Description

Tumor-infiltrating immune cells of breast cancer identified at single-cell resolution

Jae-Yong Nam^1,3*, Hye Hyeon Eum¹*, Woosung Chung^1,3, Han-Byoel Lee⁴, Wonshik Han⁴, Woong-Yang Park^1,2*, Hae-Ock Lee¹*

¹Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; ²Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea;

³Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06351, Korea;

⁴Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea

The number and type of tumor-infiltrating immune cells are often associated with clinical outcome in breast cancer. However, most results have been generated using bulk tumor samples, a mixture containing both tumor and many types of non-tumor cell populations. For the precise characterization of different type of immune cells, we performed single-cell RNA-sequencing on the triple negative breast cancer (TNBC) with high number of infiltrating immune cells. The majority of isolated single-cells were T cells (50%) and the rest were macrophages (28%), B cells (3.5%) and dendritic cells (15%). T cell receptor (TCR) analysis demonstrates the capture of diverse T cell clones suggesting the presence of multiple tumor antigens. T cell variable gene usage of both single-cell and bulk is almost identical, but some TCR genes show clear differences which are reflected in the CDR3 sequence diversity. In parallel, forty-three putative neo-antigens were discovered based on the patient HLA type, and mutant peptide-MHC binding affinity stronger than the wild peptide-MHC binding affinity. Overall, our results show that single-cell RNA sequencing allows the characterization of the diverse immune cells, especially T cell clonotypes in the tumor microenvironment.