Modelling the WNT3 Pathway

Gabrielle Bulliard, creating a model of the β-catenin destruction complex.

Author: Gabrielle Bulliard | Major: Biomedical Engineering

During the beginning of my freshman spring semester, I learned about a research program when attending one of the biomedical engineering department demos. The program was created by our school’s Biomedical Engineering Society and is called the Alpha Research Program. This program is designed to allow students to become easily involved in research within the biomedical engineering department, no matter their experience or possible time commitment. When I entered the program, I was assigned to a mentor group according to my research and career interests: mainly cancer, genetics, and therapies. Under Dr. Leonard Harris, my groupmates and I have been creating a computational model, a computer simulation, of the WNT3 signaling pathway, constructing an aid for researchers trying to find treatments for tumor-induced bone disease.

The WNT3 signaling pathway is one of many signaling pathways that are active in breast, lung, and prostate cancer cells that have metastasized to the bone. These pathways drive the expression of proteins in tumor cells, such as parathyroid hormone-related protein (PTHrP), that cause tumor-induced bone disease (TIBD), which is an umbrella term for increased fractures, spinal compression, pain, bone marrow dysfunction, and hypercalcemia due to metastasized tumors that have established in the bone. There have been many decades of research and attempts at treatment. However, because of the multiple signaling pathways that underlie TIBD and their complex interactions, there has not been a treatment that has both improved bone health and reduced tumor burden. Our computational model, in theory, should allow researchers to better predict effective treatments.

Our computational model has been built using Python and the PySB package, which allows users to create mathematical models of biochemical systems without extensive Python knowledge and large amounts of calculations. During the beginning of the 2021 summer grant term, my group and I completed the framework of our model. We had a very basic simulation of the pathway, but we were able to run the full program and create rudimentary plots of protein population and RNA production. Once we had a working model, we set to make it more biologically accurate by breaking down the basic components of our model that glossed over many processes into more detailed steps. To do this, my group and I read articles about the detailed aspects of the pathway and compiled our research to be entered into our code. The biological process we decided to first break down is the creation of a multi-protein complex known as the “destruction complex” and the ubiquitination of β-catenin, a protein that drives the expression of PTHrP.

As of this writing, one of my groupmates and I have created a basic model of the creation of the destruction complex and how it triggers degradation of β-catenin. The destruction complex binds β-catenin while still in the cytosol and phosphorylates it, allowing β-TrCP, a recognition protein, and the E3 ubiquitin ligase to ubiquitinate β-catenin and shuttle it to a proteasome, a protein complex that degrades ubiquitinated proteins. The destruction complex is a group of proteins that are bound together: Axin, GSK3β, CK1α, and APC. Axin is a scaffolding protein that holds the destruction complex together. Once β-catenin is bound to Axin, GSK3β and CK1α phosphorylate β-catenin, allowing it to unbind from Axin and instead bind to APC, which was also phosphorylated by CK1α creating an attraction between the two proteins. This then allows β-TrCP to bind to and ubiquitinate β-catenin. β-catenin is now only bound to the destruction complex by the phosphorylated APC, which is either dephosphorylated inside the complex and loses its attraction to β-catenin, thus breaking the bond, or is taken to the proteasome and separated there.

Now that we have created a basic model, my peers and I will meet with Dr. Harris to go over the destruction complex assembly model in detail, correct any mistakes in the code, and simplify it if needed. This Fall, we will continue to add more detail to our model of the WNT3 pathway and meet with Dr. Harris’ experimental collaborators at Vanderbilt University to get feedback, advice, and discuss future directions.