Spatial Multi-Omics Reveals an Immunometabolic Niche Defined by PROM1+SLC27A4+ Tumor-Initiating Cells and CD8A+ABCA12+ Exhausted T Cells in HER2-Positive Breast Cancer

Despite targeted therapy advances, drug resistance and metastasis remain the primary causes of mortality in HER2-positive breast cancer. The crosstalk between tumor-initiating cells (TICs) and specific CD8 ⁺ T cell subsets in the tumor microenvironment (TME) that may contribute to treatment failure remains poorly defined. Here, by integrating snRNA-seq (N=20), spatial transcriptomics with spatial metabolomics (N=5), spatial in situ analysis (N=42), proteomics (N=12), functional co-culture assays, and clinical tissue validation (N=279), as well as reanalysis of public datasets (N=35), we identified a PROM1 ⁺ SLC27A4 ⁺ TICs (tumor-initiating cells) – associated CD8A ⁺ ABCA12 ⁺ exhausted T cell population enriched in HER2-positive breast cancer. Spatial and functional analyses support a model in which PROM1 ⁺ SLC27A4 ⁺ TICs engage EGFR-expressing CD8A ⁺ ABCA12 ⁺ cells through an EGF-enriched signaling axis, consistent with STAT5-dependent upregulation of TIGIT and ABCA12. In turn, CD8A ⁺ ABCA12 ⁺ cells facilitate ABCA12-dependent lignoceric acid release, putatively imported by PROM1 ⁺ SLC27A4 ⁺ TICs in a SLC27A4-dependent manner, associated with peri-droplet mitochondrial (PDM) remodeling, MFN2 upregulation and enhanced ATP production. Trajectory analyses suggest that CD8A ⁺ ABCA12 ⁺ cells are transcriptionally and spatially connected to CD8A ⁺ ITGAE ⁺ tissue-resident memory cells, consistent with a putative exhaustion-associated state transition. CD8A ⁺ ABCA12 ⁺ cells were enriched in primary tumors, metastatic lesions and post-chemotherapy specimens, correlating with poor clinical outcome. These findings define an immunometabolic TIC-associated niche that may contribute to therapy resistance and metastatic progression in HER2-positive breast cancer.