G Peluffo, A Subedee, NW Harper, N Kingston, B Jovanović, F Flores, LE Stevens, F Beca, A Trinh, CS Reddy Chilamakuri, EK Papachristou, K Murphy, Y Su, A Marusyk, CS D'Santos, OM Rueda, AH Beck, C Caldas, JS Carroll, K Polyak
To define transcriptional dependencies of triple-negative breast cancer (TNBC), 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 (Engrailed 1) is overexpressed in TNBCs and its downregulation preferentially and significantly reduced viability and tumorigenicity in TNBC cell lines. By integrating gene expression changes after EN1 downregulation with EN1 chromatin binding patterns, we identified genes involved in WNT and Hedgehog signaling, neurogenesis, and axonal guidance as direct EN1 transcriptional targets. Quantitative proteomic analyses of EN1-bound chromatin complexes revealed association with transcriptional repressors and co-activators including TLE3, TRIM24, TRIM28, and TRIM33. High expression of EN1 correlated with short overall survival and increased risk of developing brain metastases in TNBC patients. Thus, EN1 is a prognostic marker and a potential therapeutic target in TNBC.