Preexisting Somatic Mutations of Estrogen Receptor Alpha (ESR1) in Early-Stage Primary Breast Cancer

Abstract

Background: More than three-quarters of primary breast cancers are positive for estrogen receptor alpha (ER; encoded by the gene ESR1), the most important factor for directing anti-estrogenic endocrine therapy (ET). Recently, mutations in ESR1 were identified as acquired mechanisms of resistance to ET, found in 12% to 55% of metastatic breast cancers treated previously with ET.

Methods: We analyzed 3217 population-based invasive primary (nonmetastatic) breast cancers (within the SCAN-B study, ClinicalTrials.gov NCT02306096), sampled from initial diagnosis prior to any treatment, for the presence of ESR1 mutations using RNA sequencing. Mutations were verified by droplet digital polymerase chain reaction on tumor and normal DNA. Patient outcomes were analyzed using Kaplan-Meier estimation and a series of 2-factor Cox regression multivariable analyses.

Results: We identified ESR1 resistance mutations in 30 tumors (0.9%), of which 29 were ER positive (1.1%). In ET-treated disease, presence of ESR1 mutation was associated with poor relapse-free survival and overall survival (2-sided log-rank test P < .001 and P = .008, respectively), with hazard ratios of 3.00 (95% confidence interval = 1.56 to 5.88) and 2.51 (95% confidence interval = 1.24 to 5.07), respectively, which remained statistically significant when adjusted for other prognostic factors.

Conclusions: These population-based results indicate that ESR1 mutations at diagnosis of primary breast cancer occur in about 1% of women and identify for the first time in the adjuvant setting that such preexisting mutations are associated to eventual resistance to standard hormone therapy. If replicated, tumor ESR1 screening should be considered in ER-positive primary breast cancer, and for patients with mutated disease, ER degraders such as fulvestrant or other therapeutic options may be considered as more appropriate.

Figure 1.

ESR1 mutation screening at diagnosis in early breast cancer. 3217 tumors from the SCAN-B cohort were analyzed for mutations in the ESR1 gene by RNA sequencing (RNA-seq). 31 ESR1 resistance mutations were identified in 30 tumor samples (0.9%), with 1 double mutant tumor, harboring both D538G and Y537S variants. Shown are the count of each mutation (A), the mutation to wild-type allele fraction in RNA-seq data (B), and the mutant allele fraction in tumor DNA for 18 of 18 cases tested (8 E380Q, 4 D538G, and 1 each for Y537C/N/S) using IBSAFE ddPCR (C). Asterisk (*) indicates not tested. See Supplementary Table 2 (available online) for additional details. (D) Lollipop plot for identified ESR1 endocrine resistance mutations in the ER protein indicating the functional domains.

Figure 2.

ESR1 mutation at diagnosis of early breast cancer and outcome in patients who receive subsequent endocrine therapy. Kaplan-Meier survival plots for overall survival (A) and relapse-free survival (B) in the endocrine therapy group.

Figure 3.

Cox regression models for ESR1 mutation at diagnosis in early breast cancer. Forest plots for overall survival (A) and relapse-free survival (B) in the endocrine-treated group. HR = hazard ratio; OS = overall survival; RFS = relapse-free survival; WT = wild-type; NHG = Nottingham histological grade.