Single-Cell Immune Map of Breast Carcinoma Reveals Diverse Phenotypic States Driven by the Tumor Microenvironment

Knowledge of the phenotypic states of immune cells in the tumor microenvironment is essential for understanding immunological mechanisms of cancer progression and immunotherapy responses, as well as the development of novel treatments. By combining single-cell RNA-seq data from over 45,000 immune cells collected from eight primary breast carcinomas, as well as matched normal breast tissue, peripheral blood, and lymph node, we created an immune map of breast cancer. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address the computational challenges inherent to single-cell RNA-seq data, enabling integration of data across patients. This atlas revealed significant similarity between normal and tumor tissue resident immune cells. However, we observed continuous tumor-specific phenotypic expansions driven by environmental cues. Our results argue against discrete activation states in T cells and the polarization model of macrophage activation in cancer, with important implications for characterizing tumor-infiltrating immune cells.