Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.
Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression 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.
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Analysis Portals
NoneProject Label
GSE114727_BreastTumorMicroenvironmentSpecies
Homo sapiens
Sample Type
specimens
Anatomical Entity
Organ Part
Selected Cell Types
Disease Status (Specimen)
Disease Status (Donor)
Development Stage
human adult stage
Library Construction Method
Nucleic Acid Source
single cell
Paired End
trueAnalysis Protocol
data_analysis_protocolsFile Format
Cell Count Estimate
72.0kDonor Count
11