Deconstructing iNKT cell development at single-cell resolution

Recent unbiased single-cell RNA sequencing of mouse invariant natural killer T (iNKT) cells revealed previously unappreciated heterogeneity. iNKT2 cell transcriptomes reveal RNA plasticity indicative of multipotency, and iNKT2 cells thus contain precursors of iNKT1 and iNKT17 pools. iNKT cell effector differentiation can occur in the thymus, or precursor cells can egress the thymus and mature in peripheral tissues. T cell receptors, signaling lymphocytic activation molecule (Slam) family receptors, and cytokine signals drive iNKT cell differentiation. Phenotypic, functional, and transcriptomic studies have begun to unravel the heterogeneity of human iNKT cells. Invariant natural killer T (iNKT) cells are increasingly regarded as disease biomarkers and immunotherapeutic targets. However, a greater understanding of their biology is necessary to effectively target these cells in the clinic. The discovery of iNKT1/2/17 cell effector subsets was a milestone in our understanding of iNKT cell development and function. Recent transcriptomic studies have uncovered an even greater heterogeneity and challenge our understanding of iNKT cell ontogeny and effector differentiation. We propose a refined model whereby iNKT cells differentiate through a dynamic and continuous instructive process that requires the accumulation and integration of various signals within the thymus or peripheral tissues. Within this framework, we question the existence of true iNKT2 cells and discuss the parallels between mouse and human iNKT cells. Invariant natural killer T (iNKT) cells are increasingly regarded as disease biomarkers and immunotherapeutic targets. However, a greater understanding of their biology is necessary to effectively target these cells in the clinic. The discovery of iNKT1/2/17 cell effector subsets was a milestone in our understanding of iNKT cell development and function. Recent transcriptomic studies have uncovered an even greater heterogeneity and challenge our understanding of iNKT cell ontogeny and effector differentiation. We propose a refined model whereby iNKT cells differentiate through a dynamic and continuous instructive process that requires the accumulation and integration of various signals within the thymus or peripheral tissues. Within this framework, we question the existence of true iNKT2 cells and discuss the parallels between mouse and human iNKT cells. a technique that enables the assessment of genome-wide chromatin accessibility (i.e., the epigenome) in bulk or single-cell experiments. Computational methods allow the identification of cell (population)-specific binding sites and transcription factors with specific activity. a non-polymorphic MHC class Ib protein composed of three α domains that are non-covalently associated with β2-microglobulin. CD1d molecules are specialized in the presentation of lipid-based antigens. a subset of mouse and human iNKT cells that are specialized in providing help to B cells during the germinal center reaction in lymphoid tissues. a gene variant that causes partial loss of function. one of the algorithms enabling pseudo-time ordering using Python as programming language. the process by which CD4/CD8 double-positive (DP) thymocytes expressing a functional TCR receive survival signals through antigen presentation. algorithms applied to single-cell (sc)RNA-seq analysis to predict cell fate trajectories. Based on the quantification of cell connectivity according to similarity in gene expression, it builds predictive graphs that map the developmental evolution of cells and distinguishes transient states, branching decisions, and endpoints. the earliest cells that have exited the thymus and can be detected in peripheral tissues. TCR gene rearrangement generates small circles of DNA in thymocytes; these are considered to be quantitative markers of thymic output. biochemical signals transduced upon TCR engagement that are translated into a complex network that activates multiple signaling pathways culminating in the regulation of transcription factors and cytoskeleton changes. the thymus is a primary lymphoid organ composed of the cortex, an outer cell-rich area containing immature thymocytes, and the medulla, an inner less dense layer in which thymocytes fulfill their developmental program. a transcriptionally defined subset of mouse MAIT cells which appears to have the potential to give rise to MAIT1 and MAIT17 cell subsets based on a pseudo-time ordering approach. a group of cytokines including IFN-α and IFN-β that signal through a common IFN-α receptor (IFNAR) and are usually involved in antiviral responses. a heterogeneous class of T lymphocytes which are not restricted to highly polymorphic MHC class I and II molecules. Unconventional T cells are donor-unrestricted and respond to non-peptidic public antigens through a relatively conserved TCR repertoire.