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Estrogen receptor β gene codes for a variety of transcript isoforms resulting from alternative splicing, which are expressed both in mammary gland and in breast cancer cells. We studied the function of two exon-deleted ERβ isoforms recently identified by our group in comparison to ERβ1 in regulation of growth, apoptosis and gene expression of two breast cancer cell lines with different ERα status. Overexpression of ERβ1, but not of the exon-deleted variants exerted strong antitumoral effects both on ERα-positive MCF-7 and ERα-negative SK-BR-3 cells. ERβ1 overexpression slowed growth of MCF-7 and SK-BR-3 cells in the absence of E2 and also inhibited E2-triggered growth stimulation of MCF-7 cells, but overexpression of the exon-skipped variants did not affect cell growth. Whereas overexpression of ERβ1 triggered an increased basal and tamoxifen-induced apoptosis of MCF-7 and SK-BR-3 cells, the isoforms ERβδ125 or ERβδ1256 did not affect cellular tamoxifen response. The observed lack of function of the exon-deleted variants in terms of regulation of proliferation was accompanied both by their inability to affect expression of cyclins D1 and A2, p21 (WAF1) and PR and their disability to modulate estrogen response element (ERE) activation. In contrast, our results demonstrating antitumoral effects of ERβ1 on breast cancer cells with different ERα-status support the hypothesis that ERβ is able to exert antitumoral actions both on ERα-positive and -negative breast cancer cells.