Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells

Authors: Wiarda, Jayne; Trachsel, Julian; SIVASANKARAN, SATHESH - Iowa State University; TUGGLE, CHRISTOPHER - Iowa State University; Loving, Crystal

Submitted to: Life Science Alliance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2022
Publication Date: 8/22/2022
Citation: Wiarda, J.E., Trachsel, J.M., Sivasankaran, S.K., Tuggle, C.K., Loving, C.L. 2022. Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells. Life Science Alliance. 5(10). Article e202201442. https://doi.org/10.26508/lsa.202201442.
DOI: https://doi.org/10.26508/lsa.202201442

Interpretive Summary: Improving health and disease resilience in pigs is crucial for a safe and secure food supply. As gut health can have major impacts on overall health and disease susceptibility, gaining a detailed understanding of porcine gut immune cells and their functions is critical for improvement strategies. A relatively new technology known as single-cell RNA sequencing was used to obtain highly-detailed descriptions of the genes expressed in thousands of individual immune cells in the pig intestine. Identities and functions of immune cells were determined by assessing gene expression, location of cells in the different parts of the intestine, and making comparisons to mouse and human gut immune cells. Gene expression in pig gut immune cells was comparable to mouse and human, though several immune cell types not been previously described in pigs were discovered, and gene expression profiles of new cell types were used to create new laboratory methods for their identification in future research. A specific immune cell type [innate lymphoid cells (ILCs)] not previously described for pigs were characterized. Overall, the data serve as a highly valuable resource, providing detailed descriptions of immune cells in the pig intestinal tract and provide foundational baseline knowledge for research pertaining to improvement of pig gut health. Data will be publicly available to the international research community as a resource for further exploration.

Technical Abstract: Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will improve utility of pigs as a biomedical model for intestinal research and promote food security. Single-cell RNA sequencing (scRNA-seq) was performed to provide highly-resolved transcriptomic profiles of lymphocytes in porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine intestine, including SELLhi gd T cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single cell transcriptomes in ileum were compared to those in in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular CD4 ab T cells, and cycling T/ILCs were enriched in ileum with Peyer’s patches, while non-cycling gd T, CD8 ab T, and group 1 ILCs were enriched in ileum without Peyer’s patches. scRNA-seq findings were leveraged to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry and in situ staining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral porcine ILCs (corresponding to NK cells), but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to those identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.