Open AccessReverse engineering a hierarchical regulatory network downstream of oncogenic KRAS
Author(s) -
StelniecKlotz Iwona,
Legewie Stefan,
Tchernitsa Oleg,
Witzel Franziska,
Klinger Bertram,
Sers Christine,
Herzel Hanspeter,
Blüthgen Nils,
Schäfer Reinhold
Publication year - 2012
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2012.32
Subject(s) - biology , kras , oncogene , gene silencing , transcription factor , gene , transcription (linguistics) , microarray analysis techniques , gene expression , computational biology , cancer research , gene regulatory network , regulation of gene expression , cell cycle , genetics , microbiology and biotechnology , mutation , linguistics , philosophy
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.