Azizi E1, Carr AJ2, Plitas G3, Cornish AE1, Konopacki C4, Prabhakaran S1, Nainys J5, Wu K6, Kiseliovas V7, Setty M1, Choi K8, Fromme RM9, Dao P1, McKenney PT10, Wasti RC11, Kadaveru K11, Mazutis L1, Rudensky AY12, Pe'er D13.
Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancerprogression and immunotherapy response. We profiled 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph nodes, using single-cell RNA-seq. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer. Our results have important implications for characterizing tumor-infiltrating immune cells.