Gene expression data and FTIR spectra provide a similar phenotypic description of breast cancer cell lines in 2D and 3D cultures

Thirteen breast cancer cell lines were grown in traditional two-dimensional (2D) monolayer and three-dimensional (3D) laminin-rich extracellular matrix (lrECM) culture models. Microarray-based transcriptional profiling data were published for these cell lines under both culture conditions. Colonies embedded in Matrigel matrix were fixed in formalin, embedded in paraffin and cut into 4 μm thick sections. The sections were mounted onto infrared-transparent barium fluoride windows and deparaffinized for Fourier transform infrared (FTIR) imaging. Samples consisting of Matrigel-coated 2D-grown cells followed the same processing procedure, simplifying comparison with 3D-cultured cells as well as with routinely prepared formalin-fixed, paraffin-embedded tissue specimens. Gene expression was found to be dominated by the cell line genome. Cluster analysis first groups the same cell line samples, independent of whether cells have been grown in 2D or 3D cultures. FTIR spectroscopy first groups by culture conditions when considering the full spectrum length. The paper reports two important results. First, both gene expression level and FTIR spectroscopy are multivariate techniques that contain sufficient information to identify uniquely both any cell line (among thirteen breast cancer cell lines) and phenotype induced by growing the cells in 2D or 3D lrECM cultures. Second, we established the presence of a strong correlation between gene expression patterns and FTIR spectral data for the thirteen breast cancer cell lines grown in both 2D and 3D lrECM cultures. These results suggest that, although based on completely different principles, the two approaches describe similarly the patterns of variations in cells.