Network analysis of gene expression reveals regulators of cell viscosity and mechanical phenotype

Abstract

Abstract Cell mechanical properties, such as cell stiffness and viscous behavior, have been proposed as biomarkers of cell disease states. Moreover, the molecular pathways that modify cell mechanics may also be potential novel targets for managing lethal diseases, such as cancer, by specifically changing the mechanical phenotype of cells along with the associated functional phenotype. This study explores the relationship between the viscosity and stiffness of cells and the underlying molecular mechanisms. We used a large linked molecular dataset to explore the correlations between gene expression, cell migration, and cell mechanical properties, which were quantified by two viscous rate constants from a standard linear solid viscoelasticity model and apparent Young’s modulus from a Hertzian contact mechanics model. Using a causal network analysis built on known relationships curated from literature in Qiagen’s Ingenuity Pathway Analysis package, we identified potential molecular control nodes that could modify the expression of multiple genes correlated with cell mechanics. We investigated the up- and down-regulation of expression by two predicted potential small molecule regulators (lacidipine and AG879) and four predicted potential gene regulators (AKT2, ITGB6, mir-183, and CD82) through small molecule inhibition, RNA interference, and introduction of microRNAs. The effects of modulation of these regulators were measured on both cell mechanical properties and gene expression in three ovarian cancer cell types. We identified several regulators that change the viscosity and stiffness of the cell with a corresponding change to the functional migratory ability in a cell-type specific manner.