Systematic variation in gene expression patterns in human cancer cell lines

We used cDNA microarrays to explore the variation in expression of approxim ately 8,000 unique genes among the 60 cell lines used in the National Cance r Institute's screen for anti-cancer drugs. Classification of the cell line s based solely on the observed patterns of gene expression revealed a corre spondence to the ostensible origins of the tumours from which the cell line s were derived. The consistent relationship between the gene expression pat terns and the tissue of origin allowed us to recognize outliers whose previ ous classification appeared incorrect. Specific features of the gene expres sion patterns appeared to be related to physiological properties of the cel l lines, such as their doubling time in culture, drug metabolism or the int erferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumour specimens rev ealed features of the expression patterns in the tumours that had recogniza ble counterparts in specific cell lines, reflecting the tumour, stromal and inflammatory components of the tumour tissue. These results provided a nov el molecular characterization of this important group of human cell lines a nd their relationships to tumours in vivo.