Noninvasive Detection of Activating Estrogen Receptor 1 (ESR1) Mutations in Estrogen Receptor–Positive Metastatic Breast Cancer

Background: Activating mutations in the estrogen receptor 1 (ESR1) gene are acquired on treatment and can drive resistance to endocrine therapy. Due to the spatial and temporal limitations of needle core biopsies, our goal was to develop a highly sensitive, less invasive method of detecting activating ESR1 mutations via circulating cell-free DNA (cfDNA) and tumor cells as a “liquid biopsy”. Methods: We developed a targeted 23 amplicon next-generation sequencing (NGS) panel for detection of hotspot mutations in ESR1, PIK3CA, TP53, FGFR1 and FGFR2 in 48 patients with ERα positive metastatic breast cancer who were receiving systemic therapy. Selected mutations were validated using digital droplet PCR (ddPCR). Results: Nine baseline cfDNA samples had an ESR1 mutation. NGS detected 3 activating mutations in ESR1, 3 hotspot mutations in PIK3CA and 3 in TP53 in baseline cfDNA, and the ESR1 p.D538G mutation in one matched circulating tumor cell sample. ddPCR analysis was more sensitive than NGS and identified 6 additional baseline cfDNA samples with the ESR1 p.D538G mutation at a frequency of < 1%. In serial blood samples from 11 patients, 4 showed changes in cfDNA, 2 with emergence of a mutation in ESR1. We also detected a low frequency ESR1 mutation (1.3%) in cfDNA of one primary patient thought to have metastatic disease, but was clear by scans. Conclusion: Early identification of ESR1 mutations by liquid biopsy might allow for cessation of ineffective endocrine therapies and switching to other treatments, without the need for tissue biopsy and prior to the emergence of metastatic disease.