The LncRNA XIST mediates resistance to estrogen receptor beta targeted therapies in triple negative breast cancer

Breast cancer accounts for nearly a quarter of all cancers in women with an estimated 2.3 million new diagnoses and over 670,000 deaths annually. Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by lack of estrogen receptor alpha (ERalpha) and progesterone receptor (PR) expression in the absence of HER2 amplification. TNBC accounts for ~15% of all incident breast cancers and is associated with poor patient outcomes. Problematically, TN tumors exhibit vast inter-patient molecular heterogeneity making the identification of novel therapeutic vulnerabilities difficult and the development of alternative treatment strategies problematic. We and others have demonstrated that estrogen receptor beta (ERbeta) is expressed in about 20% of TN tumors and potently suppresses proliferation, invasion, and migration in TNBC cells in vitro and in vivo . We thus hypothesized that endocrine therapies that selectively activate ERbeta would be an effective treatment approach for this subset of patients. We also anticipated that some tumors would display de novo or acquired resistance to ERbeta targeted therapies despite ERbeta protein expression. We therefore sought to define mechanisms of resistance to ERbeta targeted therapy and to identify synthetic lethal vulnerabilities. We generated the first models of ERbeta resistant TNBC through chronic exposure to estradiol or an ERbeta specific agonist (LY500307) and through a CRISPR genome wide knockout screen. We identified the LncRNA XIST as one of the most upregulated transcripts in multiple models of ERbeta resistant disease, and knockdown of XIST expression was shown to resensitize resistant cell to estradiol and LY500307 treatment. XIST was not found to be directly regulated by ERbeta in TNBC further suggesting that its overexpression is a bona fide mechanism of resistance to ERbeta mediated suppression of proliferation. The phenomena of chronic ligand exposure leading to activation of XIST expression in ERbeta+ cells is not shared with ERalpha suggesting that the mechanism by which XIST expression is elevated during the development of resistance is distinct between the two sister receptors. We further characterized XIST expression in patient samples of TNBC and found that XIST expression varies, but largely exhibits a bimodal distribution with most tumors displaying either low or high transcript levels. In conclusion, we have identified the X-inactivating transcript as a driver of resistance to ERbeta targeted therapies in TNBC. Future studies aimed at uncovering the consequences of XIST over-expression on global gene expression, functionality of ERbeta, and aggressiveness of TNBC are ongoing.