In partial fulfillment of the requirements for the degree of

Doctor of Philosophy in Bioinformatics

in the School of Biological Sciences

Siarhei Hladyshau

Defends his thesis:

Computational models of actin regulation driving cytoskeletal dynamics, cell polarity and motion

Wednesday, April 19, 2023

10:00 AM Eastern Time

EBB, Conference Room #4029

Zoom link:  https://gatech.zoom.us/j/97063735483

Thesis Advisors: 

Dr. Denis Tsygankov

Wallace H. Coulter Department of Biomedical Engineering

Georgia Institute of Technology and Emory University 

Committee Members:

Dr. Shuyi Nie

School of Biology

Georgia Institute of Technology

Dr. Melissa L. Kemp

Wallace H. Coulter Department of Biomedical Engineering

Georgia Institute of Technology and Emory University 

Dr. Eberhard O. Voit

Wallace H. Coulter Department of Biomedical Engineering

Georgia Institute of Technology and Emory University 

Dr. Mark Borodovsky

School of Computational Science and Engineering, Georgia Institute of Technology

and Wallace H. Coulter Department of Biomedical Engineering

Georgia Institute of Technology and Emory University 

Summary:

Cell morphodynamics is a fundamental biological process required for the healthy functioning of a eukaryotic organism. Understanding its regulatory mechanisms is needed for developing new strategies to treat numerous diseases, including cancer metastasis, excessive angiogenesis, congenital disorders, and chronic wounds. My work focuses on Rho family GTPases (RhoA, Rac1, and Cdc42), known as the key regulators of actin cytoskeleton and cell motion. I developed a computational platform that allowed me to study different configurations of GTPase signaling pathways and capture the complex spatiotemporal distribution of these proteins driving cytoskeletal organization and dynamics. I applied this platform to investigate signaling bistability and the mechanisms of polarity establishment in yeast. I also used this methodology to study wave dynamics of GTPases and F-actin in the cortex of Patiria miniata and Xenopus laevis oocytes. I quantitatively reproduced different actin behaviors in these two organisms and revealed a critical role of quasi-static, low-amplitude patterns in the emergence of complex wave dynamics. Finally, I studied the regulation of cell ruffling by Cdc42 and Rac1 in epithelial breast cancer cells and mouse embryonic fibroblasts. Using my computational approach, I showed that cell edge velocity is regulated by the kinetic rate of GTPase activation rather than the concentration of the active molecules. My analysis also suggested that the timing of Rac1 and Cdc42 activity is cell-type dependent. I developed a model that reproduced such dependences and showed that feedback from Cdc42 and Rac1 was sufficient to control the activation delay when these GTPases have a common upstream regulatorily motif. I developed a series of image analysis pipelines for these studies that allowed precise tracking of GTPase activity and cell edge motion in simulations and experimental data.