Abstract
Signaling pathways invoke interplays between forward signaling and feedback to drive robust cellular response. In this study, we address the dynamics of growth factor signaling through profiling of protein phosphorylation and gene expression, demonstrating the presence of a kinetically defined cluster of delayed early genes that function to attenuate the early events of growth factor signaling. Using epidermal growth factor receptor signaling as the major model system and concentrating on regulation of transcription and mRNA stability, we demonstrate that a number of genes within the delayed early gene cluster function as feedback regulators of immediate early genes. Consistent with their role in negative regulation of cell signaling, genes within this cluster are downregulated in diverse tumor types, in correlation with clinical outcome. More generally, our study proposes a mechanistic description of the cellular response to growth factors by defining architectural motifs that underlie the function of signaling networks.
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Acknowledgements
We thank P. Blackshear, W. Lai, M. Kracht, J. Milbrandt, S. Friedman and G. Narla for reagents. We thank P. Luu, R. Malenka and N. Citri for instructive comments on the manuscript. We thank W.L. Gerald for providing us with the prostate cancer data set. The following plasmids were gifts: ZFP36-GFP from P. Blackshear (National Institutes of Health), an IL8 reporter plasmid from M. Kracht (Medical School Hannover), EGR1 reporter plasmid from J. Milbrandt (Washington University School of Medicine) and a STAT3 reporter plasmid from A. Gertler (Hebrew University). Our laboratory is supported by research grants from Minerva, the Israel Cancer Research Fund, the German Israel Foundation, the Prostate Cancer Foundation, the European Commission and the National Cancer Institute (grants CA72981, CA102537, CA65930, CA64602 and CA099031). Y.Y. is the incumbent of the Harold and Zelda Goldenberg Professorial Chair, and E.D. is the incumbent of the Henry J. Leir Professorial Chair. A.C. acknowledges support of the Human Frontier Science Program. E.D. was supported in part by the Ridgefield Foundation, the Israel Science Fund and the European Commission (EC FP6). Requests for materials should be addressed to Y.Y. (yosef.yarden@weizmann.ac.il).
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Supplementary information
Supplementary Fig. 1
Model illustrating circuitries of feedback regulation embedded in the EGF-induced transcriptional program. (PDF 188 kb)
Supplementary Fig. 2
Ligands and cytokines induced by EGF in HeLa cells. (PDF 62 kb)
Supplementary Fig. 3
The repressive functions of MAFF and KLF2 depend on integrity of their effector domains. (PDF 354 kb)
Supplementary Fig. 4
ZFP36 governs stability of EGF-induced transcripts. (PDF 529 kb)
Supplementary Fig. 5
EGF-induced ligands and cytokines are coordinately upregulated in tumors of ovarian patients. (PDF 79 kb)
Supplementary Fig. 6
EGF and serum induce different subsets of transcription regulators and cytokines in MCF10A cells. (PDF 74 kb)
Supplementary Fig. 7
Additional potential network motifs used by the EGF-induced transcriptional program. (PDF 68 kb)
Supplementary Table 1
Phosphoprotein and gene expression profiles of EGF-stimulated epithelial cells. (PDF 183 kb)
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Amit, I., Citri, A., Shay, T. et al. A module of negative feedback regulators defines growth factor signaling. Nat Genet 39, 503–512 (2007). https://doi.org/10.1038/ng1987
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DOI: https://doi.org/10.1038/ng1987
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