Assays based on cultured cells are moving to the center of the drug discovery process, and in recent years have gained a substantial share in safety testing. Primary cells and cell lines may yield complex and often more meaningful data compared to biochemical assays, provided that the cell system is chosen or designed to fit the purpose of the assay. These requirements vary substantially however, and often a compromise must be made between practicability on one hand and a close match with the natural response on the other hand. Permanent cell lines with their capability ofcontinuous self-renewal and amplification provide a sustainable source of standardized material, much in contrast to primary tissue. However, proteome or transcriptome wide screens for pleiotropic effects suffer from substantial differences between immortalized cells and primary cells, or cultivated and primary tissue samples. The target of first, maintaining the physiological properties of a given tissue, and second, immortalizing the cells that regenerate that tissue in vitro to provide a continuous supply, represents a formidable challenge that requires complex and careful manipulations of several interlinked cellular pathways.

Once an immortalized cell line is obtained, additional layers of complexity to the screen can be added by genetic manipulation not possible with primary cells. These cell lines are designed specifically to express a single target protein or proteins assembling into a functional pathway. In addition, they may be designed to exhibit novel functional properties not found in Nature, for example to improve detection and quantification in drug screens. The convenience of set-up and handling, robustness, and the stability of assays with designed cell lines is an important advantage over primary material. Increased complexity provides the opportunity for very elaborate and unique assays, but this usually comes at the cost of further remoteness from the natural situation, such as loss of certain differentiation states or tissue markers. The focal point of this chapter is to discuss the approaches for immortalization, the application of designer cell lines, and their limitations.

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