Data and simulation code for paper 'Adhesion-driven invasion: disentangling the interplay between cell-cell and cell-matrix interactions in cancer cell migration' (Biophysical Journal, 2026)

Zenodo (CERN European Organization for Nuclear Research)

Abstract

This repository accompanies the research article “Adhesion-driven invasion: disentangling the interplay between cell-cell and cell-matrix interactions in cancer cell migration” (Biophysical Journal, 2026). In the paper, we study cell invasion into the extracellular matrix. The simulation data was generated using simulations based on the Cellular Potts model in CompuCell3D [1]. The simulations were analysed using an in-house MATLAB script based on Hou et al. (2018) [2]. UPDATE VERSION 2.0: We identified an error in the simulation code concerning cell-cell adhesion. The adhesion value was intended to be set to JCC as described in the manuscript, but due to an error in the implementation, the adhesion value remained 0. We investigated the issue and performed additional checks to assess its impact on the reported results. After discovering the error, we reran the simulations of the radial ECM network using the corrected code and repeated the analysis using the TASI-software. The results were compared with the original results, and these checks confirmed that the error does not significantly affect the quantitative results and the conclusions of the analyses reported in the manuscript remain unchanged. This version includes the corrected code together with the dataset generated using the corrected code. The simulations for the smaller and larger ECM sizes have not been rerun and are therefore not included in this version. However, the corrected code supports simulations of these size variations, which can be regenerated if needed. The original version is retained unchanged for transparency and reproducibility. However, the code from the original version should no longer be used to run the simulations. Simulation code and raw data The zip-folder 'NetworkRadialECM_LeaderOnly168' contains the simulation code and data for the parameters we ran in the manuscript. The data is for the ECM network with a radial geometry. Simulations were run for 210 conditions. For each condition, 50 independent simulations were run. Force per ECM binding site (kappa) 0, 1, 2, 3, 4, 5 Cell-cell adhesion strength (JCC) 0, 1, 2, 3, 4, 5, 6 Cell-matrix adhesion strength (JCF) 0, 1, 2, 4, 6 For each simulation, we stored the snapshots (as VTK files) every 1000 mcs. These are included in the zip-folder. We also ran simulations for a random ECM network, and for different system sizes. The processed data is avaible in the Supplementary Material of the publication and the raw simulation data is available upon request. Spheroid analysis The simulations were analysed using an in-house MATLAB script based on Hou et al. (2018). The processed data is available in the zip-folders: AnalysisTASI_*.zip. This data set contains the processed TIFF images based on the VTK files as well as the excel sheet Migration.csv with the analysis results. References [1] Swat, Thomas, Belmonte, Shirinifard, Hmeljak and Glazier. Chapter 13 - Multi-scale modeling of tissues using CompuCell3D. Methods in Cell Biology, 110 (2012). 325-366. https://doi.org/10.1016/B978-0-12-388403-9.00013-8 [2] Hou, Konen, Brat, Markus and Cooper. TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics. Scientific Reports, 8 (2018). 7248. https://doi.org/10.1038/s41598-018-25337-4

Authors 5

1. Quirine J. S. Braat

   Eindhoven University of Technology

   Affiliation as printed

   Eindhoven University of Technology

2. Klara Beslmüller Aachen

   Leiden University

   Affiliation as printed

   Leiden University

3. Cornelis Storm

   Eindhoven University of Technology

   Affiliation as printed

   Eindhoven University of Technology

4. Erik H.J. Danen Aachen

   Leiden University

   Affiliation as printed

   Leiden University

5. Liesbeth Janssen

   Eindhoven University of Technology

   Affiliation as printed

   Eindhoven University of Technology