Modelling heterogeneity of EMT
to identify main drivers of basal extrusion
Steffen Plunder
Kyoto University
Institute for the Advanced Study of Human Biology
The 1st
ASHBi-KAIST Joint Workshop
October 3th, 2024
Epithelial-to-mesenchymal transitions (EMT)
The good
Source: Gilbert, Scott F., and Michael J. F. Barresi.
Developmental Biology
(2018)
and the bad!
Source: Craene, Bram De, and Geert Berx.
“Regulatory Networks Defining EMT during Cancer Initiation and Progression.”
Nature Reviews Cancer
(2013)
Question:
Which aspect of EMT determine
the directionality of extrusion?
Yang et al.
“Guidelines and Definitions for Research on Epithelial–Mesenchymal Transition.”
Nature Reviews Molecular Cell Biology
(2020)
Challenge #1:
The spectrum of EMT phenotypes
Example in chick neural crest
Challenge #2:
Complex regulation network
Nadège Gouignard, Cyril Andrieu, and Eric Theveneau.
“Neural Crest Delamination and Migration: Looking Forward to the next 150 Years.”
Genesis
(2018)
Computational modelling for the rescue?
Our initial idea for key EMT events and factors which might drive basal extrusion:
Loss of cell-cell adhesion
Loss of cell-matrix adhesion
Change of cytoskeleton dynamics
Loss of apical-basal polarity
+ timing of events
+ order of events
+ heterogeneity of phenotypes
Approach:
Let's test first in computer simulations before doing
tons of experiments...
An
in vivo
model for EMT:
Chick neural crest
Neural tube:
Pseudostratified epithelium with interkinetic nuclear migration
(INM)
Existing computational models for epithelial tissues
Primary model for epithelial tissues:
Vertex Models
S. Alt, P. Ganguly, and G. Salbreux,
“Vertex models: from cell mechanics to tissue morphogenesis,”
Philosophical Transactions of the Royal Society B (2017)
Main limitation in our setting:
Less suitable for study of nuclei
position along apical-basal axis...
Cell shapes in PSE are not convex regions...
Existing nuclei-centered models: e.g. ya||a
P. Germann, M. Marin-Riera, and J. Sharpe,
“ya||a: GPU-Powered Spheroid Models for
Mesenchyme and Epithelium,” C
ells (2019)
S. Runser, R. Vetter, and D. Iber,
“SimuCell3D: three-dimensional simulation of
tissue mechanics with cell polarization,” Nat Comput Sci
(2024)
Models specifically for PSE
Quite complex, in particlar with since we need
to add EMT & simulation are complex
and hence studying many EMT scenarios
would be time consuming.
(and it came anyway too late for this project)
Part I:
Development of an agent-based model for PSE
(2019)
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Modelling principle: "We strictly only add rules which are known in vivo."
1. Tissue dynamics based on cell-cell interactions
2. Pseudostratified epithelium: Internuclear Migration
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Part II:
Computational Modelling of EMT
Adding EMT-like events to our computational model
A:
loss of apical cell-cell adhesion
S:
loss of straightness (polarity)
B:
loss of apical cell-cell adhesion
P:
protrusive activities after
B
ve
In our model we can now control for each individual cell
the onset of EMT-like events (yes or no) and the timing...
Evaluation of simulation results
Individual cells
Heterogeous groups
The "most logical" sequence of EMT events...
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In the model: EMT-like events
"A S B"
In the computational model this
"logical sequence" has issues...
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Part III:
In silico
and
in vivo
results
Statistical evaluation of randomized EMT scenarios
(in silico)
Ensemble simulations
150.000 simulations
~ 425 different EMT scenarios
Correlation analysis
1. Protrusions are primary factor.
2. Position of nucleus more
important than timing of events!
Result #1:
The role of INM
in silico
&
in vivo
In silico
:
INM impacts the directionality of extrusion
In vivo
:
INM regulation is less thight in the neural crest
Result #2:
early role of protrusions during epithelial destabilisation
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In silico we observe
(among randomzied EMT scenarios)
two paths towards the basal
side:
less INM
EMT cells
stop INM
basal positioning
of nuclei
BASAL EXTRUSION
protrusive
activities
protrusive
within epithelium
activities
e.g. S. H. Kil, C. E. Krull, G. Cann, D. Clegg, and M. Bronner-Fraser,
“The α4Subunit of Integrin Is Important for Neural Crest Cell Migration,”
Developmental Biology (1998)
Literature:
Knockout of α4-subunit of integrin leads to apical extrusion.
Result #2:
Upregulation of integrins contributes to epithelial destabilization
In addition to the role of integrins for
mobility, integrin expression can
contribute to epithelial destabilisation
and direction of extrusion.
EMT network hypothesis
Instead of a
"logical"
linear EMT sequence
Our data suggest multiple paths towards basal extrusion:
Extensions & furture work
Application to mouse gastrulation:
role of cell cycle length
and cytoskeleton properties
to non-apical mitosis.
Upcoming, modelling of extrusion and rosette formation in
drosophila eye-antenna.
Thanks for your attention!
Sara Merino-Aceituno
Marina A Ferreira Diane Peurichard Pierre Degond
Seirin-Lee, BiMed-Math Lab
Kyoto University,
Institute for Advanced Study of Human Biology
Eric Theveneau
Try our
S
tandalone
EMT
simula
TOR
at
semtor.github.io