Delineating breast cancer gene expression networks by RNA interference and global microarray analysis in human tumor cells
German Cancer Research Center
Last modified: April 8, 2006
Holger Sültmann, Mark Fellmann, Ruprecht Kuner, Andreas Buness, Achim Tresch*, Markus Ruschhaupt, Tim Beissbarth, and Annemarie Poustka
German Cancer Research Center Heidelberg, Germany, *current address: Johannes Gutenberg University Mainz, Germany
Apart from lung cancer, breast cancer is the most common malignant disease in human females. In recent years, many excellent genome-wide gene expression studies have attempted to elucidate the mechanisms responsible for malignant progression of breast tumors. However, though the number of genes associated with breast cancer has been increasing, the biological mechanisms of tumor development remain obscure.
To elucidate the processes of gene regulation in breast cancer, we knocked down the activity of single genes with relevance in breast cancer by using RNA interference (RNAi) in (estrogen receptor positive) MCF7 breast cell lines as models. Silencing efficiencies were measured by qRT-PCR, and amplified total cellular RNA was used for hybridization on human whole genome cDNA microarrays containing 37,500 clones (RZPD Unigene Set 3.1).
The cellular gene expression patterns were used to analyze the downstream effects of single-gene perturbances. By using the microarray data, gene expression network models were derived to elucidate the hierarchial organisation of transcriptional regulation of cancer-relevant genes related to the estrogen receptor (ESR) pathway. The results revealed novel insights into the biological processes associated with malignant tumor progression.