Developmental trajectory of unconventional T cells of the cynomolgus macaque thymus.

As nonhuman primates are immunologically the closest model to humans, a comprehensive understanding of T-cell development in these species is crucial. However, the differentiation pathways in which thymocytes participate, along with their heterogeneity, remain poorly characterized. Using single-cell RNA sequencing, we thoroughly profiled the development of various T-cell lineages in the juvenile cynomolgus monkey thymus, identifying and characterizing 12 distinct thymic cell states or types. Interestingly, we identified two unexpected cell types, an agonist-selected and a memory-like cell population. The agonist-selected cell population expressed genes associated with strong TCR signaling, such as , , , , , and but exhibiting significantly higher expression compared with cells following the conventional developmental pathway. Additionally, we identified a substantial number of memory-like cell populations characterized by high and expression. Notably, this population also highly expressed the effector-associated markers, , , and , as well as the innate cell-associated markers, , , , , and . The   memory-like cell population expressed highly , indicating the presence of an agonist-selection footprint. Our findings provide insights into the agonist-selection pathway that allows self-reactive thymocytes to survive thymic selections and differentiate into various unconventional T-cell lineages.