{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T15:02:47Z","timestamp":1791558167615,"version":"4.3.4"},"reference-count":92,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T00:00:00Z","timestamp":1772582400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3389\/fimmu.2026.1704257","type":"journal-article","created":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T05:41:29Z","timestamp":1772602889000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["A single-cell immune atlas of primary and secondary lymphoid organs in pigs"],"prefix":"10.3389","volume":"17","author":[{"given":"Jayne E.","family":"Wiarda","sequence":"first","affiliation":[{"name":"Virus and Prion Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture","place":["Ames, IA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muskan","family":"Kapoor","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Iowa State University","place":["Ames, IA, United States"]},{"name":"Bioinformatics and Computational Biology Graduate Program, Iowa State University","place":["Ames, IA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sathesh K.","family":"Sivasankaran","sequence":"additional","affiliation":[{"name":"Genome Informatics Facility, Iowa State University","place":["Ames, IA, United States"]},{"name":"Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture","place":["Ames, IA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristen A.","family":"Byrne","sequence":"additional","affiliation":[{"name":"Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture","place":["Ames, IA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crystal L.","family":"Loving","sequence":"additional","affiliation":[{"name":"Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture","place":["Ames, IA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher K.","family":"Tuggle","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Iowa State University","place":["Ames, IA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,3,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.imlet.2007.06.009","article-title":"Plasticity and heterogeneity of lymphoid organs: What are the criteria to call a lymphoid organ primary, secondary or tertiary","volume":"112","author":"Pabst","year":"2007","journal-title":"Immunol Lett"},{"key":"B2","unstructured":"2023"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abd5758","article-title":"Importance of the pig as a human biomedical model","volume":"13","author":"Lunney","year":"2021","journal-title":"Sci Trans Med"},{"key":"B4","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.molimm.2021.04.004","article-title":"Swine as biomedical animal model for T-cell research\u2014Success and potential for transmitta ble and non-transmitta ble human diseases","volume":"135","author":"K\u00e4ser","year":"2021","journal-title":"Mol Immunol"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.689406","article-title":"Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing","volume":"12","author":"Herrera-Uribe","year":"2021","journal-title":"Front Genet"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.01651","article-title":"The veterinary immunological toolbox: past, present, and future","author":"Entrican","year":"2020","journal-title":"Front Immunol"},{"key":"B7","doi-asserted-by":"publisher","first-page":"giaa051","DOI":"10.1093\/gigascience\/giaa051","article-title":"An improved pig reference genome sequence to enable pig genetics and genomics research","volume":"9","author":"Warr","year":"2020","journal-title":"GigaScience"},{"key":"B8","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1186\/s12864-019-5709-y","article-title":"Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data","volume":"20","author":"Beiki","year":"2019","journal-title":"BMC Genomics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"3620","DOI":"10.1038\/s41467-022-31388-z","article-title":"Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level","volume":"13","author":"Wang","year":"2022","journal-title":"Nat Commun"},{"key":"B10","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s12863-025-01308-3","article-title":"A dataset of single-cell transcriptomic atlas of Bama pig and potential marker genes across seven tissues","volume":"26","author":"Chen","year":"2025","journal-title":"BMC Genomic Data"},{"key":"B11","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1038\/s41597-025-04957-2","article-title":"Single cell transcriptome profiling of immune tissues from germ-free and specific pathogen-free piglet","volume":"12","author":"Zhang","year":"2025","journal-title":"Sci Data"},{"key":"B12","doi-asserted-by":"publisher","first-page":"111050","DOI":"10.1016\/j.celrep.2022.111050","article-title":"A single-cell analysis of thymopoiesis and thymic iNKT cell development in pigs","volume":"40","author":"Gu","year":"2022","journal-title":"Cell Rep"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1016\/j.mucimm.2024.08.005","article-title":"Conserved B cell signaling, activation, and differentiation in porcine jejunal and ileal Peyer\u2019s patches despite distinct immune