Endocrine Resistance Score Based on Three Key Genes Predicts Prognosis and Reveals Potential Therapeutic Targets for ER+HER2− Breast Cancer

Abstract

Endocrine resistance is a leading cause of mortality in oestrogen receptor-positive and human epidermal growth factor receptor 2-negative (ER+HER2−) breast cancer (BC), highlighting the urgent need to understand its underlying molecular mechanisms and identify potentially resistant patients for effective management. In this study, we constructed endocrine-resistant cell lines through long-term oestrogen deprivation and identified differentially expressed genes (DEGs) via transcriptome analysis. Key endocrine-resistant genes were defined through Cox regression analysis. Our findings revealed that the genes CLEC3A, PCDH10, and ST3GAL1 were significantly upregulated in endocrine-resistant cells and serve as independent prognostic factors for ER+HER2− BC patients. We developed an endocrine resistance score (ERS), and a nomogram model incorporating ERS demonstrated robust predictive capabilities for patient prognosis. Single-cell RNA sequencing analysis demonstrated that the ERS and the three core genes constituting the ERS were significantly upregulated in tissue specimens from patients with resistance to endocrine neoadjuvant therapy. Additionally, knocking down CLEC3A, PCDH10, and ST3GAL1 led to reduced malignancy progression in endocrine-resistant BC cells. Mechanistic studies revealed that CLEC3A promotes endocrine resistance by upregulating the PI3K-AKT pathway. This study suggests that CLEC3A, PCDH10, and ST3GAL1 are associated with endocrine resistance and can reflect the prognosis of ER+HER2− BC patients receiving endocrine therapy, providing potential therapeutic targets and a valuable prognostic indicator for clinicians.

Keywords

breast cancer / endocrine resistance / gene signature / oestrogen receptor / prognostic factors

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