Unveiling the heterogeneity of NKT cells in the liver through single cell RNA sequencing

Haifeng Liu,Hao Shen,Tao Liang,Fan Guo,Chan Gu,Xiaolong Liu

doi:10.1038/s41598-020-76659-1

Abstract

CD1d-dependent type I NKT cells, which are activated by lipid antigen, are known to play important roles in innate and adaptive immunity, as are a portion of type II NKT cells. However, the heterogeneity of NKT cells, especially NKT-like cells, remains largely unknown. Here, we report the profiling of NKT (NK1.1+CD3e+) cells in livers from wild type (WT), Jα18-deficient and CD1d-deficient mice by single-cell RNA sequencing. Unbiased transcriptional clustering revealed distinct cell subsets. The transcriptomic profiles identified the well-known CD1d-dependent NKT cells and defined two CD1d-independent NKT cell subsets. In addition, validation of marker genes revealed the differential organ distribution and landscape of NKT cell subsets during liver tumor progression. More importantly, we found that CD1d-independent Sca-1−CD62L+ NKT cells showed a strong ability to secrete IFN-γ after costimulation with IL-2, IL-12 and IL-18 in vitro. Collectively, our findings provide a comprehensive characterization of NKT cell heterogeneity and unveil a previously undefined functional NKT cell subset.

Highlights

Natural killer T (NKT) cells have been increasingly reported to play an important role in controlling innate and adaptive immune responses against cancers, inflammatory disorders and infectious d iseases[1]
By comparison of the clustering pattern of NKT cells from wild type (WT) mice with those of NKT cells from Jα18-deficient and CD1d-deficient mice, the NKT cells were divided into 4 distinct subsets, which we temporarily termed Cluster 1 (C1), Cluster 2 (C2), Cluster 3 (C3) and Cluster 4 (C4)
In this study, benefiting from the advantages of single-cell RNA-seq, we showed the heterogeneity of NKT cells from the mouse liver regardless of antigen specificity

Summary

Introduction

Natural killer T (NKT) cells have been increasingly reported to play an important role in controlling innate and adaptive immune responses against cancers, inflammatory disorders and infectious d iseases[1]. NKT cells are generally defined as CD1d-dependent natural killer-like T cells. The majority of the literature has defined NKT cells as a CD1d-dependent cell type[11] Both type I and type II NKT cells have been shown to play an important role in the regulation of immune responses in cancer and other diseases[1]. CD1d-independent NKT-like cells are more heterogeneous and less thoroughly characterized than CD1d-dependent NKT cells, which makes it more difficult to study their biological function precisely. By comparison of the scRNA-seq data of liver NKT cells from WT mice with those of liver NKT cells from Jα18-deficient and CD1d-deficient mice, we identified type I and type II NKT cells and divided the CD1d-independent NKT cells into two major subsets. Our research reveals the landscape of NKT cells in the liver and redefines the NKT cell subsets

Methods

Results

Conclusion