landscapes","volume":"17","author":"Wiarda","year":"2024","journal-title":"Mucosal Immunol"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.202201442","article-title":"Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells","volume":"5","author":"Wiarda","year":"2022","journal-title":"Life Sci Alliance"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1101\/2025.06.13.659514","article-title":"Porcine epidemic diarrhea virus infection promotes Peyer\u2019s patch immune induction and epithelial defense via single-cell transcriptional reprogramming","author":"Wiarda","year":"2025","journal-title":"bioRxiv"},{"key":"B16","doi-asserted-by":"publisher","first-page":"e2312150121","DOI":"10.1073\/pnas.2312150121","article-title":"Single-cell profiling of African swine fever virus disease in the pig spleen reveals viral and host dynamics","volume":"121","author":"Zhu","year":"2024","journal-title":"Proc Natl Acad Sci"},{"key":"B17","doi-asserted-by":"publisher","first-page":"692","DOI":"10.3390\/cells13080692","article-title":"Single-cell RNA-sequencing reveals heterogeneity and transcriptional dynamics in porcine circulating CD8+ T cells","volume":"13","author":"Han","year":"2024","journal-title":"Cells"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1007\/s13258-023-01456-9","article-title":"Single-cell transcriptomic analysis reveals transcriptional and cell subpopulation differences between human and pig immune cells","volume":"46","author":"Li","year":"2024","journal-title":"Genes Genomics"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1113","article-title":"Ensembl 2019","volume":"47","author":"Cunningham","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"B20","doi-asserted-by":"publisher","first-page":"giaa151","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"GigaScience"},{"key":"B21","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: computational identification of cell doublets in single-cell transcriptomic data","volume":"8","author":"Wolock","year":"2019","journal-title":"Cell Syst"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat Biotechnol"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1093\/jas\/skac318","article-title":"Regional epithelial cell diversity in the small intestine of pigs","volume":"101","author":"Wiarda","year":"2022","journal-title":"J Anim Sci"},{"key":"B25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1906-x","article-title":"scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation","volume":"21","author":"Madissoon","year":"2019","journal-title":"Genome Biol"},{"key":"B26","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat Commun"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1038\/s41422-020-0353-2","article-title":"Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly","volume":"30","author":"Ren","year":"2020","journal-title":"Cell Res"},{"key":"B28","unstructured":"Chang\n              W\n            \n            \n              Cheng\n              J\n            \n            \n              Allaire\n              JJ\n            \n            \n              Sievert\n              C\n            \n            \n              Scholoerke\n              B\n            \n            \n              Xie\n              Y\n            \n          \n          shiny: Web application framework for R\n          \n          2025"},{"key":"B29","doi-asserted-by":"publisher","first-page":"653253","DOI":"10.1101\/653253","article-title":"Presto scales Wilcoxon and auROC analyses to millions of observations","author":"Korsunsky","year":"2019","journal-title":"bioRxiv"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.01139","article-title":"Intraepithelial T cells diverge by intestinal location as pigs age","volume":"11","author":"Wiarda","year":"2020","journal-title":"Front Immunol"},{"key":"B31","doi-asserted-by":"publisher","first-page":"110865","DOI":"10.1016\/j.vetimm.2024.110865","article-title":"In situ staining with antibodies cross-reactive in pigs, cattle, and white-tailed deer facilitates understanding of biological tissue status and immunopathology","volume":"279","author":"Wiarda","year":"2025","journal-title":"Veterinary Immunol Immunopathology"},{"key":"B32","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1038\/nature25741","article-title":"Population snapshots predict early haematopoietic and erythroid hierarchies","volume":"555","author":"Tusi","year":"2018","journal-title":"Nature"},{"key":"B33","volume-title":"Tissue digestion for stromal cell and leukocyte isolation, in T-cell trafficking: methods and protocols","author":"Nayar","year":"2017"},{"key":"B34","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1186\/s13059-020-02048-6","article-title":"Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows","volume":"21","author":"Denisenko","year":"2020","journal-title":"Genome Biol"},{"key":"B35","doi-asserted-by":"publisher","first-page":"06.12.448210","DOI":"10.1101\/2021.06.12.448210","article-title":"Multimodal single-cell characterization of the human granulocyte