Spatial transcriptome to identify biomarkers for endocrine sensitivity of hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2-) early breast cancer (EBC).

Abstract

e12501 Background: Intratumor heterogeneity is associated with endocrine sensitivity in breast cancer. However, no relevant studies have elucidated the role of different regions within the tumor in regulating endocrine therapy (ET). The study aims to explore the intratumor heterogeneity and identify potential biomarkers associated with endocrine sensitivity in patients with HR+/HER2- EBC based on digital spatial profiling. Methods: Patients were stratified into the ET-resistant and ET-sensitive groups. A total of 111 spatially resolved regions in three tissue compartments defined by morphology markers [tumor (PANCK+), leucocytes (CD45+), and nonimmune stroma (CD45-/PANCK-)] were investigated. A designated panel comprising 235 ET-related genes was successfully constructed. Transcriptomic measurement, enrichment analyses, single-cell sequencing, and survival assessment were performed across three types of spatial regions. Results: A total of 27, 13, and 5 differentially expressed genes (DEGs) were identified when comparing the ET-resistant with the ET-sensitive group in PANCK+, CD45+, and CD45-/PANCK- regions. Biological processes were primarily associated with nuclear activities, cell cycle, and histone modification. Fourteen DEGs in the PANCK+ regions were significantly associated with disease-free survival (DFS), among which seven DEGs, including RAD51, KAT6A, SMARCE1, FGFR1, KDM4B, GREB1L, and CCNDBP1, were qualified to construct a model for predicting DFS. Patients with low-risk scores had a median DFS of 55.77 months, significantly longer than 21.67 months among those with high-risk scores (p=2.1e-4, HR=6.73, 95CI%=2.20-20.60). The AUC for 1-year, 3-year, and 5-year DFS was 0.98, 0.95, and 0.91, indicating its superior efficacy for predicting DFS in patients with HR+/HER2− EBC. In the CD45+ regions, MLH3 was the only DFS-related DEG, where high expression level of MLH3 led to a prolonged DFS (p=3.8e-5, HR=0.22, 95CI%=0.10-0.47). Similarly, in the CD45−/PANCK− regions, only HDAC7 upregulation was found to be significantly associated with longer DFS (p=9.2e-3, HR=0.39, 95CI%=0.18-0.81). Non-classical monocyte infiltration was significantly higher in the ET-sensitive group (p=0.03) in the CD45+ regions, and plasma cell infiltration was significantly higher in the ET-resistant group (p=0.01) in the CD45−/PANCK− regions. Conclusions: Our study has firstly demonstrated the intratumor heterogeneity of patients showing different responses to ET-based treatment, which may be helpful for disentangling the molecular mechanisms of endocrine resistance and stratifying patients who are responsive to ET.