Expression profiles at the level of miRNAs in 3D cultures.

Three-Dimensional Organotypic Cultures Reshape the microRNAs Transcriptional Program in Breast Cancer Cells Three-dimensional (3D) cell cultures have several advantages over conventional monolayer two-dimensional (2D) cultures as they can better mimic tumor biology. This study delineated the changes in microRNA (miRNA) expression patterns of breast cancer cells cultured in 3D and 2D conditions. 3D organotypic cultures showed morphological changes such as cell–cell and cell–extracellular matrix interactions associated with a loss of polarity and reorganization on bulk structures in both basal Hs578T and luminal T47D breast cancer cells. Data indicate that down-regulated miRNAs in Hs578T 3D cultures, relative to the 2D condition, contribute to a positive regulation of biological processes such as response to hypoxia and focal adhesion, whereas over-expressed miRNAs were related to negative regulation of the cell cycle. Remarkably, the repro-gramming of miRNAs’ transcriptional profiles was accompanied by changes in the expression of key miRNA/mRNA coregulation networks, such as miR-935/HIF-1A, which correlated with the expression found in clinical breast tumors and predicted poor patient outcomes. These data have implications in our understanding of cancer biology and impact the miRNA/mRNA regulatory axes of cells grown in 3D cultures. Our data represent a guide for novel miRNA candidates for functional analysis, including the response to therapy and biomarker discovery in breast cancer. We analyzed 3D culture samples compared to 2D cultures of the Hs578T triple-negative breast cancer cell line, using the Affymetrix GeneChip miRNA 4.0 platform. Array data were processed with the Affymetrix GeneChip command console software v4.0 computational tool. Samples were run in triplicate.