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GENE EXPRESSION DATA AND FTIR SPECTRA PROVIDE A SIMILAR PHENOTYPIC DESCRIPTION OF BREAST CANCER CELL LINES IN 2D AND 3D CULTURES

Abstract

Thirteen breast cancer cell lines were grown in 2D traditional monolayer and in 3D laminin-rich extracellular matrix culture models. Microarray-based transcriptional profiling data were published for these cell lines in both culture conditions. Colonies embedded in Matrigel matrix were fixed in formalin, embedded in paraffin and cut in 4µm thick sections. Sections were mounted onto IR-transparent barium fluoride windows and deparaffinized for 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 cell genomes. Cluster analysis groups first the same cell line samples, independently on whether cells have been grown in 2D or 3D cultures. FTIR spectroscopy groups first by culture condition when considering the full spectrum length. The paper reports two important results. First, both gene expression level and FTIR spectroscopy are multivariate techniques which contain sufficient information to identify uniquely both any cell line (among 13 breast cancer cell lines) and phenotype induced by growing the cells in 2D or 3D cultures. Second, we established the presence of a strong correlation between gene expression patterns and Fourier transform infrared (FTIR) spectral data for the 13 breast cancer cell lines grown in both 2D and 3D cultures. These results suggest that, although based on completely different principles, the two approaches are similarly sensitive and describe the same patterns of variations in living cells.

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Supplementary files

Publication details

The article was received on 24 Jan 2018, accepted on 08 Apr 2018 and first published on 09 Apr 2018


Article type: Paper
DOI: 10.1039/C8AN00145F
Citation: Analyst, 2018, Accepted Manuscript
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    GENE EXPRESSION DATA AND FTIR SPECTRA PROVIDE A SIMILAR PHENOTYPIC DESCRIPTION OF BREAST CANCER CELL LINES IN 2D AND 3D CULTURES

    M. Smolina and E. Goormaghtigh, Analyst, 2018, Accepted Manuscript , DOI: 10.1039/C8AN00145F

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