Genomic landscape of estrogen receptor-positive HER2-negative advanced breast cancer with acquired resistance to aromatase inhibitors: Identification of an ESR1 alteration-related gene signature

Background: Treatment of advanced estrogen receptor-positive HER-2-negative breast cancer is based on hormonal therapy with aromatase inhibitors for postmenopausal women. However, acquired endocrine resistance is unavoidable at some point in the advanced or metastatic stage, and its underlying molecular mechanisms remain to be fully elucidated. The study prospectively included patients with advanced or metastatic breast cancer who had relapsed or progressed following treatment with a non-steroidal aromatase inhibitor (AI) and were treated with exemestane (a steroidal AI) and everolimus. The objective was to perform DNA and RNA analyses in order to gain a deeper understanding of the genomic and transcriptomic landscape of endocrine-resistant advanced BC. Material and methods: We selected 65 patients included between 2015 and 2018 in the SAFIRTOR trial (NCT02444390). NGS-based gene panel of 65 genes (SAFIR02 core panel), Comparative genomic hybridization array and RNA-sequencing assessed single nucleotide variations, copy-number variations and gene expression and fusion genes of interest, respectively. Results: The most prevalent genomic alteration was ESR1, observed in 49% (32/65) of cases, with most being activating missense mutations. Two cases of ESR1 fusions were identified. The observed alterations were not mutually exclusive with those from NF1 or ERBB2. Differential expression analysis in the presence or absence of ESR1 alterations showed significant enrichment of the ESR-mediated signaling pathway in tumors with ESR1 alterations (p < 0.005). 17 genes were identified as significantly differentially expressed, forming a transcriptional signature with 81.3% sensitivity and 84.3% specificity (p < 0.0001). The oxidative phosphorylation (OXPHOS) pathway was significantly associated with resistance to everolimus (p = 5.05 × 10^-10). 16 genes were differentially expressed between responders and non-responders, forming a OXPHOS gene signature distinguishing two groups with markedly different outcomes.