Abstract P2-24-04: The ER antagonist giredestrant induces profound chromatin remodeling including activation of cis-regulatory elements bound by FOXA1 and GATA3 in HR+ breast cancer models
Authors: Ahmed Musaddeque , Guan Jane , Zhou Wei , Yao Xiaosai , Metcalfe Ciara , Hafner Marc 
Published: March 2023

Abstract
The progression of HR+ breast cancers is governed by ER signaling which makes the development of optimized ER-targeting agents a high priority. Among current therapeutics, selective ER antagonists and degraders (SERDs) have emerged as a particularly attractive class. Fulvestrant is the only SERD that is currently approved, but its clinical potential is hypothesized to be somewhat limited by poor physicochemical properties, dosage and exposure. We identified giredestrant as an orally bioavailable, highly potent non-steroidal ER antagonist, immobilizer and degrader with robust anti-proliferative activity. Giredestrant is currently being evaluated in phase III clinical trials for the treatment of ER+ breast cancer, after showing evidence of clinical activity in phase I and II trials. Here, we set out to investigate the impact of giredestrant on the transcriptome and chromatin landscape of ER+ breast cancer cells in vitro and in vivo. RNA-seq data from MCF-7 cells in vitro and three patient-derived xenograft (PDX) models in vivo showed that giredestrant inversely regulates the RNA levels of E2-regulated genes. Transcriptome wide, the expression of genes affected by giredestrant are strongly correlated (r2=0.8) with those affected by siRNA-mediated silencing of ESR1, consistent with on-target ER antagonism. Performing ATAC-seq in the three PDX models, including one ESR1 mutant model, reveals that giredestrant reduces accessibility in up to 18,173 chromatin regions that are associated with genes induced by E2. These regions are also enriched in the ER binding motif. In addition, we found up to 17,127 chromatin regions with increased accessibility upon giredestrant treatment. These regions are associated with genes suppressed by E2, and are enriched in the FOXA1 binding motif. To probe giredestrant’s role in functional modulation of cis-regulatory elements (CREs), we performed ChIP-seq targeting FOXA1 and GATA3, as key pioneer factors for ER, as well as ER itself and H3K27ac as a marker of active enhancers in MCF-7 cells. We identified 3,195 regions with significantly reduced H3K27ac signals that also exhibit significant reduction of both ER and FOXA1 binding upon giredestrant treatment, indicating that giredestrant deactivates these CREs concomitantly with suppressing ER and FOXA1 binding. ChIP-seq analysis further revealed 2,292 regions with a significant increase in H3K27ac signals upon giredestrant treatment. Interestingly, the GATA3 motif was identified as the most enriched motif in these activated CREs. Further, GATA3 and FOXA1 ChIP-seq signals were stronger in the activated CREs compared to the deactivated ones. Similar profiling of both tamoxifen, an approved selective ER modulator (SERM), as well an GNE-858, a SERM from the same chemical series as giredestrant, showed their epigenetic effects to be highly distinct from those observed for giredestrant, suggesting that the high degree of chromatin remodeling is likely related to giredestrant’s mechanism of action. Our studies here show that giredestrant profoundly alters ER binding and remodels the chromatin landscape, thus changing the transcriptional profile of cells in a manner that is associated with an anti-proliferative response. While deactivation of CREs with ER binding is perhaps in line with expectations, giredestrant treatment also leads to the activation of a number of regions associated with pioneer factors, potentially through their redistribution. This raises the question of the functional consequences of CRE activation and if this is relevant for the anti-proliferative effects of giredestrant.
Citation Format: Musaddeque Ahmed, Jane Guan, Wei Zhou, Xiaosai Yao, Ciara Metcalfe, Marc Hafner. The ER antagonist giredestrant induces profound chromatin remodeling including activation of cis-regulatory elements bound by FOXA1 and GATA3 in HR+ breast cancer models [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-24-04.