| Many protein kinases along with phosphoserine/threonine-binding domains such as 14-3-3 proteins, WW domains, FHA domains, Polo-box domains, and BRCT domains function together within signaling networks to control growth factor responses, cell cycle progression, the response to DNA damage, and the onset of apoptosis. How signals emerging from these pathways are integrated and processed as a network is unclear. To address this, we have been developing systems models of signaling where kinase activities, protein phosphorylation, binding of substrates to phosphoserine/threonine binding domains, and cellular responses such as cell cycle arrest and apoptosis are quantitatively measured at densely sampled points in time, and related mathematically using partial least squares regression and principal components analysis. We used this approach to construct a systems model of cytokine-induced apoptosis in HT-29 cells, where 7980 intracellular signaling events were linked to 1440 response outputs associated with apoptosis. The model accurately predicted multiple time-dependent apoptotic responses induced by a combination of the death-inducing cytokine tumor necrosis factor (TNF) with the pro-survival factors epidermal growth factor (EGF) and insulin. The model revealed new molecular mechanisms connecting signaling to apoptosis including the role of unsuspected autocrine circuits activated by TGF-α and IL-1α, All of the molecular signals could be divided along two primary signaling axes that constitute fundamental dimensions (molecular “basis axes”) within the apoptotic signaling network. Projections of different stimuli along these axes captures the entire observed apoptotic response, suggesting that cell survival is determined by signaling through this canonical basis set. We have developed a new technique termed “network breakpoint analysis” to probe essential features of information transfer in signaling pathways. Applying this approach to TNFα-induced cell death revealed that the p38MAPK-MAPKAP Kinase-2 pathway is optimally ‘tuned’ to maximize apoptosis in response to pro-death stimuli while minimzing death in their absence. We have now applied this methodology to study signal transduction events that control cell cycle arrest and apoptosis in response to DNA damage. Our data indicates that, in addition to the well-established ATM-Chk2 and ATR-Chk1 pathways, p53-defective tumor cells have re-wired the checkpoint signaling network to incorporate the p38MAPK-MAPKAP Kinase-2 pathway as an essential component of the DNA damage response. |
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Systems Biology Seminar |
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Date： |
July 2, 2008(Wed) 16:00～18:00 |
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Place： |
Faculty of Science Bldg.3, 4F, room 412 |
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Host： |
Shinya Kuroda(skuroda AT bi.s.u-tokyo.ac.jp) |
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