Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression

Cell Syst. 2018 Jan 24;6(1):75-89.e11. doi: 10.1016/j.cels.2017.11.010. Epub 2017 Dec 13.


Upon stimulation of cells with transforming growth factor β (TGF-β), Smad proteins form trimeric complexes and activate a broad spectrum of target genes. It remains unresolved which of the possible Smad complexes are formed in cellular contexts and how these contribute to gene expression. By combining quantitative mass spectrometry with a computational selection strategy, we predict and provide experimental evidence for the three most relevant Smad complexes in the mouse hepatoma cell line Hepa1-6. Utilizing dynamic pathway modeling, we specify the contribution of each Smad complex to the expression of representative Smad target genes, and show that these contributions are conserved in human hepatoma cell lines and primary hepatocytes. We predict, based on gene expression data of patient samples, increased amounts of Smad2/3/4 proteins and Smad2 phosphorylation as hallmarks of hepatocellular carcinoma and experimentally verify this prediction. Our findings demonstrate that modeling approaches can disentangle the complexity of transcription factor complex formation and its impact on gene expression.

Keywords: L1 regularization; Smad proteins and complexes; TGF-β signal transduction; dynamic pathway modeling; hepatocellular carcinoma; liver; mathematical modeling; quantitative mass spectrometry; regulation of gene expression; systems biology.

MeSH terms

  • Aged
  • Animals
  • Carcinoma, Hepatocellular / genetics
  • Carcinoma, Hepatocellular / metabolism
  • Cell Line, Tumor
  • DNA-Binding Proteins / genetics
  • Female
  • Hep G2 Cells
  • Hepatocytes / metabolism
  • Humans
  • Liver / metabolism
  • Liver Neoplasms / genetics
  • Liver Neoplasms / metabolism
  • Male
  • Mass Spectrometry / methods
  • Mice
  • Mice, Inbred C57BL
  • Middle Aged
  • Phosphorylation
  • Signal Transduction
  • Smad Proteins / genetics*
  • Smad Proteins / metabolism
  • Trans-Activators / genetics
  • Transcription, Genetic
  • Transforming Growth Factor beta / metabolism


  • DNA-Binding Proteins
  • Smad Proteins
  • Trans-Activators
  • Transforming Growth Factor beta