SRA

To define transcriptional dependencies of TNBCs, we identified transcription factors highly and specifically expressed in primary TNBCs and tested their requirement for cell growth in a panel of breast cancer cell lines. We found that EN1 is overexpressed in TNBCs and its downregulation preferentially and significantly reduces cellular viability and tumorigenicity in TNBC cell lines. Based on RNA-seq and ChIPseq we found that EN1 regulates genes involved in angiogenesis, neurogenesis, and axon guidance in breast cancer cells. Higher expression of EN1 correlates with shorter overall survival among TNBC patients and with higher risk of developing brain metastases. Thus, EN1 is a prognostic marker and a therapeutic target in this particularly lethal subset of TNBCs. Overall design: Bulk RNA-Seq: Gene expression analysis of SUM149 and SUM159 cell lines with TET-inducible shRNA against EN1 with the following variables: Two different shRNA labeled shEN1-1 and shEN1-2, doxycyclin (plus/treatment) and no doxycyclin (minus/control), 3 days and 5 days after doxycyclin treatment. All conditions were sequenced in biological duplicates (32 samples). For the MCF7 cellline samples, differential gene expression analysis was performed with inducible overexpression of EN1 with the following variables: doxycyclin (plus/treatment) and no doxycyclin (minus/control). All conditions were sequenced in biological duplicates (4 samples). ChIP-Seq: ChIP-Seq for exogenously expressed V5-tagged EN1 in SUM149, SUM159 and MCF7. ChIP-Seq for histone H3 lysine 27 acetyl (H3K27ac) in SUM149 and SUM159. ChIP-Seq for the transcription factor FOXA1 in MCF7 cells of both LacZ condition and EN1-expressing condition. ChIP-Seq for the transcription factor Beta-catenin in MCF7 cells of both LacZ condition and EN1-expressing condition, and in SUM149 with and without EN1 knockdown. ChIP-Seq for TLE3 in MCF7 cells of both LacZ condition and EN1-expressing condition, and in SUM149 and SUM159 with and without EN1 knockdown.