Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

Woosung Chung, Hye Hyeon Eum, Hae-Ock Lee, Kyung-Min Lee, Han-Byoel Lee, Kyu-Tae Kim, Han Suk Ryu, Sangmin Kim, Jeong Eon Lee, Yeon Hee Park, Zhengyan Kan, Wonshik Han () and Woong-Yang Park ()
Additional contact information
Woosung Chung: Samsung Genome Institute, Samsung Medical Center
Hye Hyeon Eum: Samsung Genome Institute, Samsung Medical Center
Hae-Ock Lee: Samsung Genome Institute, Samsung Medical Center
Kyung-Min Lee: Seoul National University College of Medicine
Han-Byoel Lee: Seoul National University College of Medicine
Kyu-Tae Kim: Samsung Genome Institute, Samsung Medical Center
Han Suk Ryu: Seoul National University College of Medicine
Sangmin Kim: Samsung Medical Center, Sungkyunkwan University School of Medicine
Jeong Eon Lee: Samsung Medical Center, Sungkyunkwan University School of Medicine
Yeon Hee Park: Samsung Medical Center
Zhengyan Kan: Oncology Research, Pfizer Inc.
Wonshik Han: Seoul National University College of Medicine
Woong-Yang Park: Samsung Genome Institute, Samsung Medical Center

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract Single-cell transcriptome profiling of tumour tissue isolates allows the characterization of heterogeneous tumour cells along with neighbouring stromal and immune cells. Here we adopt this powerful approach to breast cancer and analyse 515 cells from 11 patients. Inferred copy number variations from the single-cell RNA-seq data separate carcinoma cells from non-cancer cells. At a single-cell resolution, carcinoma cells display common signatures within the tumour as well as intratumoral heterogeneity regarding breast cancer subtype and crucial cancer-related pathways. Most of the non-cancer cells are immune cells, with three distinct clusters of T lymphocytes, B lymphocytes and macrophages. T lymphocytes and macrophages both display immunosuppressive characteristics: T cells with a regulatory or an exhausted phenotype and macrophages with an M2 phenotype. These results illustrate that the breast cancer transcriptome has a wide range of intratumoral heterogeneity, which is shaped by the tumour cells and immune cells in the surrounding microenvironment.

Date: 2017
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DOI: 10.1038/ncomms15081

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