A single-cell immune atlas of primary and secondary lymphoid organs in pigs

Authors: Wiarda, Jayne; KAPOOR, MUSKAN - Iowa State University; SIVASANKARAN, SATHESH - Oak Ridge Institute For Science And Education (ORISE); Byrne, Kristen; Loving, Crystal; TUGGLE, CHRISTOPHER - Iowa State University

Submitted to: Frontiers in Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/12/2026
Publication Date: 3/4/2026
Citation: Wiarda, J.E., Kapoor, M., Sivasankaran, S.K., Byrne, K.A., Loving, C.L., Tuggle, C.K. 2026. A single-cell immune atlas of primary and secondary lymphoid organs in pigs. Frontiers in Immunology. https://doi.org/10.3389/fimmu.2026.1704257.
DOI: https://doi.org/10.3389/fimmu.2026.1704257

Interpretive Summary: Understanding how the pig immune system functions is critical for developing novel strategies that target immunity to promote animal health, such as vaccinations, drugs, antibiotics, feed additives, or genetic selection. Despite the need to understand pig immunity, the ability to study unique immune cells in pigs has been limited until development of a recent technology called single-cell RNA sequencing (scRNA-seq), which allows us to study gene expression across thousands of immune cells in order to pinpoint cellular identities and functions. Using scRNA-seq, we were able to identify nearly 50,000 immune cells recovered from important immune tissues in pigs. Results indicated many cells have unique functions based on the tissue they are located in, and many immune cells are also highly similar to those identified in humans. As part of this work, we developed an online tool where individuals can investigate patterns of gene expression in the nearly 50,000 recovered cells, thus providing an open-access resource that can be utilized to understand pig immunity for downstream applications. Findings can be utilized as a much-needed knowledge base for developing strategies that target various immune cell populations to promote pig health for United States pork producers, thus solidifying pork as a reliable and safe food source for United States consumers.

Technical Abstract: Single-cell RNA sequencing (scRNA-seq) has revolutionized understandings of cellular identities and functions due to the ability to study transcriptome-wide gene expression within individual cells. Multi-tissue scRNA-seq atlases have generated holistic understandings of body-wide cell dynamics and serve as key foundational resources for further scientific studies across a variety of species. Pigs are a valuable biomedical model, and pork is an essential global food source, but minimal understanding of immune cell identities and functions across anatomical locations limits agricultural and health advancements in pigs. To address current limitations, we apply scRNA-seq to create an atlas of immune cells recovered from key immune tissues including primary lymphoid organs (bone marrow and thymus) and secondary lymphoid organs (lymph node and spleen). Thymus data was compared to a previously published scRNA-seq dataset of pig thymus and shared a general consensus while also identifying several new thymic cell populations. Comparison of spleen to a human splenic scRNA-seq dataset also revealed conserved features, including two subsets of innate lymphoid cells conserved between pigs and humans. Spatial reconstruction of lymph node structure from scRNA-seq data revealed follicular organization with similar cell type distributions and cell signaling interactions to those in human lymph nodes. To expand accessibility of the scRNA-seq atlas for biological query, we deploy an interactive application and demonstrate its use for non-computational exploration of diverse monocyte/macrophage populations recovered from bone marrow. Overall, results expand current foundational understandings of immune cell identities and functions in pig lymphoid organs and demonstrate pig-to-human immune similarities to consider for future research applications. Materials associated with this work are made readily accessible for others to investigate individual queries requiring foundational knowledge pertaining to pig immunity.