ORIGINAL RESEARCH article
Front. Immunol.
Sec. Comparative Immunology
A single-cell immune atlas of primary and secondary lymphoid organs in pigs
Provisionally accepted
Jayne E Wiarda1*
Muskan Kapoor2
Sathesh K Sivasankaran1,2
Kristen Alicia Byrne1
Crystal L Loving1
Christopher K Tuggle2*- 1USDA-ARS National Animal Disease Center, Ames, United States
- 2Iowa State University of Science and Technology, Ames, United States
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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. Inference of lymph node cell interactions and proximities from scRNA-seq data resembled some features of follicular organization and conventional germinal center reaction processes. 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 cell 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.
Keywords: atlas4, cellannotation8, FAANG1, Immune3, lymphoid6, Pig5, scRNA-seq2, single-cel7
Received: 12 Sep 2025; Accepted: 12 Feb 2026.
Copyright: © 2026 Wiarda, Kapoor, Sivasankaran, Byrne, Loving and Tuggle. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Jayne E Wiarda
Christopher K Tuggle
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