A multitissue single-cell atlas of the tree shrew reveals tissue-specific macrophage heterogeneity and evolutionarily conserved NRlH3+ immunoregulatory mechanism

Rodents are widely used in immunological research, but their evolutionary distance from humans limits their effectiveness in modeling complex human immune regulation. The tree shrew (Tupaia belangeri) is an emerging model organism that is evolutionarily closer to primates than rodents; however, a comprehensive immune cell atlas for this species is still lacking. Here, we present the first single-cell transcriptomic atlas of T. belangeri, encompassing 39 cell types across 12 organs. Notably, we confirm that T. belangeri possesses a tonsillar structure analogous to the human tonsil, a feature absent in rodents. By a cross-tissue analyses reveal two functionally specialized macrophage subsets in the spleen: an NR1H3+ immunosuppressive subset and an IRF8+ pro-inflammatory subset. In a T. belangeri EBV infection model, the NR1H3+ macrophage subset undergoes functional reprogramming during acute infection and eventually dominates the ensuing inflammatory response. We further identify an analogous NR1H3+ subset in human splenic macrophages, and we show that it mediates immunoregulatory effects by suppressing the non-canonical NF-kB signaling pathway. Comparative single-cell profiling across seven species shows that NR1H3+ macrophages are evolutionarily conserved in T. belangeri and human, but are absent in mouse. Our work provides a valuable resource for advancing immunological research, enabling cross-species comparisons, and facilitating the development of T. belangeri-specific reagents. By addressing the limitations of nontraditional models, this work significantly enhances the utility of T. belangeri in preclinical and translational studies, positioning it as a powerful alternative to nonhuman primates.