Aspros, Kirsten G. M.

Abstract 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 (ERα) 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 (ERβ) 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 ERβ 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 ERβ targeted therapies despite ERβ protein expression. We therefore sought to define mechanisms of resistance to ERβ targeted therapy and to identify synthetic lethal vulnerabilities. We generated the first models of ERβ resistant TNBC through chronic exposure to estradiol or an ERβ 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 ERβ 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 ERβ in TNBC further suggesting that its overexpression is a bona fide mechanism of resistance to ERβ mediated suppression of proliferation. The phenomena of chronic ligand exposure leading to activation of XIST expression in ERβ+ cells is not shared with ERα 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 ERβ targeted therapies in TNBC. Future studies aimed at uncovering the consequences of XIST over-expression on global gene expression, functionality of ERβ, and aggressiveness of TNBC are ongoing. Citation Format: Michael Emch, Kirsten Aspros, Matthew P. Goetz, John Hawse. The LncRNA XIST mediates resistance to estrogen receptor beta targeted therapies in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2293.

Abstract Background:. Poor patient outcomes in triple negative breast cancer (TNBC) largely stem from a lack of understanding of therapeutic vulnerabilities and an insufficient armamentarium of effective drugs. The standard of care for most early stage TNBC patients continues to be (neo)adjuvant chemotherapy and radiation. Identifying additional therapeutic options for this subset of patients represents a major unmet need. We and others demonstrated that estrogen receptor beta (ERβ) is expressed in about 20% of TN tumors. Prior research has shown that ligand-mediated activation of ERβ decreases proliferation, invasion, and migration in TNBC cell lines. In vivo, ERβ suppresses the growth of cell line xenograft models and prevents the development of metastatic lesions in a ligand dependent manner. Mechanistically, we found that ERβ repurposes EZH2 to suppress oncogenic NFκB signaling and that pharmacologic inhibition of EZH2 diminishes ERβ function and its anti-cancer effects. This research has led to an ongoing clinical trial (NCT03941730) assessing the efficacy of estradiol in ERβ+ TNBC patients with chemorefractory disease. As with all therapies, patients will exhibit de novo and acquired resistance and therefore we sought to understand the mechanisms of resistance to ERβ targeted therapies. Methods:. Using multiple models of ERβ positive TNBC, we developed ERβ resistant cell lines through chronic exposure to estradiol and the ERβ specific agonist LY500307 over a period of 8 months. We employed RNA sequencing to characterize the transcriptomic changes which occurred following ERβ resistance. We profiled XIST expression across multiple publicly available datasets, including TCGA, Metabric, BEAUTY, and GTEx. XIST expression was also modulated using CRISPR/Cas9 to assess subsequent effects on TNBC cell biology, ERβ function, and response to ERβ targeted therapies. Results:. Our resistant cell line models of ERβ positive TNBC maintained ERβ expression, but were no longer growth inhibited by ERβ agonists. RNAseq revealed substantial differences comparing the transcriptome of resistant versus sensitive cell lines, of which the most increased transcript in the resistant setting was the lncRNA XIST. XIST is best known for its role in X-chromosome inactivation through recruitment and association with the PRC2 complex, and thus EZH2. However, little is known about its functions in breast cancer. We therefore assessed the expression levels of XIST in breast tumors and cell lines. XIST expression was highly variable in breast cancer, was found in a proportion of all breast cancer sub-types and did not correlate with ERβ status. However, XIST expression was up-regulated in ERβ expressing cell lines following long term estrogen treatment. No effects on XIST expression were identified in multiple ERα positive models following estrogen, SERM/SERD treatment, or estrogen deprivation. Furthermore, upregulation of XIST was not associated with resistance to Paclitaxel or Doxorubicin, suggesting XIST is not a part of a broad resistance phenotype. Strikingly, CRISPR mediated knockout of XIST in ERβ resistant cells completely re-sensitized cells to ERβ targeted therapies suggesting that XIST expression is a critical component of ERβ resistance. Conclusions:. ERβ represents a relevant therapeutic target that is being tested in clinical trials. Using multiple in vitro models, we provide evidence that XIST expression is sufficient to induce resistance to. ERβ targeted therapies in TNBC and may therefore represent a relevant biomarker for patient stratification. Further strategies to suppress XIST expression may elicit anti-cancer effects on their own and may resensitize a sub-set of ERβ resistant tumors to ERβ agonists. Citation Format: Michael J Emch, Kirsten GM Aspros, Elizabeth S Bruinsma, Krishna R Kalari, Calley J Jones, Brandon W Simone, Matthew P Goetz, John R Hawse. The lncRNA XIST mediates sensitivity to ERβ targeted therapies in triple negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-02-09.

