Abstract P5-04-01: Functional and therapeutic significance of ESR1 fusions in metastatic ER+ breast cancer
Authors: Lei JT , Gou X , Seker S , Haricharan S , Lee AV , Robinson DR , Ellis MJ 
Published: May 2019

Abstract
Background. Next-generation sequencing methods have identified several ESR1 fusion genes in treatment refractory ER+ breast cancer, however detailed functional studies in experimental models are lacking and how they might be targeted remains poorly understood. We recently reported two transcriptionally active, in-frame ESR1 fusions, ESR1-YAP1 and ESR1-PCDH11X, identified in a small cohort of metastatic ER+ cases, that induce not only pan-endocrine therapy resistance but also metastatic disease progression (Lei et al., Cell Reports, in press). Limited characterization of ESR1-DAB2 and ESR1-GYG1, also identified in metastatic ER+ disease from a recent study, suggests these two ESR1 fusions also drive estrogen-independent gene activation (Hartmaier et al., Annals of Oncology, 2018). Here, we functionally characterize ESR1-DAB2 and ESR1-GYG1 along with additional ESR1 fusions discovered in metastatic ER+ breast tumors to further support a causal role for in-frame ESR1 fusions in driving endocrine therapy resistance and promoting metastasis-associated biology, and explore therapeutic vulnerabilities induced by ESR1 fusion gene formation.
Methods. RNA-seq identified ESR1 fusions from treatment refractory, ER+ metastatic breast tumors. In-frame ESR1 fusions constructs were generated and stably expressed in ER+ breast cancer cell lines: T47D, MCF7, and ZR75-1. Estrogen-independent and fulvestrant-resistant growth was monitored in hormone-deprived stable cell lines. mRNA-qPCR was performed to examine expression of estrogen responsive and epithelial-to-mesenchymal transition (EMT) genes. In vitro sensitivity to CDK4/6 inhibition was tested with palbociclib and abemaciclib.
Results. In addition to previously described ESR1-YAP1, ESR1-PCDH11X, ESR1-DAB2, and ESR1-GYG1, that follow a pattern retaining the first 6 exons of ESR1 (ESR1-e6) fused in-frame to C-terminal sequences provided by the partner gene, additional in-frame ESR1-e6 fusions, ESR1-PCMT1, ESR1-ARNT2, and ESR1-ARID1B, all identified in metastatic ER+ samples, were found to follow the same fusion pattern. ESR1-DAB2 and ESR1-GYG1 produced stable ESR1 fusion proteins in ER+ breast cancer cell lines. In T47D, these two fusions drove estrogen-independent and fulvestrant-resistant growth. In addition, T47D and ZR75-1 models revealed that ESR1-DAB2 drove estrogen-independent expression of estrogen responsive genes and also EMT genes, including SNAI1, suggesting this fusion, like ESR1-YAP1 and ESR1-PCDH11X, could also drive metastasis. Treatment with CDK4/6 inhibitors suppressed growth induced by ESR1-DAB2 and ESR1-GYG1.
Conclusion. The majority of in-frame ESR1 exon 6 fusions found in metastatic ER+ breast are transcriptionally active, drive endocrine therapy resistant proliferation, and induce an EMT-like transcriptional program. The ability to block ESR1 fusion induced growth with a CDK4/6 inhibitor is clinically significant as ESR1 fusion gene formation renders ER insensitive to all endocrine therapies that target the ligand binding domain. Furthermore, clinical diagnosis of an active ESR1 fusion could potentially stratify patients for CDK4/6 inhibitor treatment. This presentation is the most complete description of the role for ESR1 fusions in endocrine therapy resistance and metastasis described to date.
Citation Format: Lei JT, Gou X, Seker S, Haricharan S, Lee AV, Robinson DR, Ellis MJ. Functional and therapeutic significance of ESR1 fusions in metastatic ER+ breast cancer [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 P5-04-01.