Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer

Abstract

BackgroundEstrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer.Patients and methodsTo identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287–395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots.ResultsWe identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3′ partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations.ConclusionsCollectively, these data indicate that N-terminal ESR1 fusions involving exons 6–7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.

Mechanisms of resistance in estrogen receptor positive breast cancer: overcoming resistance to tamoxifen/aromatase inhibitors

“…Known mechanisms of resistance to hormone therapies are complex and include epigenetic regulation of ESR1 expression [5,6], ESR1 mutations [7–12], alternative splicing events [3], ESR1 truncation and fusion events [13], post-translational modifications [14,15], alterations in the hormone binding domain [7,16], alter-native recruitment sites within the genome [17], differential recruitment of coregulators [18], feedback loops by ER target genes on expression/activity of ER [19 ● ], downstream actions of ER target genes on growth factor pathways and other signaling networks [20,21 ●● ], influences of the tumor microenvironment [22], and many others (Figure 1). The details of these mechanisms are beyond the scope of this review but have been thoroughly described by others [23,24].…”

Therapeutic role of recurrent ESR1-CCDC170 gene fusions in breast cancer endocrine resistance

“…When introduced into breast cancer cells, ESR1-CCDC170 proteins enhance ligand-independent growth factor signaling, leading to increased cell aggressiveness and tumorigenesis [13]. To date, ESR1-CCDC170 remains the most frequent gene fusion detected in luminal B breast cancer, and its recurrence has been subsequently supported by several recent studies [5,[16][17][18][19]. In addition, this fusion is also detected as a recurrent event in ovarian cancer, and its presence has been associated with exceptional short-term survival [20].…”

“…About a quarter of the patients with primary tumor and almost all patients with metastases will present with or eventually develop endocrine resistance [3]. Tremendous efforts have been made to study the mechanism of endocrine resistance, and emerging evidence suggests that ESR1 mutations or fusions that mutate or eliminate its ligand binding domain constitute one of the most important driving mechanisms [3][4][5][6].Recurrent gene fusions resulting from chromosome translocations are a critical class of genetic aberrations causing cancer [7], which have fueled modern cancer therapeutics. Recently, several milestone studies have identified recurrent gene fusions in different types of solid tumors with tremendous clinical impact.…”

Targeted mutation detection in breast cancer using MammaSeq™

“…High-throughput genotyping of solid tumors and continual monitoring of disease burden through sequencing of cfDNA represent potential clinical applications for NGS technologies. It should be noted that targeted DNA sequencing panels such as MammaSeq™ are far less comprehensive than whole exome sequencing and they do not allow for evaluation of structural variants, which can often lead to gene fusions that function as drivers [34]. Nevertheless, as a focused panels represent cost-effective and useful alternatives to whole exome sequencing for targeted mutation detection.…”