Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness [array]

Remodeling and increased stiffness of the extracellular matrix is a hallmark of solid cancers and contributes to tumor progression through increased proliferation, survival and migration. Mechanotransduction, the process in which cells sense and transduce mechanical signals, can result in transcriptional changes that in turn alter cellular behavior. In vitro culturing of MCF10ACA1a (CA1a) breast cancer cells on polyacrylamide-based hydrogels of variable stiffness revealed drastic changes in morphology, indicating a stiffness dependent induction of a malignant phenotype. We used DNA microarray to characterize the transcriptome of CA1a cells on low (400 Pa) and high (5000 Pa) stiffness, corresponding to the stiffness of normal breast and breast cancer, respectively. In vitro cultures of MCF10CA1a cells on polyacrylamide-based hydrogels of variable stiffness revealed drastic stiffness-dependent morphology. To elucidate how this phenotypic switch is reflected by changes in mRNA levels, we used DNA-microarrays (initially) and RNA sequencing (later) and studied MCF10CA1a cells cultured for five days on stiffness mimicking normal breast tissue or breast cancer.