lineage","volume":"2021","author":"Qi","year":"2021","journal-title":"bioRxiv"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-019-0420-3","article-title":"Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage","volume":"20","author":"Dress","year":"2019","journal-title":"Nat Immunol"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1016\/j.jot.2024.06.010","article-title":"Osteostaticytes: A novel osteoclast subset couples bone resorption and bone formation","volume":"47","author":"Wei","year":"2024","journal-title":"J Orthopaedic Translation"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1007\/s11914-021-00708-5","article-title":"The osteocyte transcriptome: discovering messages buried within bone","volume":"19","author":"Wee","year":"2021","journal-title":"Curr Osteoporosis Rep"},{"key":"B39","doi-asserted-by":"publisher","first-page":"e10631","DOI":"10.1002\/jbm4.10631","article-title":"Interspecies single-cell RNA-seq analysis reveals the novel trajectory of osteoclast differentiation and therapeutic targets","volume":"6","author":"Omata","year":"2022","journal-title":"JBMR Plus"},{"key":"B40","doi-asserted-by":"publisher","first-page":"23115","DOI":"10.1038\/srep23115","article-title":"Identification of early myeloid progenitors as immunosuppressive cells","volume":"6","author":"Pu","year":"2016","journal-title":"Sci Rep"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.11.013","article-title":"Transcriptional heterogeneity and lineage commitment in myeloid progenitors","volume":"163","author":"Paul","year":"2015","journal-title":"Cell"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1093\/jmcb\/mjy063","article-title":"Assembly of a parts list of the human mitotic cell cycle machinery","volume":"11","author":"Giotti","year":"2019","journal-title":"J Mol Cell Biol"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E19-01-0013","article-title":"Unbiased Boolean analysis of public gene expression data for cell cycle gene identification","volume":"30","author":"Dabydeen","year":"2019","journal-title":"Mol Biol Cell"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2025.1639553","article-title":"Unraveling porcine dendritic-cell diversity: welcome tDC and DC3","author":"Baillou","year":"2025","journal-title":"Front Immunol"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2020.02.034","article-title":"CD163 expression defines specific, IRF8-dependent, immune-modulatory macrophages in the bone marrow","volume":"146","author":"Fischer-Riepe","year":"2020","journal-title":"J Allergy Clin Immunol"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2022.01.003","article-title":"Unraveling B cell trajectories at single cell resolution","volume":"43","author":"Morgan","year":"2022","journal-title":"Trends Immunol"},{"key":"B47","doi-asserted-by":"publisher","first-page":"117693510700300004","DOI":"10.1177\/117693510700300004","article-title":"Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): analysis of molecular predictors, signatures, cell cycle state and patient survival","volume":"3","author":"Blenk","year":"2007","journal-title":"Cancer Inf"},{"key":"B48","doi-asserted-by":"publisher","first-page":"10836","DOI":"10.1038\/ncomms10836","article-title":"EAF2 mediates germinal centre B-cell apoptosis to suppress excessive immune responses and prevent autoimmunity","volume":"7","author":"Li","year":"2016","journal-title":"Nat Commun"},{"key":"B49","doi-asserted-by":"publisher","first-page":"112512","DOI":"10.1016\/j.celrep.2023.112512","article-title":"STAT3 signaling in B cells controls germinal center zone organization and recycling","volume":"42","author":"Fike","year":"2023","journal-title":"Cell Rep"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.03.016","article-title":"B cell responses: cell interaction dynamics and decisions","volume":"177","author":"Cyster","year":"2019","journal-title":"Cell"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1016\/S0002-9440(10)63637-1","article-title":"Two newly characterized germinal center B-cell-associated genes, GCET1 and GCET2, have differential expression in normal and neoplastic B cells","volume":"163","author":"Pan","year":"2003","journal-title":"Am J Pathol"},{"key":"B52","doi-asserted-by":"publisher","first-page":"151421","DOI":"10.1016\/j.anndiagpath.2019.151421","article-title":"The life and death of the germinal center","volume":"44","author":"Gars","year":"2020","journal-title":"Ann Diagn Pathol"},{"key":"B53","doi-asserted-by":"publisher","first-page":"3013","DOI":"10.1038\/s41467-020-16828-y","article-title":"An Erg-driven transcriptional program controls B cell lymphopoiesis","volume":"11","author":"Ng","year":"2020","journal-title":"Nat Commun"},{"key":"B54","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1016\/j.stemcr.2017.02.009","article-title":"Latexin inactivation enhances survival and long-term engraftment of hematopoietic stem cells and expands the entire hematopoietic system in mice","volume":"8","author":"Liu","year":"2017","journal-title":"Stem Cell Rep"},{"key":"B55","doi-asserted-by":"publisher","first-page":"6843","DOI":"10.1038\/s41467-021-27232-5","article-title":"Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation","volume":"12","author":"Lee","year":"2021","journal-title":"Nat