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Updated: Aug 15, 2026
Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Identification of VDR-responsive gene signatures in breast cancer cells
Kelly Towsend1, Victor Trevino, Francesco Falciani
1Institute of Biomedical Research, Endocrinology and Metabolism, Medical School, University of Birmingham Edgbaston, Birmingham, UK.
Objectives:
Defining transcriptional profiles which predict cancer cell anti-proliferative responsiveness towards 1,25-dihydroxyvitamin D(3) [1alpha,25(OH)(2)D(3)] is required to improve and tailor the chemotherapeutic application of this seco-steroid hormone to individual cancer patients.
Methods:
We undertook a transcriptomic approach with Affymetrix human U133 GeneChips to determine responsive and resistant gene signatures in MCF-7 breast cancer cells and 1alpha,25(OH)(2)D(3)-resistant MCF-7(Res) cells, respectively. Principal component and hierarchical clustering analyses demonstrated that the patterns of responsiveness between the 2 cell types differed clearly and were used to generate heat maps. Differentially regulated gene targets were validated with Q-RT-PCR and the biological impact upon proliferation measured.
Results:
In untreated MCF-7(Res) cells, 163 genes were up-regulated and 274 down-regulated (with a log(2) ratio of >0.5) compared to the MCF-7 controls. Using the same gene expression threshold, 1alpha,25(OH)(2)D(3) treatment (100 nM, 6 h) of MCF-7 cells up-regulated 91 genes and down-regulated 5, whereas in MCF-7(Res), despite their resistance to the anti-proliferative effects, 156 genes were modulated with 91 being down-regulated. Strikingly, CYP24 was the only induced gene that was common to the genetic profiles of the 2 sets of 1alpha,25(OH)(2)D(3)-treated cells. Heat map analyses defined 2 sub-clusters of genes: (1) basal expression patterns associated with insensitivity towards 1alpha,25(OH)(2)D(3) and (2) regulated expression patterns associated with 1alpha,25(OH)(2)D(3) sensitivity. This latter cluster contained BAX, GADD45alpha, IGFBP-3, EGFR, MAPK4 and TGF-beta(2). Time course studies confirmed the 1alpha,25(OH)(2)D(3) regulation of TGF-beta(2) in MCF-7 and non-tumourigenic MCF-12A cells but not in MCF-7(Res) cells. Co-treatment of MCF-7(Res) cells with exogenous TGF-beta(2) plus 1alpha,25(OH)(2)D(3) enhanced anti-proliferative and vitamin D receptor transcriptional effects.
Conclusions:
Basal and regulated gene patterns can be used to predict and monitor the cellular response towards vitamin D(3) compounds and may possibly be applied as a further diagnostic tool.
