Annotating cell transcriptomes in four immune tissues to establish a porcine single-cell immune atlas
A single cell-level understanding of the porcine immune system will provide tools for improving both disease resistance and use of the pig in biomedical modeling. We performed scRNA-seq on bone marrow, lymph node, spleen, and thymus from healthy adult pigs. After quality control to remove duplicate cells and cells with high mitochondrial content, > 50,000 cells were used for downstream analysis. Using a combination of model defined and canonical immune cell markers, we were able to annotate each cluster as part of a diverse set of immune cell types identified. We used our previously published porcine PBMC scRNA-seq dataset to compare peripheral blood against tissue specific cell types. We were also able to confirm our cell type annotations across shared cell types. We further validated these annotations using publicly available human scRNA-seq datasets specific for each corresponding porcine immune tissue. We compared expression profiles between similarly annotated cell types between human and pig, and identified cells with expression profiles that were unique to pig immune tissues. Our single cell-level transcriptomic study of immune tissues will be an important resource for improved annotation of porcine immune genes and cell types, including providing information for directed development of immune reagents to distinguish these cell types. These data can be compared to human single cell transcriptomes to inform human translational biomedical research using pigs as a biomedical model.