Abstract Triple Negative Breast Cancer (TNBC) affects approximately 15-20% of BC patients, yet accounts for a disproportionately higher rate of BC morbidity and mortality, in part due to lack of targeted therapies. We have shown that estrogen receptor beta (ERβ) is expressed in approximately 20% of TN breast tumors and that ligand-mediated activation of ERβ with estradiol (E2) or ERβ-selective agonists decreases tumor cell proliferation, invasion and migration in vitro and in vivo. Therefore, we aimed to elucidate the mechanisms by which ERβ elicits its anti-cancer effects in TNBC. RNAseq analysis of ERβ-expressing MDA-MB-231 cells demonstrated that ERβ significantly downregulates NFκB signaling in the presence of E2. ChIPseq for ERβ in these cells revealed that ERβ primarily associated with estrogen response elements, but 12% of all ERβ binding sites were located at NFκB consensus motifs. Using an NFκB reporter construct and qPCR, ERβ was shown to block TNFα-mediated induction of NFκB signaling and NFκB target gene expression. RNAseq analysis of MDA-MB-231-ERβ cells treated with TNFα or E2+TNFα revealed substantial global inhibition of TNFα regulated genes in the presence of E2. ChIPseq for NFκB demonstrated that ERβ significantly alters NFκB’s cistrome whereby it can both diminish NFκB binding and redistribute NFκB throughout the genome. ChIPseq also demonstrated that ligand-mediated activation of ERβ significantly diminished an activating histone mark (H3K27Ac) at many of these NFκB target genes while enhancing a repressive mark (H3K27Me3). The addition of H3K27Me3 at these loci was shown to occur through the recruitment of the histone methyltransferase, EZH2. Drug-mediated blockade of EZH2 activity reversed suppression of NFκB target gene expression by ERβ. Knockdown of NFκB or Mutation of ERβ’s DNA binding domain rendered ERβ incapable of associating with DNA, recruiting EZH2, methylating NFκB target gene loci, repressing NFκB target gene expression and inhibiting proliferation. Interestingly, ERβ was shown to elicit more potent anti-cancer effects in TNBC cells expression a constitutively active form of NFκB. These finding suggest that a primary mechanism by which ERβ functions as a tumor suppressor is through inhibition of NFκB pathway activity. Our studies have also revealed that ERβ functions as a molecular switch for EZH2 and repurposes it for tumor suppressive activities, as EZH2 has previously been reported to enrich NFκB signaling in TNBC. These findings could address the paradox that high EZH2 expression is associated with worse TNBC patient outcomes, while high H3K27Me3 expression is associated with improved patient outcomes. Currently, a Mayo Clinic Breast Cancer SPORE prospective phase II clinical trial is underway to investigate the efficacy of estradiol for the treatment of metastatic ERβ+TNBC and to further evaluate the cross-talk between ERβ, EZH2 and NFκB signaling.

Abstract Background: Triple Negative Breast Cancer (TNBC) affects approximately 15-20% of BC patients, yet accounts for a disproportionately higher rate of BC morbidity and mortality, in part due to lack of targeted therapies. Using well-validated antibodies, we have found that estrogen receptor beta (ERβ) protein is expressed in approximately 20% of TN breast tumors. We have demonstrated that ligand-mediated activation of ERβ with estradiol (E2) or ERβ-selective agonists decreases tumor cell proliferation, invasion, and migration in vitro, as well as primary tumor growth and metastatic spread in vivo. As such, we aimed to elucidate the mechanisms by which ERβ elicits its anti-cancer effects in TNBC. Methods: RNAseq and ChIPseq were used to identify ERβ and NFκB regulomes and cistromes in TNBC cells. The global effects of ERβ on H3K27Ac and H3K27Me3 were also assessed via ChIPseq. The influence of ERβ on NFκB signaling was determined using co-immunoprecipitation, luciferase assays transcriptional readouts and ChIPseq. The involvement of EZH2 in mediating ERβ’s suppression of NFκB signaling and cancer cell phenotypes was determined using pharmacological approaches. Results: Pathway analysis of ERβ-regulated genes identified NFκB and inflammatory signaling as being highly suppressed in response to E2 treatment. Numerous NFκB target genes were among the most down-regulated genes by ERβ. ChIPseq revealed that ERβ primarily associated with estrogen response elements (EREs), but was also highly enriched at NFκB binding sites following E2 treatment. However, ERβ had no impact on TNFα-mediated NFκB phosphorylation or nuclear localization, but was shown to physically associate with NFκB protein. Using an NFκB reporter construct and qPCR, ERβ was shown to block TNFα-mediated induction of NFκB signaling and NFκB target gene expression. Globally, RNAseq identified 373 genes to be significantly regulated by TNFα in TNBC cells, of which 107 were blocked in the presence of E2+TNFα. Interestingly, E2+TNFα treatment induced novel NFκB binding sites compared to TNFα alone as identified by ChIPseq for NFκB. ChIPseq also demonstrated that ligand-mediated activation of ERβ significantly diminished an activating histone mark (H3K27Ac) at many of these NFκB target genes while enhancing a repressive mark (H3K27Me3). These modifications were shown to occur through the recruitment of the histone methyltransferase, EZH2, to enhancer elements of these NFκB target genes. Drug-mediated blockade of EZH2 activity reversed suppression of NFκB target gene expression by ERβ. Finally, knockdown of NFκB expression inhibited the anti-cancer effects of ERβ while expression of a constitutively active form of NFκB enhanced ERβ’s inhibitory effects. Conclusions: Our data suggest that ERβ elicits its anti-cancer effects, in part, via formation of a novel co-repressor complex consisting of ERβ, NFκB, and EZH2. These data are in keeping with prior observations of the importance of NFκB signaling as it relates to TNBC cell proliferation and invasion, and that decreased expression of NFκB target genes is associated with improved outcomes in TNBC patients. Currently, a Mayo Breast SPORE prospective study is underway to investigate the efficacy of estradiol for the treatment of metastatic ERβ+TNBC and to further evaluate the cross-talk between ERβ and NFκB signaling. Citation Format: Kirsten GM Aspros, Adam W Nelson, Zhenqing Ye, Zhifu Sun, Igor Chernukhin, Jason S Carroll, James N Ingle, Matthew P Goetz, John R Hawse. Estrogen receptor beta repurposes EZH2 to inhibit oncogenic NFκB signaling in triple negative breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-05-02.

