StemCellFactory – characterizing cells during reprogramming and differentiation

The recent progress in reprogramming of adult cells towards pluripotency, referred to as “induced pluripotent stem cells” (iPS cells), introduces a new dimension to the field of drug development and regenerative medicine, since it allows the generation of tissue-, disease- and patient-specific cells. In vitro reprogramming and differentiation of cells is a work intensive process, which is currently performed manually in a non-standardized manner. The StemCellFactory project is an interdisciplinary research project aiming to develop a prototype of a factory that automizes, standardizes and parallelizes these processes in order to produce iPSC-derived cell products in an industrial scale. One major challenge in this process is the proper characterization of reprogrammed and differentiated cells for quality control purposes.

Using large scale gene expression microarray data, we developed mathematical and bioinformatics methods to assess the pluripotency of  reprogrammed cells [Mueller et al. 2011, Williams et al. 2011, Goldmann et al. 2012, Shao et al. 2012, MacArthur et al] and to track the cells during their differentiation process in a physiological reference space [Lenz et al. 2013]. The methods use large amounts of public available microarray data to detemine tissue or cell type specific gene expression patterns and map data from new experiments onto the identified patterns.

These methods will be further extended to distinguish between several sub cell types, e.g. of the brain, and can also be used for characterization of cancer cells and comparison of various stress response patterns in humans as well as in plants.