A FOXA1/SPDEF Co-regulatory Axis Maintains Luminal Identity in HER2-Positive Breast Cancer by Driving ERBB2 Expression and Suppressing a TEAD/YAP-Driven EMT Program [RNA-Seq]

The function of the pioneer factor forkhead box A1 (FOXA1) in estrogen receptor (ER)-negative, human epidermal growth factor receptor 2 (HER2, encoded by the ERBB2 gene)-positive breast cancer represents a critical gap in our understanding of lineage identity in tumorigenesis. Here, we solve this enigma by addressing this question through the identification of an indispensable, co-dependent regulatory circuit formed between FOXA1 and the SAM pointed domain containing ETS-family transcription factor (SPDEF). Using integrative multi-omics analyses of patient tumors and experimental models, we demonstrate that this circuit functions as the master guardian of the HER2-positive luminal state. It executes this role via two distinct, essential mechanisms: it directly binds regulatory elements to drive high-level expression of the ERBB2 oncogene, and it simultaneously preserves epithelial identity by suppressing a latent program of epithelial-to-mesenchymal transition (EMT). Mechanistically, the FOXA1/SPDEF circuit promotes the expression of the transcriptional repressor TRPS1, which in turn antagonizes the pro-mesenchymal activity of the TEAD/YAP complex. Our findings define a central regulatory node that couples lineage fidelity to oncogenic output in HER2-positive cancer, revealing the FOXA1/SPDEF–TRPS1 axis as a critical determinant of tumor plasticity and a potential therapeutic target for overcoming resistance in HER2-positive breast cancer. Overall design: To investigate the effect of SPDEF on HER2-related pathways, a stable cell line expressing shRNA directed against SPDEF was generated by transducing cells with commercially prepared lentiviruses containing three individual shRNA directed against SPDEF mRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells. Comparateive gene expression profiling analysis of RNA-seq data for MCF7 and SKBR3 cells and its KD derivates (SPDEFKD).