Transcriptomic effects of ERRa repression in human 3D-cultured breast cancer cells.

Estrogen Related Receptor a (ERRa) is a member of the nuclear receptor superfamily that acts as a transcription factor. In vivo, ERRa exerts diverse physiological functions such as modulation of bone mass and of energy metabolism. In addition, it plays a strong role in cancer progression. Transcriptional targets of ERRa and co-regulators of ERRa transcriptional activity have been identified using two-dimensional (2D) cell culture systems, which only partially reflect the three dimensional (3D) conditions under which a tumor develops. The aim of the study is to determine specific targets of ERRa during cancer progression and to identify new transcriptional co-regulators of ERRa under 3D conditions using a combination of bioinformatics, molecular and cellular biology approaches. Overall design: MDA-MB-231 cells were cultured in 3D using hanging drop method. They were inactivated for ERRa using two different siRNAs. One control siRNA was used for comparison. In each condition, triplicate samples were analyzed in RNA-seq experiments.