|Elucidating the Control Mechanism for DNA Damage Repair with the p53-Mdm2 System: Single Cell Data Analysis and Ensemble Modeling |
Chemical and Biochemical Engineering
|Babatunde A. Ogunnaike, Univ.of Delaware, Chemical Engineering Dept.|
10:20 AM, Fiber Optics Auditorium
The p53-Mdm2 system, which plays a crucial role in DNA damage repair, is one of the best-studied of the “negative feedback motifs” known to be present in human cells (see for example, Piette, et al, 1997; Vogelstein et al, 2000; and Michael and Oren, 2003). Such studies typically involve perturbing cell populations with appropriate stimuli and monitoring total population response with immunoblots. Often such measurements of ensemble behavior are sufficient for understanding the molecular mechanism underlying the phenomenon in question. In the case of DNA damage repair using the p53-Mdm2 system however, Lahav et al, (2004), recently published experimental evidence that the dynamic behavior of the ensemble is fundamentally different from that of individual cells, creating a dilemma about the underlying control system mechanism.
Specifically, in response to DNA damage, the observed ensemble response is a damped oscillation in p53 levels whose amplitude increases with increased DNA damage. This behavior is consistent with “analog” control and a model by Bar-Or et al., (2000), predicts it reasonably well. However, the data in Lahav, et al., (2004) shows that at the single cell level, the response to DNA damage is rather a series of discrete pulses in p53; furthermore, with increase in DNA damage, neither the mean height nor the duration of the pulses changed, but the mean number of pulses increased. In addition, genetically identical cells each showed a different number of pulses of p53. Taken together, the observed single cell behavior is consistent with “digital” control (Lahav et al., 2004), raising the obvious question: how can “digital” behavior at the single cell level appear “analog” at the ensemble level? The more fundamental issue concerning the underlying DNA damage response mechanism is captured by the following challenge stated by Lahav, et al.:
What is the mechanism for digital oscillations in this system? Digital undamped oscillatory behavior is a challenge to modelers because the simplest theoretical models of this negative feedback loop show damped analog oscillations.
In this seminar we present a comprehensive, systems engineering model that uses the Lahav data to elucidate this mechanism and resolve the dilemma. First, we develop a simple model of the p53-Mdm2 effector system that reproduces the single non- oscillatory response to a stress signal experimental observed by Lahav et al. Next, from a careful analysis of the Lahav data we develop a probabilistic model of the distribution of pulses observed in a cell population. Finally, we combine the two with the simplest possible digital control algorithm to show how oscillatory responses whose amplitudes grow with DNA damage can arise from single cell behavior in which each single pulse response is independent of the extent of DNA damage.
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