E-GEOD-9959 - Understanding Vitamin D resistance using Nonsense Mediated Decay arrays

Released on 1 June 2008, last updated on 2 May 2014
Homo sapiens
Samples (8)
Array (1)
Protocols (6)
Vitamin D is the strongest known natural anti-proliferative. A large number of studies in a wide spectrum of cancers, including epidemiological, in vitro and animal models, demonstrate that the active form of Vitamin D has anti-cancer benefits, affecting both progression and metastasis. Alike the role in calcium Vitamin D regulation, its anti-proliferative effect is thought to function through the Vitamin D receptor (VDR), although convincing evidence is lacking. Notwithstanding, separation of the calcemic and the anti-proliferative activity of Vitamin D analogues has been a major obstacle in developing new drugs for the treatment of cancer. The work presented attempts to unveil the molecular mechanism behind the anti-proliferative action of Vitamin D using genomic tools. For that purpose four independently developed Vitamin D sensitive/resistant MCF7 cell line pairs were collected. These unique biological replicates enabled us, both to increase the power of our study and to omit the use of Vitamin D. We deem this omission crucial since in the presence of Vitamin D only downstream genes involved in proliferation and cell cycle would be identified rather than causal resistance genes. The use of a variety of genomic techniques including expression, NMD and oligo CGH arrays reveal in the resistant cell lines the 11q13-14 as a region of DNA copy number loss and an altered expression of EGFR signaling pathway genes. Surprisingly, no genes known from calcium Vitamin D regulation were identified, nor did the VDR silencing by RNAi induce resistance to the sensitive cell lines. Keywords: Expression microarray, NMD array, cell type comparision Several MCF7 breast tumor cell lines independently derived from the human breast cancer cell line, both resistant and sensitive to Vitamin D, were used. The pairs of cell lines (parental-resistant) were developed in different laboratories and using different methodologies; while some cell lines acquired resistance by long exposure to the physiological concentration of Vitamin D (100nM), others were induced to resistant by being exposed to increasing amounts of Vitamin D. A total of 4 microarray expression experiments were carried out. In all microarray experiments RNA from the Vitamin D resistant cell line treated with Emetine was hybrizided agains RNA from the respsective sensitive/parental cell line treated with emetine.
Experiment type
transcription profiling by array 
Serge Smeets <s.smeets@vumc.nl>, Bauke Ylstra, Carmen J Narvaez, Derk ten Berge, Fernando Schmitt, JoEllen Welsh, Jose L Costa, Mark van de Wiel, Paul Eijk
Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-down. Costa JL, Eijk PP, van de Wiel MA, ten Berge D, Schmitt F, Narvaez CJ, Welsh J, Ylstra B. , Europe PMC 19863778
Investigation descriptionE-GEOD-9959.idf.txt
Sample and data relationshipE-GEOD-9959.sdrf.txt
Processed data (1)E-GEOD-9959.processed.1.zip
Array designA-GEOD-2826.adf.txt