Abstract PO2-16-03: ESR1 genomic alterations (GAs) and coexistent putative resistance alterations in comprehensive genomic profiling (CGP) of metastatic breast cancer (MBC)
Authors: Heather McArthur, Hanna Tukachinsky, Alexa Schrock, Russell Madison, Oliver Holmes, Smruthy Sivakumar, Ethan Sokol, Ryon Graf, Julia Quintanilha, Kali Dougherty, Lincoln Pasquina, Geoffrey Oxnard, Mia Levy, Eric Winer
Journal: Cancer Research (2024)

Abstract Background: ESR1 mutations (ESR1mut) are an established biomarker of endocrine therapy (ET) resistance in patients (pts) with hormone receptor positive (HR+) MBC. Moreover, ESR1mut acquired in response to standard-of-care ET now confer access to novel ET recently approved by health authorities. However, the nuanced genomic landscape beyond the simple presence or absence of ESR1mut may be critically important. We report on detailed ESR1 GAs detected by tissue and liquid biopsies (TBx, LBx) and examine the prevalence of co-occurring GAs in other genes reported to confer intrinsic or acquired resistance to ET. Methods: CGP results from MBC biopsies were retrospectively analyzed (TBx 33,653 pts; LBx 7,134 pts) using FoundationOne® CDx and FoundationOne® Liquid CDx, hybrid-capture based sequencing platforms profiling 324 cancer-related genes. Foundation Medicine’s ctDNA tumor fraction (TF) is a composite algorithm prioritizing aneuploidy at higher levels to avoid germline signal and prioritizing variant allele frequency (VAF) of canonical alterations at lower levels to maximize dynamic range. Results: ESR1mut were detected in 3,755 (11.2%) TBx and 1,513 (21.2%) LBx. Among samples with ESR1mut, multiple ESR1mut were more common in LBx (19% 2, 12% 3+) than in TBx (6% 2, 0.5% 3+), with up to 10 different ESR1mut seen in one LBx. The most common mutations were D538G (39% and 52% of TBx and LBx with ESR1mut), Y537S (27%, 38%), Y537N (10%, 15%), and E380Q (10%, 14%). Activating ESR1 insertion-deletion mutations (indels) were detected in 81 TBx and 62 LBx (2% and 4%), representing 23 distinct variants at the protein level, including V422del (107), indels affecting codons 532-538 (29), G344_L345insC (7), and Y328_S329del (6). 28 fusions of the ESR1 DNA binding domain to 13 unique gene partners were detected; 10/28 (36%) were ESR1-CCDC170 fusions. ESR1 amplifications (ESR1amp) were detected in 704 (2.1%) TBx; 62 (8.8%) also harbored ESR1mut. ESR1amp were detected among 34 (0.5%) LBx; 8 (24%) also had ESR1mut. In TBx with ESR1mut and LBx collected from the same pt within 8 months (43 pairs), LBx sensitivity of detection of ESR1mut was 96% (26/27, 95% confidence interval CI [95%CI]: 79%-99%) when TF was ≥1%, but only 6% (1/16, 95%CI: 0.3%-32%) when LBx had TF &amp;lt; 1%. In 988/1,513 (65%) of LBx with ESR1mut, ≥1 mutations or fusions in genes associated with alternative ET resistance pathways were detected, including PIK3CA (46% of ESR1mut LBx), RB1 (12%), PTEN (10%), NF1 (7%), ARID1A (7%), AKT1 (5%), FGFR2 (4%), and KRAS (4%) and ERBB2 (3%). Prevalence of co-occurring GA associated with ET resistance was higher in LBx than in TBx (RB1, NF1, FGFR2, PTEN, EGFR, KRAS, PIK3CA, FDR &amp;lt; 0.001). Moreover, prevalence was higher in 240 LBx where ESR1 was a minor allele (VAF/TF &amp;lt; 10%) compared to 1,273 LBx were ESR1 was a major allele (FGFR2, PIK3CA, FGFR3, BRAF, ERBB2, RB1, FDR &amp;lt; 0.05). In pts with ESR1mut LBx and a historical TBx collected &amp;lt; 5 years earlier (182 pairs), GAs in RB1, FGFR2, KRAS, EGFR, and BRAF were detected primarily on the LBx but not the preceding TBx. Conclusions: CGP detects a wide spectrum of mutations in ESR1, including missense and indel mutations and fusions. When LBx TF is &amp;lt; 1%, sensitivity for ESR1mut is reduced and repeat testing should be considered. ESR1mut can coexist with complementary or competing resistance mechanisms, particularly when ESR1 is a minor allele, which could impact benefit from novel ET approved for patients with ESR1 mutations. Currently, CGP of LBx informs therapeutic recommendations for pts with HR+ MBC based on the binary presence or absence of ESR1mut; however, the clinical implications of the ESR1 mutation spectrum described herein and the potential impact of co-expression of other key pathway signals warrant further investigation. Citation Format: Heather McArthur, Hanna Tukachinsky, Alexa Schrock, Russell Madison, Oliver Holmes, Smruthy Sivakumar, Ethan Sokol, Ryon Graf, Julia Quintanilha, Kali Dougherty, Lincoln Pasquina, Geoffrey Oxnard, Mia Levy, Eric Winer. ESR1 genomic alterations (GAs) and coexistent putative resistance alterations in comprehensive genomic profiling (CGP) of metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-16-03.