Agent-based modelling of heterogeneous EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion Steffen PlunderKyoto University Institute for the Advanced Study of Human BiologyESTMB 2024 ToledoMinisymposium on Multiscale mathematical models in physiological processes and cancer. From sub-cellular mechanisms to phenotype switching and metastasis (II)
OutlinePSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxAn agent-based model for pseudostratified epithelial tissueModelling of epithelial-to-mesenchymal transitions (EMT)In silico study of key factors for basal extrusionIn vivo results: Early onset of inhibition of INM and central role of protrusions
apical basalapical basalPseudostratified epithelium and neural crest cells
PSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxAgent-based model for pseudostratified epitheliumBased on: Ferreira, Marina A., Evangeline Despin-Guitard, Fernando Duarte, Pierre Degond, and Eric Theveneau. “Interkinetic Nuclear Movements Promote Apical Expansion in Pseudostratified Epithelia at the Expense of Apicobasal Elongation.” PLoS Computational Biology (2019)
Interkinetic nuclear migration (INM)PSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT Networkxx
Epithelial-to-mesenchymal transitions (EMT)Embryo development, wound healing, ...The goodSource: Gilbert, Scott F., and Michael J. F. Barresi. Developmental Biology (2018)Gouignard, Nadège, Cyril Andrieu, and Eric Theveneau. “Neural Crest Delamination and Migration: Looking Forward to the next 150 Years.” Genesis (2018)Cancer, fibrosis, ...and the bad!Source: Craene, Bram De, and Geert Berx. “Regulatory Networks Defining EMT during Cancer Initiation and Progression.” Nature Reviews Cancer (2013)
The spectrum of EMT phenotypesYang et al. “Guidelines and Definitions for Research on Epithelial–Mesenchymal Transition.”Nature Reviews Molecular Cell Biology (2020)EpithelialMesenchymalprotrusionsloss of polaritycell-matrixremodellingloss of adhesion
Key question: What drives basal extrusion?In enbryo development: Good!During cancer: Bad!Gouignard, Nadège, Cyril Andrieu, and Eric Theveneau. “Neural Crest Delamination and Migration: Looking Forward to the next 150 Years.” Genesis (2018)
Adding EMT-like events to our existing model
A: loss of apical adhesion B: loss of basal adhesion S: loss of polarity
Possible factors leading to basal extrusionPSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxOur simulation study:Vary to following parameters- number of cells 'n' individual or group- number of EMT events none, 1, 2 or all- timing of EMT events early, normal, late- INM on/off- heterogeneity of on/off EMT-like events- Protrusions on/off
PSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxSingle EMT-like events lead to apical and basal extrusion!with INM without INMINM has significant effect on direction of extrusion
In vivo evidence for early onset of inhibition of INMPSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT Networkxx
In vivo evidence for early onset of inhibition of INMPSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT Networkxx
Next: Multiple EMT-like events
Textbook strategy for 'optimal setup' leading to basal extrusion:PSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxIn our model: Event ASBExpectation:Order of events matter + timing.
PSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxHomogeneous group with multiple EMT-like events
Early protrusive activities might requirement for basal extrusionPSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxExisting results: Inhibition of cell-matrix adhesion leads to apical extrusionS. H. Kil et al. The alpha4 subunit of integrin is important for neural crestcell migration. Developmental Biology (1998)Timing of protrusions might be critical.In vivo overexpression of integrin alpha5:In vivo experiments show apical extrusion
Until now: all EMT cells followed the same EMT-like events...However, in reality EMT is highly heterogeneous, more like:
Simulation study of heterogeneityPSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxSimulation"Black-Box"Input:Timing (never, early, later) of phenotype changes:A: loss of apical adhesionB: loss of basal adhesionS: loss of polarityP: protrusive activitiesINM: rapid apical movementHeterogeneity between cells!
Heterogeneous EMT scenarios could increase group efficiencyPSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxHowever, like for homogeneous groups,main in silico factors for basal extrusion are: 1. protrusive activities (P)2. early inhibition of INM
Correlation analysis in heterogeneous casePSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT NetworkxxOrder and timing of EMT events almost irrelevantPositioning of nucleus at onset of EMTcorrelated with direction of extrusion.
Network hypothesis for EMT progressionPSEG1 S G2 MINMEMThomogen.n = 1homogen.n > 1heterogen.n > 1Early INMProtrusionsEMT Networkxx
Details:SP, Cathy Danesin, Bruno Glise, Marina A. Ferreira, Sara Merino Aceituno, and Eric Theveneau. “Modelling Variability and Heterogeneity of EMT Scenarios Highlights Nuclear Positioning and Protrusions as Main Drivers of Extrusion.” bioRxiv, (2023) [accepted in Nature Communications]Despin-Guitard, Evangéline, SP, Navrita Mathiah, Eric Theveneau, and Isabelle Migeotte. “Occurrence of Non-Apical Mitoses at the Primitive Streak, Induced by Relaxation of Actomyosin and Acceleration of the Cell Cycle, Contributes to Cell Delamination during Mouse Gastrulation.” bioRxiv, (2024)Numerical method:SP and Sara Merino-Aceituno“Convergence Proof for First-Order Position-Based Dynamics: An Efficient Scheme for Inequality Constrained ODEs.” arXiv (2023)
Thanks for your attention!Sara Merino-AceitunoMarina A Ferreira Diane Peurichard Pierre DegondSeirin-Lee, BiMed-Math LabKyoto University, Institute for Advanced Study of Human BiologyEric Theveneau