Title: Graph Vertex Model of 3D Cell Aggregates

Speaker: Dr. Tanmoy Sarkar (Jožef Stefan Institute, Ljubljana, Slovenia)

Abstract: Topological transformations, including cell neighbor rearrangements and cell divisions, play a pivotal role in tissue deformation, morphogenesis and cancer metastasis. Tissues are most conveniently modeled as collections of polyhedral cells within 3D cell aggregates. However, due to the complexity of the vertex model’s data structure, it is very hard to implement any topological transformations. Existing solutions to this problem are often not reproducible because of their customized nature. In the talk, I will demonstrate a reformulation of the classical vertex model we recently developed, also known as the graph vertex model (GVM) [1]. The uniqueness of GVM lies in storing the topology of the cell network in a knowledge graph, enabling topological transformations through simple and intuitive graph transformations. Additionally, the simplified data structure of GVM unifies topological transformations in both 2D and 3D. Moreover, we have applied a similar approach to develop GRAPE, an online queryable graph database that allows interactive analyses of an entire embryo, where all surface cells are accurately segmented and tracked, and cell divisions are identified. In summary, GVM can potentially revolutionize the field of tissue mechanics.

[1] T Sarkar, M Krajnc, Graph topological transformations in space-filling cell aggregates, PLoS Comput Biol 20(5): e1012089 (2024).