Mechanogenomics: A Systems-Level Genomics Investigation of Cell-Matrix Mechanobiology

Cell-extracellular matrix (ECM) mechanotransduction, the conversion of ECM biophysical cues into cellular biochemical signals – primarily through ECM receptors (i.e. integrins) – is essential to the maintenance of tissue homeostasis. Disruptions in mechanotransduction underlie many tissue remodeling diseases, including fibrosis and cancer. In lung fibrosis, resident fibroblasts lose the expression of a cell-surface integrin regulator, THY1, leading to dysregulated patterns of integrin activation, defective cytoskeletal activity, and a loss of normal cell mechanoperception. THY1-lacking fibroblasts acquire an apoptosis-resistant, ECM synthetic and chronically contractile myofibroblast phenotype that drives a pathological positive feedback loop. However, little is known of the genomic mechanisms that contribute to the emergence and persistence of these, and other, defective force sensing phenotypes. In this dissertation, I elucidate how normal and aberrant mechanosensing fibroblasts adapt their chromosomal and transcriptional networks to defined mechanical signals. I leverage a multi-omics workflow employing parallel ATAC- and RNA-sequencing in wild-type and mechanosensing defective fibroblasts generated by CRISPR knock-out of THY1 and a close relative, SEMA7a, across an array of substrate stiffnesses and culture times. In this work I confirmed and extended previously described mechanisms regarding mechanotransduction feedback and identified novel mechanosensitive genomic programs including the unique discovery of mechanics-mediated silencing of HOXA5, a pioneer factor crucial in pattern specification and lung development, thus linking aberrant mechanoperception to the loss of (re)generative gene modules. These works provide new insights into the fibroblast genomic response to mechanical signaling and establish new connections between the interplay of ECM mechanics, developmental gene circuitry, and pathogenesis.