High-throughput cellular models

Coordinator:    Prof. Dr. Michael Boutros
Institution: DKFZ Heidelberg
Systems biology of signaling pathways in colorectal carcinomas.

Cancer is characterized by aberrant growth of cells or by the inability of cells to initiate or execute programmed cell death. Cells are constantly exposed to signals from surrounding tissues that determine whether they divide, differentiate or die. In this respect, signaling pathways within the cells play a crucial role in controlling the cell state, and deregulation of signaling pathways has been implicated in many tumors. For example, deregulated Wnt signaling pathways have been shown to be particularly important for the onset of colorectal cancer. Wnt signaling is tightly regulated at multiple levels and the crosstalk between Wnt and other signaling cascades have been reported. As part of the proposed subproject, we will functionally analyze the network of interactions that are relevant in colorectal cancer.

The sequence of the human genome has recently enabled new approaches to rapidly analyze functions of all genes in a highly parallel fashion. There is still a significant challenge in the direct rapid functional analysis and validation of putative targets, and methods to predict a target’s relevance in preclinical and clinical studies. A key advance in recent years has been the discovery of RNA interference (RNAi), which allows the silencing of genes. Genome-wide RNAi approaches have become a powerful genetic approach to systematically identify pathway-specific genes.

By using high-throughput RNAi assays, we will establish a systems biology framework for cellular pathways in colon cancer and control cell lines. These genome-wide surveys will generate a network of components in relevant pathways. We will subsequently systematically identify pathway signatures to reconstruct a topology framework for the analysis of signaling pathways during colorectal cancer. Furthermore, candidate genes identified in germline mutations and somatic screens performed by other subprojects will be analyzed in CRC cell-based assays. Taken together, this approach will allow us to build a comprehensive picture of signaling dysfunction in CRC.


High-throughput RNAi screening. Cell-based assays were performed in 384-well plate formats. Cells in each well were treated with RNAi molecules targeting specific genes. Shown is the assay readout and signal intensities refer to the pathway activity.

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