A single-cell analysis of thymopoiesis and thymic iNKT cell development in pigs

Highlights

* A comprehensive atlas of thymocytes in the early-adolescent pig thymus

* Detection of unconventional subsets and characterization of transcriptional heterogeneity

* scRNA-seq on iNKT cells found more than 95% resemble murine iNKT2 and minor pig-specific subsets

* Porcine iNKT cells lack clusters that overlap with mouse iNKT1 or iNKT17 subsets

SUMMARY

Many aspects of the porcine immune system remain poorly characterized, which poses a barrier to improving swine health and utilizing pigs as preclinical models. Here, we employ single-cell RNA sequencing (scRNAseq) to create a cell atlas of the early-adolescent pig thymus. Our data show conserved features as well as species-specific differences in cell states and cell types compared with human thymocytes.We also describe several unconventional T cell types with gene expression profiles associated with innate effector functions. This includes a cell census of more than 11,000 differentiating invariant natural killer T (iNKT) cells, which reveals that the functional diversity of pig iNKT cells differs substantially from the iNKT0/1/2/17 subset differentiation paradigm established in mice. Our data characterize key differentiation events in porcine thymopoiesis and iNKT cell maturation and provide important insights into pig T cell development.