Single cell analysis of iNKT cell phenotype, functionality and metabolism

Abstract

Abstract iNKT cells have been identified as potent regulators of diverse physiological responses ranging from tumor immunity to homeostatic regulation of adipose tissue. Recent studies have also established that iNKT cells are heterogeneous, and include distinct NKT1, NKT2, NKT17 and NKT10 subsets. To date, these subsets have been broadly characterized using various transcriptomic-based approaches, providing a basis for further analysis and exploration. However, many studies characterizing the iNKT cell transcriptome have been limited to resting iNKT cells, or have focused on iNKT cell development, and thus have not captured the dramatic changes in iNKT phenotype and function that have been observed following antigen exposure. Here, we took advantage of single cell RNA-Sequencing to characterize adipose and splenic iNKT cells before and after activation, and performed integrated analysis of novel and published data to construct a comprehensive overview of the iNKT cell response to antigen. We find that all iNKT cells undergo rapid and profound transcriptional remodeling in response to αGalCer, and identify conserved features of iNKT cell activation, including dynamic reprogramming of cellular metabolism. We also find differences between activated iNKT cell subsets, and we demonstrate that oxidative metabolism functionally segregates NKT2 and NKT17 cells from NKT1 cells. Furthermore, we find that key features of iNKT cell activation are blunted in regulatory iNKT cell populations, which are enriched in adipose tissue, and we identify a conserved network of gene signatures associated with NKT10 cells. Overall, this study provides novel insights into the biology of iNKT cells, and the interplay between their biology and metabolism.