Association of <i>ESR1</i> amplification with survival and benefit from CDK4/6 inhibition in breast cancer.

Abstract

1093 Background: While ESR1 mutations are established mediators of endocrine resistance in breast cancer (BC), the significance of ESR1 amplification (amp) remains poorly understood with reported amp rates vary widely due to platform-specific differences. We leveraged a large clinico-genomic real-world database and applied a stringent NextGen sequencing (NGS) approach to test ESR1 amp. We identify ESR1 amp as a molecular entity distinct from canonical estrogen-driven resistance mechanisms. Methods: Breast tumors underwent NGS of DNA and RNA (WES/WTS; NextSeq and NovaSeq; Caris Life Sciences, Phoenix, AZ). Gene copy number was determined by CNVKit with &gt;=6.0 copies defined as amp to identify focal, high-level copy number events, minimizing misclassification of chromosome 6 copy gains. Real-world clinical data were obtained from insurance claims. Time on treatment (TOT) was defined treatment start to end; overall survival (OS) from tissue collection to last contact. Cox proportional hazards model and log-rank tests were used for survival analysis. Molecular comparisons used χ² or Mann-Whitney U with multiple-testing adjustment (q&lt;0.05). Gene set enrichment analysis was performed, with significance defined as FDR&lt;0.05. Results: Among 27,979 BC tumors, 165 were ESR1 amp (0.6%), a prevalence much lower than prior reports. ESR1 amp was significantly enriched in the Luminal B (LumB) subtype (1.4%, 81/5,915) versus other subtypes (0.1–0.4%, p&lt;0.0001). ESR1 amp tumors exhibited features of genomic instability, including higher genomic loss of heterozygosity (61% vs 24%), TP53 mutations (59% vs 27%), and amplifications on chromosomes 6, 8, and 11 (q&lt;0.05). Transcriptomically, ESR1 amp tumors had significant enrichment of G2M checkpoint and MYC target gene sets by GSEA in the overall cohort (G2M NES 2.61, MYC NES 2.41,) and in LumB (G2M NES 3.18; MYC NES 3.04, all FDR&lt;0.001), consistent with CDK4/6-independent cell-cycle progression. Unlike ESR1 mutations, ESR1 amplification was not associated with increased GREB1 expression (4.4 vs 4.2 TPM, p&gt;0.05), consistent with the absence of estrogen-response pathway enrichment. Clinically, ESR1 amp was associated with reduced OS in the overall cohort (HR 1.296, p=0.016) and LumB subset (HR 1.43, p=0.009). Palbociclib TOT was significantly shorter in ESR1 amp vs. non-amp tumors (all BC: 7.0 vs 11.0 months, HR 1.39 [95% CI 1.045–1.85], p=0.023; LumB: 4.9 vs 11.4 m, HR 1.57 [1.1–2.2], p=0.01). This effect was significant after adjusting for TP53, gLOH, and CDH1 alterations (adjusted HR 1.47 [1.04–2.06], p=0.027). No TOT difference was observed with aromatase inhibitors. Conclusions: In this large real-world analysis, ESR1 amplification defines a rare, genomically unstable breast cancer subset with proliferative signaling and reduced clinical benefit from CDK4/6 inhibition, supporting its potential role as a negative predictive biomarker.