs.

RNA interference (RNAi) is an evolutionarily conserved mechanism in plant and animal cells that directs the degradation of messenger RNAs homologous to short double-stranded RNAs termed small interfering RNA (siRNA). The ability of siRNA to direct gene silencing in mammalian cells has raised the possibility that siRNA might be used to investigate gene function in a high throughput fashion or to modulate gene expression in human diseases. The specificity of siRNA-mediated silencing, a critical consideration in these applications, has not been addressed on a genomewide scale. Here we show that siRNA-induced gene silencing of transient or stably expressed mRNA is highly gene-specific and does not produce secondary effects detectable by genomewide expression profiling. A test for transitive RNAi, extension of the RNAi effect to sequences 5' of the target region that has been observed in Caenorhabditis elegans, was unable to detect this phenomenon in human cells.

Comprehensive analysis of the gene expression profiles in human gastric cancer cell lines.

Gastric adenocarcinoma is one of the major malignancies worldwide. Gastric cell lines have been widely used as the model to study the genetics, pharmacology and biochemistry of gastric cancers. Here we describe a comprehensive survey of the gene expression profiles of 12 gastric carcinoma cell lines, using cDNA microarray with 43 000 clones. For comparison, we also explored the gene expression patterns of 15 cell lines derived from lymphoid, endothelial, stromal and other epithelial cancers. Expression levels of specific genes were validated through comparison to protein expression by immunohistochemistry using cell block arrays. We found sets of genes whose expression corresponds to the molecular signature of each cell type. In the gastric cancer cell lines, apart from genes that are highly expressed corresponding to their common epithelial origin from the gastrointestinal tract, we found marked heterogeneity among the gene expression patterns of these cell lines. Some of the heterogeneity may reflect their underlying molecular characteristics or specific differentiation program. Two putative gastric carcinoma cell lines were found to be B-cell lymphoma, and another one had no epithelial specific gene expression and hence was of doubtful epithelial origin. These cell lines should no longer be used in gastric carcinoma research. In conclusion, our gene expression database can serve as a powerful resource for the study of gastric cancer using these cell lines.