Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS

• Published in: Molecular systems biology 2012, Vol.8 (1), p.601-n/a
• Main Authors: Stelniec‐Klotz, Iwona, Legewie, Stefan, Tchernitsa, Oleg, Witzel, Franziska, Klinger, Bertram, Sers, Christine, Herzel, Hanspeter, Blüthgen, Nils, Schäfer, Reinhold
• Format: Article
• Language: English
• Subjects: Algorithms; Analysis of Variance; Animals; cancer systems biology; Cell Line, Tumor; Cell Proliferation - drug effects; Cell Transformation, Neoplastic - genetics; Cell Transformation, Neoplastic - metabolism; Deregulation; DNA microarrays; EMBO24; EMBO26; Epithelial cells; Epithelial Cells - drug effects; Epithelial Cells - metabolism; Epithelial Cells - pathology; Female; Functional groups; Gene expression; Gene Expression Regulation, Neoplastic - physiology; Gene regulation; Gene Regulatory Networks - physiology; Gene silencing; Genes, ras; Growth factors; HMGA2 Protein - antagonists & inhibitors; HMGA2 Protein - genetics; HMGA2 Protein - metabolism; Human behavior; Humans; K-Ras protein; Kinases; Kruppel-Like Factor 6; Kruppel-Like Transcription Factors - antagonists & inhibitors; Kruppel-Like Transcription Factors - genetics; Kruppel-Like Transcription Factors - metabolism; Microarray Analysis; Models, Biological; modular response analysis; Mutation; oncogenes; Ordinary differential equations; Ovarian cancer; ovarian carcinoma model; Ovarian Neoplasms - genetics; Ovarian Neoplasms - metabolism; Ovary - drug effects; Ovary - pathology; Perturbation; Phenotypes; Predictions; Proto-Oncogene Proteins - antagonists & inhibitors; Proto-Oncogene Proteins - genetics; Proto-Oncogene Proteins - metabolism; Proto-Oncogene Proteins c-fos - antagonists & inhibitors; Proto-Oncogene Proteins c-fos - genetics; Proto-Oncogene Proteins c-fos - metabolism; Proto-Oncogene Proteins p21(ras); ras Proteins - genetics; ras Proteins - metabolism; Rats; Reverse engineering; Reverse Transcriptase Polymerase Chain Reaction; RNA, Small Interfering - metabolism; RNA, Small Interfering - pharmacology; Signal Transduction; Transcription factors; Transcription Factors - antagonists & inhibitors; Transcription Factors - genetics; Transcription Factors - metabolism; Tumors
• ISSN: 1744-4292; 1744-4292
• DOI: 10.1038/msb.2012.32

RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here, we used a reverse‐engineering approach in an ovarian cancer model to reconstruct KRAS oncogene‐dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT–PCR and western blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions, we analysed growth parameters and transcriptional deregulation in the KRAS‐transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype. Systematic RNA interference perturbations within ovarian cancer cells reveal a hierarchically organized transcription factor network downstream of the oncogenic RAS pathway. Modules within the network are shown to control distinct aspects of cell growth and migration. Synopsis Systematic RNA interference perturbations within ovarian cancer cells reveal a hierarchically organized transcription factor network downstream of the oncogenic RAS pathway. Modules within the network are shown to control distinct aspects of cell growth and migration. Cellular transformation by KRAS oncogenes results in the upregulation of a multitude of transcription factors and a general deregulation of the transcriptome To exploit the network organization of selected transcriptional regulators responding to chronic RAS pathway activation, we used an integrated strategy combining experimental perturbation of transcription factor and signalling kinase expression with a reverse‐engineering approach based on modular response analysis (MRA). The network shows strong modularity, high connectivity and hierarchical organization. The network hierarchy is reflected in distinct phenotypic consequences of perturbation within modules that separately control cellular proliferation