Commun"},{"key":"B56","doi-asserted-by":"publisher","first-page":"109626","DOI":"10.1016\/j.celrep.2021.109626","article-title":"Mutant U2AF1-induced alternative splicing of H2afy (macroH2A1) regulates B-lymphopoiesis in mice","volume":"36","author":"Kim","year":"2021","journal-title":"Cell Rep"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2024.01.006","article-title":"Gut-associated lymphoid tissue: a microbiota-driven hub of B cell immunity","volume":"45","author":"Bemark","year":"2024","journal-title":"Trends Immunol"},{"key":"B58","doi-asserted-by":"publisher","first-page":"7784","DOI":"10.1038\/s41467-024-51767-y","article-title":"Unraveling the spatial organization and development of human thymocytes through integration of spatial transcriptomics and single-cell multi-omics profiling","volume":"15","author":"Li","year":"2024","journal-title":"Nat Commun"},{"key":"B59","doi-asserted-by":"publisher","first-page":"4706","DOI":"10.1038\/s41467-019-12464-3","article-title":"Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease","volume":"10","author":"Szabo","year":"2019","journal-title":"Nat Commun"},{"key":"B60","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.3390\/vaccines9101171","article-title":"Kr\u00fcppel-like factor 2 (KLF2) in immune cell migration","volume":"9","author":"Wittner","year":"2021","journal-title":"Vaccines"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.165.9.5069","article-title":"The role of thymus-expressed chemokine and its receptor CCR9 on lymphocytes in the regional specialization of the mucosal immune system1","volume":"165","author":"Papadakis","year":"2000","journal-title":"J Immunol"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1038\/nri1781","article-title":"Journey through the thymus: stromal guides for T-cell development and selection","volume":"6","author":"Takahama","year":"2006","journal-title":"Nat Rev Immunol"},{"key":"B63","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/s41421-020-00238-x","article-title":"Cross-species single-cell transcriptomic analysis reveals pre-gastrulation developmental differences among pigs, monkeys, and humans","volume":"7","author":"Liu","year":"2021","journal-title":"Cell Discov"},{"key":"B64","doi-asserted-by":"publisher","first-page":"1478","DOI":"10.1038\/s42003-024-07163-9","article-title":"Single-cell transcriptomic and cross-species comparison analyses reveal distinct molecular changes of porcine testes during puberty","volume":"7","author":"Wang","year":"2024","journal-title":"Commun Biol"},{"key":"B65","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1186\/s13567-024-01418-3","article-title":"Developmental patterns of intestinal group 3 innate lymphoid cells in piglets and their response to enterotoxigenic Escherichia coli infection","volume":"55","author":"Huang","year":"2024","journal-title":"Veterinary Res"},{"key":"B66","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.767530","article-title":"The natural cytotoxicity receptor NKp44 (NCR2, CD336) is expressed on the majority of porcine NK cells ex vivo without stimulation","volume":"13","author":"Mair","year":"2022","journal-title":"Front Immunol"},{"key":"B67","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.2300463","article-title":"Single-cell transcriptional analysis of lamina propria lymphocytes in the jejunum reveals innate lymphoid cell\u2013like cells in pigs","volume":"212","author":"Wang","year":"2023","journal-title":"J Immunol"},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.1048708","article-title":"Intraepithelial lymphocytes in the pig intestine: T cell and innate lymphoid cell contributions to intestinal barrier immunity","volume":"13","author":"Wiarda","year":"2022","journal-title":"Front Immunol"},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3482","article-title":"NK cells and type 1 innate lymphoid cells: partners in host defense","volume":"17","author":"Spits","year":"2016","journal-title":"Nat Immunol"},{"key":"B70","doi-asserted-by":"crossref","DOI":"10.1007\/978-981-10-5987-2_11","article-title":"The development and diversity of ILCs, NK cells and their relevance in health and diseases","volume-title":"Regulation of inflammatory signaling in health and disease","author":"Zhang","year":"2017"},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2020.08.009","article-title":"Tissue-specific features of innate lymphoid cells","volume":"41","author":"Meininger","year":"2020","journal-title":"Trends Immunol"},{"key":"B72","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.cytogfr.2022.07.003","article-title":"Revisiting PD-1\/PD-L pathway in T and B cell response: Beyond immunosuppression","volume":"67","author":"Lu","year":"2022","journal-title":"Cytokine Growth Factor Rev"},{"key":"B73","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1016\/j.it.2024.07.005","article-title":"BCR signaling in germinal center B cell selection","volume":"45","author":"Inoue","year":"2024","journal-title":"Trends Immunol"},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.1164\/ajrccm.162.supplement_3.15tac5","article-title":"Costimulation