Single-cell RNA sequencing reveals cellular and molecular heterogeneity and distinct immunosuppressive traits in the MMTV-R26Met syngeneic TNBC model

Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous subtype of breast cancer with limited targeted therapies. To model TNBC heterogeneity in an immunocompetent setting, we established syngeneic grafts derived from the TNBC MMTV-R26Met genetically engineered mouse model, which preserve both the molecular identity and immune landscape of primary tumors. These grafts recapitulate features of distinct TNBC subtypes, providing a physiologically relevant preclinical platform to investigate tumor–immune interactions and therapy response. Here, we performed single-cell RNA sequencing (scRNA-seq) on four syngeneic tumors (S34, S35, S37, and S39), generating transcriptomic profiles from 22,046 cells. Clustering identified cell populations spanning malignant epithelial, stromal, endothelial, and diverse immune subsets. Tumors displayed subtype-specific traits, including oxidative phosphorylation programs with N2-like neutrophils and epithelial–mesenchymal transition with M2-like macrophages. Despite overall low T cell infiltration, inhibitory receptors and myeloid checkpoint ligands were broadly expressed, highlighting strongly immunosuppressive microenvironments. These datasets provide a resource for dissecting TNBC subtype heterogeneity in an immunocompetent context and offer a preclinical framework to explore mechanisms of immune evasion and therapeutic response. Overall design: Single-cell RNA sequencing was performed on four independent syngeneic tumors (S34, S35, S37, S39) derived from the MMTV-R26Met triple-negative breast cancer mouse model. Tumors were dissociated into single-cell suspensions and processed using the 10x Genomics Chromium pipeline.