Single-cell Transcriptomics Reveal Different Maturation Stages and Sublineages Commitment of Human Thymic Invariant Natural Killer T cells

Invariant natural killer T (iNKT) cells are a subset of heterogenous T-cells with potent cytotoxic and immunomodulatory properties. During thymic development, murine iNKT cells go through different maturation stages and differentiate into distinct sublineages, namely iNKT1, iNKT2, and iNKT17 cells. To define maturation stages and to assess sublineage commitment of human iNKT cells during thymic development, we performed single-cell RNA sequencing analysis on human thymic iNKT cells. We show that these iNKT cells displayed heterogeneity and unsupervised analysis identified two clusters: one with an immature profile with high expression of genes that are important for iNKT cell development and enriched in cells expressing an iNKT2 signature, whereas a second cluster displayed a mature, terminally differentiated profile resembling murine iNKT1 cells. Trajectory analysis suggested an ontological relationship between the two clusters. Our work provides the first single cell transcriptomic analysis of thymic human iNKT cells offering new insights into their developmental process in humans.