Profiling of the TNBC Tumor Microenvironment's Functional Heterogeneity by CITE-seq to Guide Personalized Medicine

Introduction / Objective: Triple-negative breast cancer (TNBC) is an aggressive subtype with few effective treatments and frequent resistance to immune checkpoint inhibitors. The heterogeneous and plastic tumor microenvironment (TME) is a dynamic, complex ecosystem. This study aims to deconstruct the TNBC immune ecosystem and generate a cellular atlas of its tumor microenvironment. Methods: In this study, we apply three CITE-seq datasets from murine TNBC tumors, totaling 2,356 cells. After correcting for technical batch effects, we perform clustering to identify major cell types, followed by focused sub-clustering of tumor-associated macrophages (TAMs) and T cells to analysis their functional states and potential differentiation trajectories. Results: Batch-corrected analysis resolves six primary cell populations within the TNBC microenvironment. TAMs segregate into three distinct subpopulations: a classical antigen-presenting subset, a metabolically active subset enriched for mitochondrial gene expression, and a unique subset with an erythroid-like gene signature consistent with active erythrophagocytosis. T-cell analysis reveals five major states. Furthermore, we identify several therapeutic targets. Discussion: These findings reveal substantial functional diversity within key immune compartments of TNBC, particularly TAMs and T cells, including metabolically specialized and erythrophagocytic TAMs, as well as distinct T cells. Besides, we also identify several potential drug targets for targeted treatment. Conclusion: This work provides a detailed single-cell atlas of the TNBC tumor microenvironment and uncovers functional heterogeneity in its immune cells. The resulting map offers a foundation for precision medicine, facilitating patient stratification and the design of tailored therapies that target the specific cellular ecosystems driving TNBC progression.