A single cell analysis of porcine thymopoiesis and thymic iNKT cells

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 employed single-cell RNA sequencing (scRNA-seq) to create a cell atlas of the postnatal pig thymus. Our data found conserved features as well as species-specific differences in cell states and cell types compared to 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 >11,000 differentiating invariant natural killer T (iNKT) cells, which revealed that the functional diversity of pig iNKT cells differs substantially from the paradigm of iNKT0/1/2/17 subset differentiation established in mice. Collectively, our data characterizes key differentiation events in porcine thymopoiesis and iNKT cell maturation, which provide new insights into pig T cell development. Overall design: We performed single-cell RNA-seq on the pig total thymocytes and iNKT thymocytes purified from the same thymi.