The selective dependency of tumor cells on signaling pathways, oncogenes and critical downstream effectors opens a promising window for the identification of novel therapeutic targets. RNA interference can be used to induce a gene-specific loss-of-function phenotype allowing a quick determination of these genes relevance for cell proliferation and survival. Recently, we established a high-throughput method to screen large pools of shRNAs, targeting the whole genome or functional groups of genes, in a wide range of cells in vitro. Cells are infected with pooled lentiviral shRNAs and cultured in the presence or absence of a selective pressure. shRNAs that negatively affect the growth and/or survival of the cells will be depleted in the cell population and vice versa. These changes in frequency are precisely measured by a combination of next generation sequencing and a data analysis pipeline that was specifically set-up for this purpose. We successfully applied this screening technology to a range of different projects including “synthetic lethality” screens, negative selection screens and positive selection (“rescue”) screens.
Liu, L., Ulbrich, J., Müller, J., Wüstefeld, T., Aeberhard, L., Kress, T.R., Muthalagu, N., Rudalska, R., Moll, R., Kempa, S., Zender, L., Eilers, M.*, and Murphy, D.J.*, (2012) Deregulated MYC expression induces dependence upon AMPK-related kinase 5 Nature, 483:608-12* corresponding authors
Kress, T.R., Cannell, I.G., Brenkman, A.B., Gaestel, M., N`Burgering, B.M., Bushell, M., Rosenwald, A., and Eilers, M. (2011) The MK5/PRAK Kinase and Myc Form a Negative Feedback Loop that Is Disrupted during Colorectal Tumorigenesis Molecular Cell, Molecular Cell. 41:445-57.
Popov, N., Schülein, C., Jaenicke, L. and Eilers, M. (2010) Ubiquitination of the Myc amino-terminus by beta-TrCP antagonizes Fbw7-mediated degradation. Nature Cell Biology, 12,973-81.
Otto, T. Horn, S., Brockmann, M., Eilers, U., Schüttrumpf, L., Popov, N., Kenney, A.-M., Eggert, A., Beijersbergen. R., Christiansen. H., Berwanger, B. and Eilers, M. (2009) Stabilization of N-Myc is a critical function of Aurora-A in human neuroblastoma Cancer Cell 15: 67-78.