Identification of immune‐infiltrated and stroma‐enriched subtypes in HER2+ breast cancer
Ying Yang, Wei Zeng, Xin Wei, Juan Li, Xuelian Chen, Zuyi Zhou, Bo Yang, Jie Li, Li LiAbstract
Background
Human epidermal growth factor receptor 2‐positive (HER2+) breast cancer exhibits substantial biological heterogeneity, yet the diversity of its tumour immune microenvironment has not been fully characterised. This study aimed to systematically define immune–stromal variation within HER2+ breast cancer and explore its prognostic relevance.
Methods
Transcriptomic and clinical data from The Cancer Genome Atlas Breast Invasive Carcinoma cohort (TCGA‐BRCA) and four Gene Expression Omnibus (GEO) cohorts were integrated. Immune and stromal infiltration was quantified using single‐sample gene set enrichment analysis, MCP‐counter and Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data (ESTIMATE). Consensus clustering was performed to identify microenvironmental subtypes. Survival analysis and weighted gene co‐expression network analysis were further conducted to evaluate subtype‐specific prognostic features and hub genes.
Results
Five microenvironmental subtypes were identified. Among them, an immune‐infiltrated subtype (C3) and a stroma‐dominant subtype (C2) emerged as the major phenotypes. Cluster C3 showed high infiltration of adaptive and innate immune cells and enrichment of chemotaxis‐ and cytokine‐related pathways, suggesting robust immune activation. In contrast, cluster C2 was characterised by increased fibroblast and endothelial cell infiltration, together with strong activation of extracellular matrix (ECM) organisation and collagen remodelling pathways. Survival analyses across TCGA‐BRCA and GEO cohorts showed that the immune‐infiltrated subtype had better disease‐free survival, progression‐free survival and overall survival than the stroma‐enriched subtype. Weighted gene co‐expression network analysis identified an immune activation‐related MEblue module associated with C3 and an ECM‐remodelling MEturquoise module associated with C2, each containing subtype‐specific hub genes.
Conclusion
These findings reveal clinically meaningful immune–stromal heterogeneity within HER2+ breast cancer and support microenvironment‐based stratification for improved prognostic assessment and therapeutic decision making.