Cell shape is important for the dynamics of cellular signaling. We investigated the time and space dependency of cellular signaling on the cell shape by combining experimental time- resolved data for the activation of cell signaling with image analysis of the affected cells during a wound-healing experiments and spatio-temporal agent-based modeling. We performed systematic stochastic simulations and analyzed the resulting temporal behavior and spatial distribution of different signaling compounds for different cell shapes. As an input for the simulation pipeline, we adapted a method to create meshes for the surfaces of arbitrary cell shapes that subsequently can take real image data as input. Systematic simulation of the network (here exemplified for the ERK signaling pathway) in different cell shapes and under different conditions led to following insights: (i) Shape influences the dynamics of signaling molecules in the cytoplasm. (ii) The distribution of receptor molecules at the surface was not found to be affected by cell shape. (iii) The time needed by phosphorylated ERK to reach the nucleus is dependent on cell shape, where elongated cell shapes lead to longer delay between first signal and signal output reaching nucleus. (iv) Small sub-volumes such cell protrusions can restrict the diffusion of signaling molecules affecting signal transduction and creating locally different concentrations of signaling molecules.

We have combined the different analysis steps into a prototypical pipeline. This will in future allow to investigate the spatio-temporal dynamics of signaling pathways in specific cell shapes typical for different conditions such as cells in a confluent cell layer, cells invading empty space, single cells under microscope or migrating tumor cells. This will allow for a deeper understanding of the mutual dependence of cell shape and signaling.