Transcriptomic profiling of DU4475 cells in 3D cell culture matrices and suspension

The extracellular matrix (ECM)-regulated phenotypic plasticity is crucial for metastatic progression of triple negative breast cancer (TNBC). To investigate the effect of matrix cues on phenotypic plasticity, we embedded triple negative DU4475 cells from suspension culture into mechanically tunable fibrin gels or basement membrane extract (Matrigel). Cells in suspension culture and matrix cultures showed divergent gene expression profiles, with specific gene expression signatures depending on the biochemical composition and stiffness of the matrix. Overall design: DU4475 cells were embedded into soft fibrin (10 mg/mL), stiff fibrin (30 mg/mL) or Matrigel. RNA-seq analysis was performed after culturing DU4475 cells in the matrices for one week. Cells maintained in liquid suspension provided a reference for native cell phenotype. Three replicates were done for each condition.