Comparative gene expression profiling reveals partially overlapping but distinct genomic actions of different antiestrogens in human breast cancer cells

Abstract

Antiestrogens used for breast cancer (BC) treatment differ among each other for the ability to affect estrogen receptor (ER) activity and thereby inhibit hormone-responsive cell functions and viability. We used high-density cDNA microarrays for a comprehensive definition of the gene pathways affected by 17beta-estradiol (E2), ICI 182,780 (ICI), 4OH-tamoxifen (Tamoxifen), and raloxifene (RAL) in ER-positive ZR-75.1 cells, a suitable model to investigate estrogen and antiestrogen actions in hormone-responsive BC. The expression of 601 genes was significantly affected by E2 in these cells; in silico analysis reveals that 86 among them include one or more potential ER binding site within or near the promoter and that the binding site signatures for E2F-1, NF-Y, and NRF-1 transcription factors are significantly enriched in the promoters of genes induced by estrogen treatment, while those for CAC-binding protein and LF-A1 in those repressed by the hormone, pointing to novel transcriptional effectors of secondary responses to estrogen in BC cells. Interestingly, expression of 176 E2-regulated mRNAs was unaffected by any of the antiestrogens tested, despite the fact that under the same conditions the transcriptional and cell cycle stimulatory activities of ER were inhibited. On the other hand, of 373 antiestrogen-responsive genes identified here, 52 were unresponsive to estrogen and 25% responded specifically to only one of the compounds tested, revealing non-overlapping and clearly distinguishable effects of the different antiestrogens in BC cells. As some of these differences reflect specificities of the mechanism of action of the antiestrogens tested, we propose to exploit this gene set for characterization of novel hormonal antagonists and selective estrogen receptor modulators (SERMs) and as a tool for testing new associations of antiestrogens, more effective against BC.

Selective recruitment of breast cancer anti-estrogen resistance genes and relevance for breast cancer progression and tamoxifen therapy response

“…The probability of recovery of a particular gene under different selection conditions may depend on the integration position modulating its level of expression and on the consequences of the particular anti-estrogen on the biology of the ZR-75-1 cells. Our observations that the mechanisms underlying resistance against diverse anti-estrogens differ are in line with previous observations in breast cancer cell models (Soulez & Parker 2001, Faridi et al 2003, Frasor et al 2004, Martin et al 2005, Fan et al 2006, Kuske et al 2006, Scafoglio et al 2006, Shaw et al 2006, Osipo et al 2007. Accordingly, patients with breast tumors failing on tamoxifen have been shown to respond to the pure anti-estrogen fulvestrant (Howell et al 2002, Osborne et al 2002, Howell 2006, indicating subtle differences in the underlying mechanisms of tumor growth control.…”

Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays

“…To evaluate the effect of estrogens, cells were grown in phenol red-free Dulbecco's modified Eagle's medium containing 5% dextran-charcoalstripped FBS for 5 days and stimulated with 10 À8 M 17b-estradiol (E2) as described previously. 12,13 Tumor Tissue Samples All bioptic tissues for this study were obtained from different patients following their informed consent and belong to the Tumor Bank collections of the Department of Obstetrics and Gynecology, University of Turin. All samples were FFPE invasive ductal carcinomas, according to standard tissue acquisition protocols.…”

“…12,13 FFPE tissue samples were cut into 5 mm-thick sections on a microtome with a disposable blade, and the sections were stored in xylene at room temperature until use, before washing in fresh xylene and RNA extraction.…”

Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?

“…20,21 Y/CCAAT is Enriched in Promoters of 'Cancer' Genes Analysis of transcriptome profiles during cellular transformation identified the Y/CCAAT box as over-represented in promoters of genes overexpressed in diverse types of cancers, breast, colon, thyroid, prostate and leukemias. [22][23][24][25][26][27][28][29] Treating cells with cytotoxic drugs, or overexpressing growth suppressors, led to the downregulation of genes with CCAAT in their promoters. 30,31 However, it is important to remark that these exercises were performed with matrices included in TRANSFAC and JASPAR; hence, they could be highly biased, as the lists of transcription factor-binding sites (TFBS) present in databases certainly do not recapitulate all possible TF-binding sequences.…”