Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis

• Published in: Mathematical biosciences 2022-02, Vol.344, p.108759-108759, Article 108759
• Main Authors: Tikka, Pauli, Mercker, Moritz, Skovorodkin, Ilya, Saarela, Ulla, Vainio, Seppo, Ronkainen, Veli-Pekka, Sluka, James P., Glazier, James A., Marciniak-Czochra, Anna, Schaefer, Franz
• Format: Article
• Language: English
• Subjects: Adhesion; Agglomeration; Cell adhesion; Cell adhesion & migration; Cell culture; Cell migration; Cell Movement; Cells (biology); Cellular potts model; Chemotaxis; CompuCell3D; Computer applications; Computer Simulation; Crosstalk; Early nephrogenesis; Epithelial cells; Epithelium; Kidney; Kidneys; Mesenchyme; Nephrons; Organogenesis; Organogenesis - genetics; Organoids; Parameter estimation; Particle swarm optimization; Pattern formation; Phenotypes; Progenitor cells; Python analysis functions; Self organizing maps; Stem Cells; Ureter
• ISSN: 0025-5564; 1879-3134
• DOI: 10.1016/j.mbs.2021.108759

During early kidney organogenesis, nephron progenitor (NP) cells move from the tip to the corner region of the ureteric bud (UB) branches in order to form the pretubular aggregate, the early structure giving rise to nephron formation. NP cells derive from metanephric mesenchymal cells and physically interact with them during the movement. Chemotaxis and cell–cell adhesion differences are believed to drive the cell patterning during this critical period of organogenesis. However, the effect of these forces to the cell patterns and their respective movements are known in limited details. We applied a Cellular Potts Model to explore how these forces and organizations contribute to directed cell movement and aggregation. Model parameters were estimated based on fitting to experimental data obtained in ex vivo kidney explant and dissociation–reaggregation organoid culture studies. Our simulations indicated that optimal enrichment and aggregation of NP cells in the UB corner niche requires chemoattractant secretion from both the UB epithelial cells and the NP cells themselves, as well as differences in cell–cell adhesion energies. Furthermore, NP cells were observed, both experimentally and by modelling, to move at higher speed in the UB corner as compared to the tip region where they originated. The existence of different cell speed domains along the UB was confirmed using self-organizing map analysis. In summary, we saw faster NP cell movements near aggregation. The applicability of Cellular Potts Model approach to simulate cell movement and patterning was found to be good during for this early nephrogenesis process. Further refinement of the model should allow us to recapitulate the effects of developmental changes of cell phenotypes and molecular crosstalk during further organ development. •Computational modelling for developmental biology.•Initial causes of cell movements and aggregations during early kidney development revealed.•Optimization of simulations using experimental data.•Parameter, e.g. diffusion constant, estimation method developed together with Cellular Potts Model.