Identification and validation of the ESR1 Y537S mutant-enriched enhancer and its downstream target IGFBP3

Endocrine therapy that inhibits estrogen receptor (ER) mediated signaling is a cornerstone treatment for ER-positive breast cancer, a subtype that accounts for more than 75% of all breast cancer cases. However, resistance to endocrine therapy occurs in a significant proportion of patients, and hotspot missense point mutations of the ESR1 gene that codes ER is one of the major underlying mechanisms for such resistance. While recent research has provided novel insights into the functions and activities of mutant ER, effective therapeutics that can overcome this mutant ER mediated endocrine resistance remain elusive. Using a circulating tumor cell line derived from a metastatic breast cancer patient and harboring the ESR1 Y537S mutation, together with genetically engineered breast cancer cell lines carrying the same mutation, we identified a novel enhancer region that preferentially occupied by Y537S mutant ER. Deletion of this enhancer region reduced cell proliferation and adhesion in vitro, decreased tumorigenicity in vivo, and enhanced sensitivity to fulvestrant specifically in cells harboring Y537S ER mutation. We subsequently identified IGFBP3 as a functional downstream target of this enhancer and validated its contribution to a subset of the phenotypes associated with Y537S mutant ER.