Novel epigenomic liquid biopsy assay to predict estrogen receptor (ER) status and to infer ER pathway activation in breast cancer.
Authors: Morganti Stefania , Beagan Jonathan , D'Ippolito Anthony , Smith Kalie , Hughes Melissa E. , Chmielecki Juliann , Gorthi Aparna , Painter Corrie , Barrett J. Carl , Eaton Matthew L , Freedman Matthew , Tolaney Sara M. , Lin Nancy U. , Parsons Heather Anne 
Published: June 2024

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Background: Endocrine therapy (ET) is the cornerstone of treatment for ER-positive (ER+) breast cancer (BC). However, BC may lose ER expression over the disease course, and ER+ tumors may become resistant to ET regardless of ER expression. Blood-based biomarkers to infer ER expression and to predict ET sensitivity are lacking. Methods: We identified 44 patients (pts) with metastatic BC seen at Dana-Farber Cancer Institute from 2012-2023, who had blood samples drawn in Streck tubes within 6 weeks of tumor biopsy with ER scored via immunohistochemistry (IHC). We applied a novel, multi-analyte, liquid biopsy assay to capture genome-wide epigenomic signals, mapping enhancers, promoters, and DNA methylation data from 1mL of plasma. First, we applied a previously developed, IHC-benchmarked, regularized logistic regression model to infer ER status from plasma-based epigenomic profiles (Parsons et al., SABCS 2023). Second, we applied a novel ER pathway activity score involving promoters and enhancers of certain genes previously associated with ER activity (Guan et al., Cell 2019). The ER activity score was corrected for the circulating tumor DNA (ctDNA) fraction as assessed by low pass whole genome sequencing (ichorCNA algorithm). We evaluated the association between the ER activity score and the ER status by IHC using the Wilcoxon rank-sum test. ER expression ≥1% was considered positive. Results: The ER classifier and the ER activity score have been applied to 19 of 44 samples (43%) all of which had detectable ctDNA. Eleven out of 19 (58%) pts had ER+ BC by IHC (ER IHC range 80-95%). Overall, 18/19 (95%) were correctly classified as ER+ or ER- by the ER classifier (AUC=1). Three of 19 (16%) samples were collected from pts with ER+ BC at primary diagnosis and ER- BC at time of tissue sampling. For them, the ER classifier correctly predicted ER- status. We observed a significantly higher ER activity score in samples from pts with ER+ BC than pts with ER- BC as measured by IHC (p= 0.0012). For pts with ER+ BC, we observed an association between lower ER activity scores and a higher number of lines of ET prior to blood sampling, with lower scores for pts who received >4 prior lines. We will present full results from this cohort and an expanded cohort and correlate the ER score with response to ET. Conclusions: We applied a novel blood-based epigenomic classifier able to infer ER status and a novel epigenomic activity score to predict ER signaling from a minimal plasma volume. We plan to validate our findings on a larger cohort and correlate with response to ET. If confirmed, this assay may represent a valuable, minimally invasive tool to help guide treatment selection for patients with ER+ BC and predict response to novel endocrine agents.