Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS

Mol Syst Biol. 2012;8:601. doi: 10.1038/msb.2012.32.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Analysis of Variance
  • Animals
  • Cell Line, Tumor
  • Cell Proliferation / drug effects
  • Cell Transformation, Neoplastic / genetics
  • Cell Transformation, Neoplastic / metabolism
  • Epithelial Cells / drug effects
  • Epithelial Cells / metabolism
  • Epithelial Cells / pathology
  • Female
  • Gene Expression Regulation, Neoplastic / physiology*
  • Gene Regulatory Networks / physiology*
  • Genes, ras
  • HMGA2 Protein / antagonists & inhibitors
  • HMGA2 Protein / genetics
  • HMGA2 Protein / metabolism
  • Humans
  • Kruppel-Like Factor 6
  • Kruppel-Like Transcription Factors / antagonists & inhibitors
  • Kruppel-Like Transcription Factors / genetics
  • Kruppel-Like Transcription Factors / metabolism
  • Microarray Analysis
  • Models, Biological
  • Ovarian Neoplasms / genetics*
  • Ovarian Neoplasms / metabolism
  • Ovary / drug effects
  • Ovary / pathology
  • 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)
  • RNA, Small Interfering / metabolism
  • RNA, Small Interfering / pharmacology
  • Rats
  • Reverse Transcriptase Polymerase Chain Reaction
  • Signal Transduction
  • Transcription Factors / antagonists & inhibitors
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • ras Proteins / genetics
  • ras Proteins / metabolism*

Substances

  • HMGA2 Protein
  • KLF6 protein, human
  • KRAS protein, human
  • Kruppel-Like Factor 6
  • Kruppel-Like Transcription Factors
  • Proto-Oncogene Proteins
  • Proto-Oncogene Proteins c-fos
  • RNA, Small Interfering
  • Transcription Factors
  • fos-related antigen 1
  • Proto-Oncogene Proteins p21(ras)
  • ras Proteins