Single-cell analysis reveals differences among i NKT cells colonizing peripheral organs and identifies Klf2 as a key gene for i NKT emigration

Invariant natural killer T cell ( i NKT) subsets are differentially distributed in various immune organs. However, it remains unclear whether i NKT cells exhibit phenotypical and functional differences in different peripheral organs and how thymic i NKT cells emigrate to peripheral organs. Here, we used single-cell RNA-seq to map i NKT cells from peripheral organs. i NKT1 cells from liver, spleen, and lymph node appear to have distinct phenotypic profiles and functional capabilities. However, i NKT17 transcriptomes were comparable across peripheral organs. In addition, by integrating data with a thymic i NKT cell study, we uncovered a transient population of recent thymic emigrants, a cluster of peripheral i NKT cells with high expression of transcription factor Kruppel-like factor 2 ( Klf2 ). Deletion of Klf2 led to a severe impairment of i NKT differentiation and migration. Our study revealed that i NKT subsets are uniquely distributed in peripheral organs with some inter-local tissue variation, especially for i NKT1 cell, and identified Klf2 as a rheostat for i NKT cell migration and differentiation.