Title: Understanding cell behaviour during pathological morphogenesis using simulations integrated with in vitro and in vivo experiments
Funder: The Francis Crick Institute

Abstract: My lab investigates how cells adapt their behaviour during morphogenesis: how changes to local tissue conditions alter cell behavior such that the system either finds a new functioning structure/pattern or collapses into maladapted turmoil. By integrating multiscale modeling with in vitro experiments, and in vivo experiments performed by our close collaborators, we aim to elucidate cellular-level links between signaling perturbations and tissue-level phenotypes. One example of our work is with the endothelial cell (EC) Notch signaling pathway, where by integrating simulations and experiments, we identified alternative pathways that selectively modulate the speed at which Notch selects migratory ECs. This could form the basis of novel cancer and retinopathy treatments with fewer side effects. We aim to 1) identify “temporal modulators” of vascular branch spacing, opening new therapies to normalize angiogenesis in disease and improve vascularization in tissue engineered scaffolds; 2) unravel how pathological vascular tufts, which cause blindness in retinopathies, form and predict new strategies to treat them. 3) promote the wider use of robust and accessible computational models across cell systems, such as by developing a novel simulation language for non-specialists, potentially contributing major advances in integrated biological modeling and reducing the number of animals used in biomedical research. In silico: 1) We will develop a dynamic model of VEGF diffusion and binding to VEGFR-2 using Partial Differential Equations and reaction-diffusion equations, integrated to an advanced agent-spring model of actin driven-membrane deformation. We will simulate how cell shape signalling feedback impacts cell decisions and movement during sprouting, aiming to predict optimal doses of combinatorial targets identified in our in vitro screen. 2) we will extend the model into a testbed for retinal vascular tuft formation utilizing the immersed boundary method to capture fluid pressure changes in the vitreous. 3) working with software engineers (Steffen Szchaler, KCL) we will develop a suite of higher-level modelling languages that generate a full C++ implementation of the cell simulations above automatically - with the hope that experimentalists will be able to directly understand and drive simulation design themselves. In vitro: 1) we will screen human and mouse EC lines to identify new pathways that alter Notch patterning (using the high throughout STP). 2) We will investigate pathways identified in micropatterning and microfluidic devices (developed at the Making Lab STP), quantify cell shape, motile behavior during sprouting, as well as changes in Notch-Dll4 patterning (using static-Fluorescent-ISH and live imaging with fluorescent reporters) and overall network topology. The assays will provide parameters to the in silico model and a testbed to validate new model predictions on combinatorial doses of target inhibitors to alter network density. In vivo: 1) Predictions of temporal regulatory pathways that can alter vascular sprouting will be confirmed in vivo in the zebrafish by Shane Herbert (Manchester University). 2) mouse retinopathy experiments will be performed by Claudio Franco (Lisbon) and imaged and analyzed using our new 4D lightsheet microscopy retinal imaging protocol to calibrate and test our tuft morphogenesis model.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: EYE;GENERIC HEALTH RELEVANCE