A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3 T cell development.

The neonatal thymus generates Foxp3 regulatory T (tT) cells that are critical in controlling immune homeostasis and preventing multiorgan autoimmunity. The role of antigen specificity on neonatal tT cell selection is unresolved. Here we identify 17 self-peptides recognized by neonatal tT cells, and reveal ligand specificity patterns that include self-antigens presented in an age- and inflammation-dependent manner. Fate-mapping studies of neonatal peptidyl arginine deiminase type IV (Padi4)-specific thymocytes reveal disparate fate choices. Neonatal thymocytes expressing T cell receptors that engage IA-Padi4 with moderate dwell times within a conventional docking orientation are exported as tT cells. In contrast, Padi4-specific T cell receptors with short dwell times are expressed on CD4 T cells, while long dwell times induce negative selection. Temporally, Padi4-specific thymocytes are subject to a developmental stage-specific change in negative selection, which precludes tT cell development. Thus, a temporal switch in negative selection and ligand binding kinetics constrains the neonatal tT selection window.