The PROM1+SMAD5+ Tumor-Initiating Subpopulation Shapes Premetastatic Niches through Spatial Multi-Omics Landscapes in HER2-Positive Breast Cancer

Abstract

Background: Human epidermal growth factor receptor 2 (HER2)-positive breast cancer exhibits high metastatic potential, linked not only to intrinsic cancer cell traits but also to critical crosstalk with the tumor microenvironment. However, the coevolutionary mechanisms between cancer cells and multiple stromal subpopulations in driving distant metastasis remain poorly understood. Therefore, this study aimed to explore the microenvironmental regulatory mechanisms of breast tumor-initiating cells and their roles in HER2-positive breast cancer metastasis. Methods: Integrated multi-omics analyses (spatial transcriptomics, metabolomics, spatial in situ analysis, and proteomics) were used to identify novel cell subpopulations and their interactions. High-throughput sequencing of exosomal microRNAs (miRNAs) and single-nucleus RNA from the same tissue was performed to explore the molecular mechanisms underlying cell crosstalk. In vitro experiments were conducted to verify the interaction between stromal cells and prominin 1 (PROM1)+ SMAD family member 5 (SMAD5)+ cells. In vivo murine breast cancer models were established to confirm the role of stromal subpopulations in pulmonary metastasis, and parabiosis assays were carried out to compare key cell subpopulations between tumor-bearing mice and normal mice. Clinical samples were analyzed to correlate key cell subpopulations with clinicopathological features and prognosis. Results: A breast tumor-initiating subpopulation, PROM1+ SMAD5+ cells, and its interactions with stromal cells, specifically adiponectin (ADIPOQ)+ notch receptor 4 (NOTCH4)+ adipocytes and decorin (DCN)+ transmembrane 4 L six family member 1 (TM4SF1)+ fibroblasts, were identified by integrated multi-omics analyses. Mechanistically, these 2 stromal subpopulations delivered functional miRNAs and mediated coatomer protein complex subunit alpha (COPA)-dependent epidermal growth factor receptor (EGFR) activation in PROM1+SMAD5+ cells, thereby triggering the EGFR–SMAD5–cytochrome P450 family 3 subfamily A member 4 (CYP3A4) axis to induce partial epithelial–mesenchymal transition (pEMT) and metastasis. Additionally, stroma-secreted exosomal miR-671-3p down-regulated Claudin1 in PROM1+SMAD5+ cells, promoting their evolution into PROM1+SMAD5+Claudin1− subpopulations with enhanced stemness and metastatic potential. In vivo experiments confirmed that the 2 stromal subpopulations markedly promoted pulmonary metastasis, and the 3 identified subpopulations preferentially accumulated in the primary tumors, lymph nodes, and pulmonary metastatic lesions of tumor-bearing mice. Clinically, these 3 subpopulations form a “trinity niche”, whose aggregation associated with HER2 positivity, high malignancy, and lymph node/pulmonary metastasis, and predicted poor prognosis. Conclusion: This study clarified the microenvironmental regulation of breast tumor-initiating cells and provided new insights into precision therapy.