Abstract Background: Triple Negative Breast Cancer (TNBC) affects approximately 15-20% of BC patients, yet accounts for a disproportionately higher rate of BC morbidity and mortality, in part due to lack of targeted therapies. Using well-validated antibodies, Estrogen Receptor Beta (ERβ) protein has been shown to be expressed in approximately 25% of TNBCs and is associated with improved patient outcomes. Using multiple ERβ +/- TNBC cell lines and PDX models, we have demonstrated that ligand-mediated activation of ERβ by estradiol (E2) decreases cell proliferation, invasion, and migration in vitro, as well as primary tumor growth and metastatic spread in vivo. Methods: To determine the mechanisms by which ERβ elicits these anti-cancer effects, we elucidated the ERβ transcriptome and cistrome via Microarray and ChIPseq, respectively, in TNBC cells stably expressing ERβ in a doxycycline-inducible manner. We also performed gene expression and luciferase assays to assess the impact of ERβ on NFκB signaling, followed by ChIP-PCR and ChIPseq to assess how ERβ modifies chromatin architecture near NFκB target genes. Results: Pathway analysis of ERβ-regulated genes identified NFκB signaling as one of the most suppressed pathways in response to E2 treatment. Indeed, numerous NFκB target genes were among the most down-regulated genes following E2 treatment but only in the presence of ERβ expression. Chromatin Immunoprecipitation followed by sequencing (ChIPseq) revealed that ERβ primarily associated with estrogen response elements (EREs), but was also enriched around NFκB binding sites following E2 treatment. In fact, 12% of all ERβ binding sites were enriched for NFκB response elements and ERβ was shown to physically associate with NFκB protein. Using an NFκB reporter construct and qPCR, ERβ was shown to block TNFα-mediated induction of NFκB signaling and NFκB target gene expression. Globally, RNAseq identified 200 genes to be significantly regulated by TNFα in TNBC cells, of which 81 were significantly altered in the presence of E2+TNFα. ChIPseq demonstrated that ligand-mediated activation of ERβ significantly diminished an activating histone mark (H3K27Ac) at many of these NFκB target genes while enhancing a repressive mark (H3K27Me3). These modifications are also associated with recruitment of the histone methyltransferase, EZH2, to enhancer elements of these NFκB target genes. Drug-mediated blockade of HDAC and EZH2 activity reversed suppression of NFκB target gene expression by ERβ. Conclusions: Our data suggest that ERβ may elicit its anti-cancer effects in part via formation of a novel co-repressor complex consisting of ERβ, NFκB, and EZH2. These data are in keeping with prior observations of the importance of NFκB signaling as it relates to TNBC cell proliferation and invasion, and that decreased expression of NFκB target genes is associated with improved outcomes in TNBC patients. Currently, a Mayo Breast SPORE prospective study is underway to investigate the role of estradiol in ERβ expressing TNBC and to further evaluate the cross-talk between ERβ and NFκB signaling in TNBC. Citation Format: Aspros K, Nelson A, Ye Z, Sun Z, Chernukhin I, Carroll J, Ingle J, Goetz M, Hawse J. Estrogen receptor beta elicits anti-cancer effects in triple negative breast cancer through suppression of NFκB signaling [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-05-03.