Characterization of circulating porcine immune cells using single-cell RNA-sequencing and comparison to human datasets

Abstract

Pigs are part of global food security and serve as a valuable human biomedical model. Immunoreagent unavailability limits resolution of pig leukocyte populations by protein markers; thus, single-cell RNA-sequencing (scRNA) was used to characterize pig peripheral blood mononuclear cell (PBMC) populations and infer function based on transcriptional profiles and comparison to human datasets. Across seven PBMC samples partitioned and sequenced, 28,810 cells distributed across 36 clusters were classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, more than ten B cell clusters including plasmablasts, conventional CD4 and CD8 αβ T cells, NK cells, and four clusters of γδ T cells. Signature gene sets for a publicly available human bulk RNA-seq dataset were assessed for relative enrichment in genes expressed in pig cells and substantial overlap in gene expression between specific pig and human PBMC populations was detected. Integration of pig scRNA with a public human scRNA dataset provided further validation for similarity between human and pig. Of four pig γδ T cell clusters, two had high prediction and mapping scores with human γδ T cells. The other two pig γδ T cell clusters had gene expression profiles predictive of human γδ T cells, but also human CD4 T central memory (Tcm) and innate lymphoid cells, suggesting innate and adaptive function of some pig γδ T cells. Pigs have a population of circulating double-positive (DP) CD4⁺CD8αα⁺ αβ T cells, and putative DP clusters had high prediction scores to human CD4 Tcm cells, supporting their classification in literature as memory cells. Overall, the data provided the first single-cell atlas for porcine PBMCs and comparison to human datasets.