Abstract P5-01-06: Cell-free DNA (cfDNA) analysis of ESR1-mutant advanced breast cancer (aBC): Impact of subsequent therapy on mutation persistence
Authors: Weipert Caroline M. , Rich Thereasa A. , Nagy Rebecca J. , Croessmann Sarah , Park Ben H. , O'Shaughnessy Joyce , Nezami Mohammad , Cristofanilli Massimo , Bardia Aditya , Lanman Richard B. 
Published: March 2020

Abstract
Background: Acquired ESR1 mutations (ESR1MUT) are common resistance mechanisms in estrogen receptor positive (ER+) aBC following aromatase inhibitor (AI) therapy. ESR1MUT can be identified using plasma-based cfDNA testing in patients with progressive aBC and may be cleared (i.e. become undetectable) following response to effective therapeutic interventions. Optimal treatment for ESR1MUTaBC has not been established. We retrospectively examined the impact of various treatments on ESR1MUT detection among patients with aBC undergoing serial cfDNA testing.
Methods: The deidentified Guardant Health database was queried for patients with aBC (stage IIIB/IV) with multiple cfDNA samples, at least one of which had an ESR1MUT detected (patients tested between March 2014-March 2019 using a 54-73 gene cfDNA next-generation sequencing panel, Guardant360™). Consecutive sample pairs were identified in which the first sample had ≥1 ESR1MUT and subsequent treatment could be determined from the test request form. For patients receiving combination therapy, each therapy was counted individually (e.g. a patient receiving a CDK4/6 inhibitor and an AI would be counted once for each). Each sample pair was classified as to whether any ESR1MUT persisted in the subsequent cfDNA sample. Additionally, the change in ESR1 variant allele fraction (αVAF) between the first and subsequent sample was calculated for each ESR1MUT identified. We considered ESR1MUT that had lower VAF on the subsequent sample (e.g. a negative αVAF) as evidence of a therapeutic response against ESR1MUT for the purpose of this study. The proportion of sample pairs in which the ESR1MUT was cleared, as well as the proportion of any ESR1MUT with decreased VAF was compared by treatment type using Fisher’s exact test.
Results: A total of 262 ESR1 mutations were found in 167 unique sample pairs from 124 aBC patients. The median time between sample collection for each pair was 17 weeks (range: 0.7 - 133 weeks). ESR1MUT were cleared in a minority (30/167, 18%) of sample pairs with an overall minimal change in observed VAF (median αVAF of -0.01). A negative ESR1MUT VAF was observed for more than half of all ESR1MUT in patients receiving certain endocrine therapies, including fulvestrant, tamoxifen, and goserelin, and non-endocrine therapies, including chemotherapy, anti-HER2, and CDK4/6 inhibitors, suggesting these agents may still have some efficacy against ESR1MUT (Table 1). The proportion of sample pairs with ESR1MUT clearance was not significantly different for those on endocrine therapy versus those not on endocrine therapy (16% vs 19%). Similarly, there was no significant difference between these groups when examining the proportion of ESR1MUT with decreased VAF (50% vs 50%).
Conclusions: In this exploratory analysis of serial cfDNA testing of ESR1MUTin aBC, some variation was observed in the efficacy of commonly used therapies as measured by the proportion of sample pairs with clearance of ESR1MUT and by the proportion of all ESR1MUT with a decreased VAF. We believe these data may be useful in guiding future analysis into optimal therapy for patients with ESR1MUTaBC. Notably, none of the therapies stood out as having promising efficacy against a large proportion of ESR1MUT subclones suggesting that additional therapeutic options may be needed to effectively target and provide long-term disease control of ESR1MUT aBC.
Table 1. Temporal changes in ESR1MUT in cfDNA by therapy in aBCTreatmentNo. Sample PairsESR1MUT ClearedNo. ESR1MUTESR1MUT with VAF DecreaseMedian αVAFAI2520%3842%0.09SERD (Fulvestrant)3312%4553%-0.03Estrogen Receptor Agonist (Tamoxifen)30%667%-0.18GnRH Agonist (Goserelin)813%1464%-0.09Chemotherapy8319%13052%-0.09Anti-HER2229%2752%-0.02Everolimus2512%3749%0.05CDK4/6 Inhibitor3119%4953%-0.05Immune Checkpoint520%838%0.02Any Endocrine Therapy6316%9250%-0.01No Endocrine Therapy10419%17050%-0.01OVERALL16718%26250%-0.01
Citation Format: Caroline M. Weipert, Thereasa A. Rich, Rebecca J. Nagy, Sarah Croessmann, Ben H. Park, Joyce O'Shaughnessy, Mohammad Nezami, Massimo Cristofanilli, Aditya Bardia, Richard B. Lanman. Cell-free DNA (cfDNA) analysis of ESR1-mutant advanced breast cancer (aBC): Impact of subsequent therapy on mutation persistence [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 P5-01-06.