Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells

Abstract

Cellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity. The resulting data-driven model reproduced all features of measured signaling responses and is sufficient to explain their heterogeneity in individual cells. We present evidence that heterogeneity in the levels of the feedback regulator Wip1 sets cell-specific thresholds for p53 activation, providing means to modulate its response through interacting signaling pathways. Our results demonstrate how excitable signaling networks can provide high specificity, sensitivity and robustness while retaining unique possibilities to adjust their function to the physiology of individual cells.To ensure reliable information processing, cellular signaling systems need to faithfully sense inputs in noisy environments while maintaining the flexibility to adjust their function to different physiologies. A commonly observed strategy to enable robust signal detection is the pulsed activation of signaling pathways in a digital-like response 1 . To understand how pulsatile dynamics can mediate robust yet versatile signal processing, it is necessary to identify the design principles that enable molecular networks to switch between different dynamic states and the mechanisms that allow modulation of their activity.A well-known example of a pulsatile signaling pathway in mammalian cells is the tumor suppressor p53. As a central hub of the cellular stress response, p53 maintains genomic integrity in proliferating cells and during tissue homeostasis 2 . In healthy cells, p53 levels are low due to poly-ubiquitination by the E3-ligase Mdm2 and subsequent proteasomal degradation 3,4 . Upon stress, p53 is activated by kinases that serve as primary damage sensors. One particularly dangerous insult is DNA damage in the form of double strand breaks (DSB), which may cause genomic rearrangements such as translocations, deletions and chromosome fusions. The primary sensor for DSBs is the PI3K-like kinase ataxia telangiectasia mutated (ATM) 5 , which gets phosphorylated and activated within minutes after damage induction 6 . Active ATM then stabilizes p53 by at least two distinct mechanisms: it phosphorylates Mdm2, which induces its auto-ubiquitination and subsequent degradation 7 , and p53, which interferes with Mdm2 binding 8,9 . As a consequence, p53 accumulates in the nucleus, where it acts as a transcription factor activating the expression of hundreds of target genes 10 .A key feature ...

Theoretical study of the impact of adaptation on cell-fate heterogeneity and fractional killing

“…In relation to our result, the transient and stochastic characteristics of these signaling dynamics may also suggest a role for promoting cell-fate heterogeneity. This is supported by some experimental evidences that have mapped the cell-cell variability of the pulsing dynamics of Erk 10,11 , p53 62,63 , β-catenin 13 and NF-κB 12 with the heterogeneity of cell-fate outcomes. Data-driven and fine-grained modeling of specific dynamic signaling and fate-regulatory pathways 11,20,62,64 are definitively the step further to evaluate on a case-by-case basis to which extent transient adaptation or pulsing dynamics may contribute, fortuitously or functionally, to cell-fate heterogeneity.…”

p53 dynamics in single cells are temperature-sensitive

“…This led to the appearance of damped pulses in the median p53 level of cell populations (Fig. 1E) 60 .…”

Deciphering p53 dynamics and cell fate in DNA damage response using mathematical modeling

“…The existence of ATM switch by MRN or MDC1 complex has been extensively explored (Mouri et al 2009;Sun et al 2009). Switchlike ATM activation in response to DSBs upstream of p53 was experimentally verified and guarantees undamped p53 pulses in a recent work (Monke et al 2017).…”