A Boolean network model of hypoxia, mechanosensing and TGF-β signaling captures the role of phenotypic plasticity and mutations in tumor metastasis
Authors: Greene Grant , Zonfa Ian , Ravasz Regan Erzsébet 
Published: December 2024

AbstractThe tumor microenvironment aids cancer progression by promoting several cancer hallmarks, independent of cancer-related mutations. Biophysical properties of this environment, such as the stiffness of the matrix cells adhere to and local cell density, impact proliferation, apoptosis, and the epithelial to mesenchymal transition (EMT). The latter is rate-limiting step for invasion and metastasis, enhanced in hypoxic tumor environments but hindered by soft matrices and/or high cell densities. As these influences are often studied in isolation, the crosstalk between hypoxia, biomechanical signals, and the classic EMT driver TGF-β is not well mapped, limiting our ability to predict and anticipate cancer cell behaviors in changing tumor environments. To address this, we built a Boolean regulatory network model that integrates hypoxic signaling with a mechanosensitive model of EMT, which includes the EMT-promoting crosstalk of mitogens and biomechanical signals, cell cycle control, and apoptosis. Our model reproduces the requirement of Hif-1α for proliferation, the anti-proliferative effects of strong Hif-1α stabilization during hypoxia, hypoxic protection from anoikis, and hypoxia-driven mechanosensitive EMT. We offer experimentally testable predictions about the effect of VHL loss on cancer hallmarks, with or without secondary oncogene activation. Taken together, our model serves as a predictive framework to synthesize the signaling responses associated with tumor progression and metastasis in healthy vs. mutant cells. Our single-cell model is a key step towards more extensive regulatory network models that cover damage-response and senescence, integrating most cell-autonomous cancer hallmarks into a single model that can, in turn, control the behavior of in silico cells within a tissue model of epithelial homeostasis and carcinoma.Author SummaryThe cellular environment in and around a tumor can aid cancer progression by promoting several cancer hallmarks. This environment can affect growth and cell death, as well as a phenotype change that renders cells migratory and invasive: the epithelial to mesenchymal transition. Hypoxia (low oxygen availability) is known to promote this transition, while the attachment of cells to soft matrices or high cell density environments hinders it. These influences are often studied in isolation. As a result, their crosstalk is poorly understood. To address this, we have built a network model of cellular regulation that integrates a cell’s responses to hypoxia, the biophysical environment, and growth signals to model cell division, death, and the epithelial to mesenchymal transition in environments cells encounter during metastatic tumor progression. Our model reproduces a wide range of experimental cell responses and offers experimentally testable predictions about the emergence of cancer hallmarks driven mutations that affect the hypoxic response. Our single-cell model is a key step towards more extensive cell-scale models that also include cell aging and damage response. These, in turn, can serve as building blocks of a larger tissue model of healthy vs. cancerous epithelia.