The Group of Merks researches the development of blood vessels using computer models.
Best practice: Computer models show the formation of new blood vessels
How do new blood vessels develop? This question is important for wound healing or in case of diseases such as cancer. The group of Prof. Dr. Roeland Merks, senior researcher at the National Research Institute for Mathematics and Computer Science CWI, works with models that use the National Compute Cluster Lisa.
The research into the formation of new blood vessels is called angiogenesis. Roeland Merks, who complements his activities at CWI with his work as a professor in Multiscale Mathematical Biology at Leiden University, explains: “We want to know how cells are capable of building a blood vessel together. We see the formation of a blood vessel as the collective behaviour of cells and we want to unravel the rules underlying this behaviour. Most researchers concentrate on the molecular scale, the mutations in the DNA and the signals cells give. We approach the issue from a different angle: what are the properties at cellular level we need to address? These can be the cell's shape, the adhesion between cells or another aspect such as contact inhibition.”
Merks and his colleagues study the formation of blood vessels with computer models. “We started with a standard model of angiogenesis. This model only has one cell type: the endothelial cell. However, there are two types of endothelial cells: tip cells and stalk cells. Experiments have shown that tip cells play a central role in angiogenesis, but the underlying mechanism is not exactly known. We have given part of the cells in the model a different colour to then change the behaviour of these cells. We can change the tip cells so that they are positioned at the front of a new blood vessel. A new side branch of the vessel originates because a stalk cell is pushing the tip cell to the front as it were. This affects the network that is developing.”
“We go back and forth between the simulations on Lisa and the biomedical reality in the laboratories.”
The results of the model are tested in a real biomedical environment, for which Merks seeks the advice of his colleagues at AMC: “They had already examined the differences in tip cell and stalk cell gene expression and found that one of the genes is responsible for the production of a substance that causes the cells’ mutual attraction. This substance is less apparent in the tip cells. So we go back and forth between the simulations on Lisa and the biomedical reality in the laboratories.”
“Our collaboration with SURFsara is very smooth. Our PHD students and postdoctoral researchers have been able to do a lot of computing work and problems are always solved quickly.”
For the computing and manipulation of computer models, Merks and his colleagues use SURFsara's National Compute Cluster Lisa. “Our collaboration is very smooth”, says Merks. “Our PHD students and postdoctoral researchers have been able to do a lot of computing work and problems are always solved quickly. We will continue with the research for a while yet: our staff re still putting in a lot of computing hours.”