A Kit Targeting Detection of ESR1 Mutations from Circulating Exosomal RNA and Cell-Free DNA Supports Longitudinal Studies into Endocrine Therapy Resistance in a Broadly Accessible RT-qPCR Format

Abstract Introduction: The most prevalent subtype of breast cancer is HR+/HER2- (positive for hormone receptor, negative for human epidermal growth factor receptor 2). For metastatic breast cancer (mBC), a frequent occurrence is resistance to the aromatase inhibitors used in endocrine therapy (ET). Resistance is mediated through mutations in the ligand binding domain of estrogen receptor 1 (ESR1). Approval of elacestrant, a second-line agent for HR+/HER2-/ESR1 mutated mBC , underscores the need for early detection of ESR1 resistance mutations. We have developed sensitive RT-qPCR reagents for targeted longitudinal studies into the emergence of ESR1 resistance mutations in plasma. This all-inclusive kit analyzes circulating exosomal RNA (exoRNA) and cell-free DNA (cfDNA) to accurately identify low copy number mutations with a rapid turnaround time. Methods: Challenge panels were constructed using blends of synthetic nucleic acids of known mutational status in a background of partially fragmented wild-type DNA from cell lines. Additionally, plasma samples collected from subjects with stage IV mBC (HR+/HER2-) on active aromatase inhibitor therapy, +/- CDK 4/6 inhibitor for a minimum of one year, were subjected to an in-house method optimized to co-enrich exoRNA and cfDNA. Multiplex RT-qPCR-based target enrichment performed on 11 ESR1 mutations and an internal control were evaluated on widely used thermal cycler and qPCR instruments. Results: We developed technology that interrogates 11 key ESR1 mutations associated with ET resistance in HR+/HER2- mBC cases. Earlier studies performed in simplex analyzed plasmid-based ESR1 mutations with detection of 10 or fewer mutant copies, estimating analytical sensitivity of at least 0.1% (5 mutant copies in a background of 5,000 WT copies). Herein, we describe the subsequent work to complete the methodology employed in the kit, including the incorporation of an endogenous control, external batch run control materials (positive, negative), deeply optimized reagents (RT, pre-amplification, qPCR), and automated analysis. We report on the results of studies into the kit’s performance characteristics against their targets: analytical sensitivity of the equivalent of 5 copies of mutation per mL plasma, high precision across replicates at 0.1% allele fraction, analytical specificity of ≥90% negative results in mutation-negative replicates, as well as workflow attributes (reduced pipetting steps and turnaround time). Conclusion: Our solution to detect ESR1 resistance mutations facilitates the generation of nucleic acid sample to results within one day using liquid biopsy samples and a multiplexed RT-qPCR. Enhancing mutation detection sensitivity by complementing cfDNA with exoRNA will facilitate future research into breast cancer treatment options. Citation Format: Justin T. Brown, Julie R. Thibert, Liangjing Chen, Melissa Church, Holli Dale, Jamie Myers, Elliot Hallmark, Megan Yociss, J Aquiles Sanchez, Kurt Franzen, Johan Skog, Gary Latham, Brian Haynes, Sarah Statt. A kit targeting detection of ESR1 mutations from circulating exosomal RNA and cell-free DNA supports longitudinal studies into endocrine therapy resistance in a broadly accessible RT-qPCR format [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4626.