Naive CD4+ T cell heterogeneity

Abstract

Although naive T cells comprise about 90% of circulating and 20% of tissue restricted T cells, most studies on T cells emphasize effector, regulatory or memory functions. The consensus that all naive cells comprise a functionally monomorphic population is challenged by our recent findings. A redefinition of the naive T cell state shows that these cells are heterogeneous, with pre-programed differentiation trajectories. VISTA (V-domain Ig suppressor of T cell activation) is an immune checkpoint restricted to the hematopoietic compartment. Here, using single cell sequencing, we demonstrate unexpected loss of quiescence in VISTA deficient CD4+ T cells compared to Wild Type CD4+ T cells. The quiescence module, defined by Klf2, Klf6, Btg1, Btg2 expression, is lost in VISTA deficient mice. Conversely, there is an expansion of the stem-cell memory-like cluster, defined by Tcf7, Bcl2, and Il7r. This altered subset make-up due to VISTA deficiency demonstrates that naive T cell heterogeneity is tightly regulated. Consequently, we identified 5 subsets in healthy adult mice using single cell sequencing of naive CD4+ T cells. These include a quiescence cluster, memory-like cluster, TCR reactive cluster, IFN responsive cluster and T cell undifferentiated cluster. This heterogeneity is imprinted in the thymus, maintained in the periphery, and is not influenced by the TCR repertoire. Tracking the differentiation trajectory of these naive CD4+ T cells shows biased lineage commitment dependent on progenitor cluster identity. Thus, thymic imprinting and peripheral maintenance of varied naive T cell identities determines T cell fate. Supported by 5R01AR070760-05