(343c) Hierarchical Modeling and Control of ERK Signaling

Cell
signaling is the process by which extracellular information is transmitted into
the cell. Cell signaling pathways are interconnected networks of signaling
proteins that communicate through complex molecular mechanisms. As a case in
point, ERK (extracellular signal-regulated kinases)
signaling plays an important role in numerous cellular processes such as
proliferation, apoptosis, DNA synthesis and differentiation. Signaling faults due to mutations and failures in the regulatory
mechanisms are known to result in different types of cancers. A
complex network of cellular interactions and feedback loops are usually arranged
in a hierarchical fashion in space and time to transform the information
content of extracellular signals to the DNA in the nucleus of the cell which in
turn leads to several cellular functions (see Fig.1).

Activation of EGFR (Epidermal Growth Factor Receptor) by binding
of its specific ligands, namely epidermal growth factor and transforming growth
factor α (TGF α), starts ERK signaling pathway, as shown in Fig.1.Upon
ligand binding, two subunits of EGFR are dimerized, leading to increase in the
enzymatic activity of its cytoplasmic tyrosine kinase domain. Adaptor protein
Grb2 binds to the phosphorylated RTK (Receptor tyrosine kinase)  followed by
recruitment of SOS forming Grb2-SOS complex  Membrane-bound protein Ras, which is a small GTP binding protein,
interacts with Grb2-SOS complex, and it is transformed to its active
conformation by exchanging GDP for GTP.  Active Ras acts as an important
switch which starts the sequential phosphorylation of
MAPK pathway that consists of the Raf/MEK/ERK signaling
cascade.

Activated
ERK, when translocated to the nucleus, phosphorylates nuclear transcription
factors (e.g. Myc), that govern cellular responses. Phosphorylated
transcription factors stimulate transcription of genes which are responsible
for encoding different proteins, including ones required for cell cycle
progression (e.g. Cyclin D)

We
decompose and analyze the ERK signaling pathway in two interacting functional
subsystems with distinct characteristics: First, EGFR-Ras-MAPK subsystem, and second
nuclear reactions triggered by activated ERK, including transcriptional
processes. These subsystems operate at different time scales (e.g. the nuclear reactions
are much slower than EGFR signaling throughout cytoplasm) and they interact
with each other via several inhibiting and activating feedback loops. For
instance, autocrine loop with positive feedback regulates amplitude and
duration of MAPK activation, by incorporating a ligand-releasing protease (i.e.
TACE). We have modeled the complete ERK signaling pathway shown in Fig.1 using mass-action
kinetics and conservation laws. Numerous models exist in the literature for
different parts of the pathway. Our model is more comprehensive as it combines
all the significant parts and treats the system as a whole. It is
well-established that each specific cellular response is determined by the duration,
magnitude, frequency and localization of ERK signaling.

The
developed dynamic nonlinear model exhibits very rich dynamics that is needed to
tune the steady-state and dynamic characteristics of ERK signaling. Simulations
show that ERK signaling can be modulated by a nested set of negative and
positive feedback loops to deliver the desired cellular action. Bistability
(i.e. ability to switch between two stable
steady-states separated by an unstable steady-state) is the hallmark of
cellular responses. Using bifurcation analysis, we
establish conditions for the existence of bistability in different parts of the
network and illustrate how the desired cellular function can be regulated by
modulating the bistability characteristics and on-off switching behavior of ERK
signaling.

Using
this model, we are able to explain the biological phenomena and the clinical
observations reported in the literature and postulate possible new mechanisms
to improve understanding of an important cellular signaling network.

Avraham, R., & Yarden, Y.
(2011). Feedback regulation of EGFR signaling: decision making by early and
delayed loops. Nature Reviews. Molecular Cell Biology, 12(2),
104–17. https://doi.org/10.1038/nrm3048.

Dhillon, A., Hagan, S., Rath,
O., & Kolch, W. (2007). MAP kinase signalling pathways in cancer. Oncogene,
26, 3279–3290. https://doi.org/10.1038/sj.onc.1210421

Figure 1. The
hierarchy of ERK signaling. Dashed lines represent the feedback signals with
arrow ends for activation and blunt ends for inhibition. DUSP: Dual-specificity phosphatase; TACE: (TNF)-alpha
converting enzyme, also called ADAM17.