sEMTor – The EMT simulator

Developed by Steffen Plunder, see the companion article:

Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion
Steffen Plunder, Cathy Danesin, Bruno Glise, Marina A Ferreira, Sara Merino Aceituno and Eric Theveneau, Nature Communications (2024).

An interactive, agent-based model to simulate epithelial-to-mesenchymal transition-like events in a pseudostratified epithelium.
The simulation has epithelial control cells (green) and experimental cells (red). Experimental cells can be instructed to perform some or all of the following events in various orders:

→ A Loss of apical adhesion (detachment from neighboring apical points).
→ B Loss of basal adhesion (detachment from basal line).
→ S Relaxation of straightness (apical/basal points and nuclei are no longer forced to align).
→ P Protrusive activities (seek-and grab behavior of basal points in direction of the polarity, typically basally, can only occur if B is part of the selected EMT-like scenario).

Note: Our scientific conclusions from the model are based on statistics obtained from thousands of simulations of the model shown below. Please note that in some instances, single simulations can differ substantially from the average behavior.

Simulation Apical side (red)

Basal side (black)

Time = 10

0h 12h 24h 36h 48h

A B S

Parameters

(Restart required)

Number of experimental cells

0 1 11

Number of cells undergoing EMT-like events.

Interkinetic nuclear movements

Determines if nuclei of experimental cells perform pre-mitosis rapid apical movement (PRAM).

EMT: Protrusions

Determines if the basal point of experimental cells display a seek-and-grab behavior (P). This can only occur if the EMT scenario includes B (loss of basal adhesion).

Heterogeneity

If checked, each experimental cell randomly picks an EMT-like scenario. Then users can set the probability of INM and Protrusions to 0, 50 or 100%.

EMT-like scenarios

Determines which EMT-like scenario experimental cells will perform.

Parameters

(Restart required)

EMT scenarios per cell