Genomic characterization of AI resistance in hormone receptor-positive breast cancer using LTED cell line models

Breast cancer, the most frequently diagnosed malignancy among women globally, often relies on estrogen signaling for growth, particularly in hormone receptor-positive cases. Long-term estrogen deprivation (LTED) mimics the therapeutic effects of aromatase inhibitors (AIs), standard treatments for post-menopausal patients with hormone receptor-positive breast cancer, by creating a state where cancer cells adapt to survive without estrogen. The molecular mechanism underlying LTED state involves complex adaptations that enable cancer cells to bypass estrogen dependency. Current treatment options, primarily AIs, improve survival but face challenges due to resistance development in over 30% of patients, leading to relapse. Here, we established a model to study LTED by generating two MCF7-derived LTED cell lines, MCF7-LTED-R1 and MCF7-LTED-R2, to investigate resistance mechanisms. We performed an integrated genome and transcriptome analysis using whole-exome sequencing and whole-transcriptome sequencing. Our analysis reveals that the resistant cells established acquired alterations in insulin signaling pathway genes (IGF1R, IRS1, IRS2), significant upregulation of ESR1, and a novel ESR1-PPP3CA fusion transcript not previously identified. Differentially expressed genes suggested deregulation of ER signaling, activation of insulin secretion, and aldosterone synthesis pathways, indicating compensatory survival mechanisms. We performed validation through qPCR to confirm gene expression changes. Overall, we provide a comprehensive genomic characterization of AI resistance in hormone receptor-positive breast cancer using LTED cell line models, identifying potential therapeutic targets to overcome endocrine resistance.