of T cells","volume":"162","author":"Bugeon","year":"2000","journal-title":"Am J Respir Crit Care Med"},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.02469","article-title":"Regulation of the germinal center response","volume":"9","author":"Stebegg","year":"2018","journal-title":"Front Immunol"},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.01858","article-title":"Synaptic interactions in germinal centers","volume":"9","author":"Papa","year":"2018","journal-title":"Front Immunol"},{"key":"B77","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1046\/j.1365-2567.1996.d01-705.x","article-title":"Phenotypic classification of porcine lymphocyte subpopulations in blood and lymphoid tissues","volume":"89","author":"Yang","year":"1996","journal-title":"Immunology"},{"key":"B78","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.dci.2014.02.008","article-title":"CD2 and CD8\u03b1 define porcine \u03b3\u03b4 T cells with distinct cytokine production profiles","volume":"45","author":"Sedlak","year":"2014","journal-title":"Dev Comp Immunol"},{"key":"B79","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1101879","article-title":"Ileal peyer\u2019s patches are not necessary for systemic B cell development and maintenance and do not contribute significantly to the overall B cell pool in swine","volume":"187","author":"Sinkora","year":"2011","journal-title":"J Immunol"},{"key":"B80","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201141989","article-title":"NKp46 expression discriminates porcine NK cells with different functional properties","volume":"42","author":"Mair","year":"2012","journal-title":"Eur J Immunol"},{"key":"B81","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1297-9716-44-13","article-title":"Porcine CD8\u03b1dim\/-NKp46high NK cells are in a highly activated state","volume":"44","author":"Mair","year":"2013","journal-title":"Veterinary Res"},{"key":"B82","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.00953","article-title":"Macrophage-B cell interactions in the inverted porcine lymph node and their response to porcine reproductive and respiratory syndrome virus","volume":"10","author":"Bordet","year":"2019","journal-title":"Front Immunol"},{"key":"B83","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4615-9017-0_13","article-title":"Lymph node function and lymphocyte circulation in the pig","volume-title":"Adv Exp Med Biol.","author":"McFarlin","year":"1973"},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.a.24777","article-title":"Impact of enzymatic digestion on single cell suspension yield from peripheral human lung tissue","volume":"103","author":"Bondonese","year":"2023","journal-title":"Cytometry Part A"},{"key":"B85","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.663487","article-title":"Cryopreservation preserves cell-type composition and gene expression profiles in bone marrow aspirates from multiple myeloma patients","author":"Chen","year":"2021","journal-title":"Front Genet"},{"key":"B86","doi-asserted-by":"publisher","DOI":"10.1016\/j.tplants.2024.03.010","article-title":"Lost in space: what single-cell RNA sequencing cannot tell you","volume":"29","author":"Adema","year":"2024","journal-title":"Trends Plant Sci"},{"key":"B87","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s41592-020-01033-y","article-title":"Method of the Year: spatially resolved transcriptomics","volume":"18","author":"Marx","year":"2021","journal-title":"Nat Methods"},{"key":"B88","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-08338-4","article-title":"The Human Cell Atlas from a cell census to a unified foundation model","volume":"637","author":"Rood","year":"2025","journal-title":"Nature"},{"key":"B89","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1146\/annurev-animal-020518-114913","article-title":"Functional annotation of animal genomes (FAANG): current achievements and roadma","volume":"7","author":"Giuffra","year":"2019","journal-title":"Annu Rev Anim Biosci"},{"key":"B90","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002820","article-title":"Chapter 5: network biology approach to complex diseases","volume":"8","author":"Cho","year":"2012","journal-title":"PloS Comput Biol"},{"key":"B91","doi-asserted-by":"publisher","DOI":"10.1038\/ni.2787","article-title":"Unifying immunology with informatics and multiscale biology","volume":"15","author":"Kidd","year":"2014","journal-title":"Nat Immunol"},{"key":"B92","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat Methods"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1704257\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T05:41:35Z","timestamp":1772602895000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1704257\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,4]]},"references-count":92,"alternative-id":["10.3389\/fimmu.2026.1704257"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1704257","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.09.11.675613","asserted-by":"object"}]},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,4]]},"article-number":"1704257"}}