A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

Abstract

Summary Breast cancer is a heterogeneous disease. Tumor cells and associated healthy cells form ecosystems that determine disease progression and response to therapy. To characterize features of breast cancer ecosystems and their associations with clinical data, we analyzed 144 human breast tumor and 50 non-tumor tissue samples using mass cytometry. The expression of 73 proteins in 26 million cells was evaluated using tumor and immune cell-centric antibody panels. Tumors displayed individuality in tumor cell composition, including phenotypic abnormalities and phenotype dominance. Relationship analyses between tumor and immune cells revealed characteristics of ecosystems related to immunosuppression and poor prognosis. High frequencies of PD-L1 + tumor-associated macrophages and exhausted T cells were found in high-grade ER + and ER − tumors. This large-scale, single-cell atlas deepens our understanding of breast tumor ecosystems and suggests that ecosystem-based patient classification will facilitate identification of individuals for precision medicine approaches targeting the tumor and its immunoenvironment.

CD163+ tumor‐associated macrophage accumulation in breast cancer patients reflects both local differentiation signals and systemic skewing of monocytes

“…We identified about 25% of total immune cells infiltrating BCs as CD14 + TAMs that express variable levels of CD163, underlying the phenotypic heterogeneity in TAMs. Through high‐dimensional analysis approaches, several recent reports have uncovered TAM heterogeneity at the single‐cell level in distinct tumor types, including BC, clear cell renal cell carcinoma, melanoma and lung adenocarcinoma . These studies revealed a great variety of distinct phenotypic TAM subsets that co‐exist by sharing the expression of well‐established M1 and M2 markers.…”

Phenotype molding of T cells in colorectal cancer by single‐cell analysis

“…By compiling and then comparing the levels of expression of many proteins across multiple cell types, single-cell mass cytometry is a robust readout to clarify the differentiation of expression patterns in multiple immune cell types. 20,22,23,25 Our comprehensive single-cell analysis of tumor, nontumorous colorectal tissue and blood demonstrate that the immunosuppressive/exhausted T cells were recruited/induced by the tumor microenvironment, even at the early stage of tumor development. To improve the response of immunotherapy targeting immune checkpoints, it is important to reverse the immunosuppressive tumor microenvironment.…”

“…In contrast, a previous study found that patients with breast cancer exhibited most PD-1+ T cells within the CD8+ compartment, whereas the mean expression of PD-1 was higher in CD4+ than in CD8+ T cells. 25 The mean expression level of PD-1 and PD-1 T-cell frequency strongly correlated with CD4+ and CD8+ subsets, indicating that these cells originated from T-cell expansion (Fig. 3e).…”

“…RNA‐sequencing determines the mRNA levels of huge number of genes in the bulk of tumor, while mass cytometry is a powerful single‐cell proteomic analysis technique. By compiling and then comparing the levels of expression of many proteins across multiple cell types, single‐cell mass cytometry is a robust readout to clarify the differentiation of expression patterns in multiple immune cell types …”

Microfluidic Single‐Cell Omics Analysis

“…The outcome showed that programmed cell death‐ligand 1 positive (PD‐L1 + ) tumor‐associated macrophages and exhausted T cells were abundant in high‐grade ER + and ER − tumors. This comprehensive single‐cell atlas of breast tumor indicated the significance of ecosystem‐based patient classification for precision medicine approaches …”