Overexpression of NFIB and YBX1 in MCF-7 cells

Studying transcription factor (TF) interactions and gene regulatory networks in breast cancer, we have recently identified two distinct and opposing clusters of TFs associated with estrogen receptor-positive and -negative breast cancer and breast cancer risk. The relative activity of these two groups of TFs has a dramatic effect on patient outcomes and is likely to influence the phenotypic plasticity observed in breast cancer. We have identified two novel interactors (NFIB and YBX1) of the estrogen receptor (ESR1) using Rapid Immunoprecipitation Mass Spectrometry of Endogenous Proteins (RIME), co-immunoprecipitation and microscopy experiments. Both NFIB and YBX1 are members of the group of risk TFs that oppose the activity of the risk TFs associated with estrogen receptor-positive disease, and we have demonstrated that they both repress the transcriptional activity of ESR1. Here, we examine the effect of NFIB and YBX1 overexpression on the transcriptome of an estrogen receptor-positive breast cancer cell line to see if these risk TFs are able to repress the ESR1 regulon and drive cells towards a less estrogen-dependent phenotype. Overall design: Data consists of three different cell lines (MCF-7 parental, MCF-7 stably overexpressing FLAG-tagged NFIB, and MCF-7 stably overexpressing FLAG-tagged YBX1), analysed to detect gene expression differences. Each cell line was tested in triplicate (biological replicates consisting of three separate clones of stable cells).