Multi-omics investigation reveals molecular determinants of cancer cell evolution on soft extracellular matrix

Abstract

Cancer cell adaptation to their physical tumor microenvironment is a key driver of malignancy. Recent experimental evolution experiments show that the soft extracellular matrix (ECM) can impose a selection pressure on genetically variable tumor populations. Over months of sustained culture, the selection pressure leads to enrichment of specific genetic variants with high fitness, but the mechanisms underlying the high fitness of these soft-selected clones are not fully understood. Here, we used a combination of RNA-seq, ATAC-seq, and RRBS-seq to compare soft-selected populations with non-selected ancestral populations cultured on soft ECM. We demonstrate that ancestral populations grown on soft ECM for short durations are characterized by a stressed cell state with low fitness marked by cell cycle arrest and distinct metabolic shifts, whereas sustained culture selects for a robust proliferative phenotype. Mechanistically, selected cells exhibit a silenced ancestral stress response through epigenetic modifications, characterized by reduced chromatin accessibility and de novo DNA methylation, including CDH1 promoter hypermethylation. This repressive landscape supports a high-fitness state defined by elevated MYBL2 and FAK levels. An in-silico mechanism-based model shows that these molecular differences, together with high YAP1 nuclear localization in soft-selected cells, are salient features of genetic clones capable of FAK upregulation. These findings uncover a coordinated genetic and epigenetic mechanism driving cancer cell evolution in mechanically soft microenvironments.