{"doi":"10.1038/s42003-025-08507-9","title":"Single-cell antigen receptor sequencing in pigs with influenza","abstract":"Single-cell RNA sequencing (scRNAseq) has accelerated characterizing cellular phenotypes in pigs under healthy and diseased conditions. To pair scRNAseq with immune receptor profiling, we developed porcine-specific T cell receptor (TCR) and B cell receptor (BCR) enrichment primers that are compatible with the 10 × Genomics VDJ sequencing protocol. Using these assays, we profiled the immune repertoire of cryopreserved lung cells from CD1D-expressing and CD1D-deficient pigs after one or two infections with influenza A virus (IAV) to examine whether natural killer T (NKT) cells influence pulmonary TCR and BCR receptor repertoires. We also profiled T cells longitudinally sampled from the lung fluid of IAV-vaccinated and -infected pigs to track clonal expansion. While all pigs presented highly diverse repertoires, pigs re-exposed to IAV had more expanded T cell clonotypes with activated phenotypes, suggesting potential IAV-reactive clones. Our results demonstrate the utility of high throughput single cell TCR and BCR sequencing in pigs. We developed porcine-specific primers for TCR and BCR, enabling paired single-cell RNA and receptor sequencing of pig T and B cells. Using this assay, we tracked treatment-induced changes in TCR and BCR repertoires in pig lung tissue.","journal":"Communications Biology","year":2025,"id":514835,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9173,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1271638,"name":"Darling Melany de Carvahlo Madrid","orcid":null,"position":1,"is_corresponding":false},{"id":1378238,"name":"Yuhan Wen","orcid":"0000-0002-8137-7218","position":2,"is_corresponding":false},{"id":1147275,"name":"Sadie Clements","orcid":null,"position":3,"is_corresponding":false},{"id":1269017,"name":"Laurie Touchard","orcid":null,"position":4,"is_corresponding":false},{"id":258516,"name":"Nathan J. Bivens","orcid":"0000-0002-6023-8729","position":5,"is_corresponding":false},{"id":388398,"name":"Grant M. Zane","orcid":"0000-0002-3357-3097","position":6,"is_corresponding":false},{"id":1355107,"name":"Mingyi Zhou","orcid":"0000-0002-4696-6586","position":7,"is_corresponding":false},{"id":1268572,"name":"Kiho Lee","orcid":"0000-0003-1548-0513","position":8,"is_corresponding":false},{"id":397274,"name":"John P. Driver","orcid":"0000-0002-6714-3335","position":9,"is_corresponding":false},{"id":1146846,"name":"Weihong Gu","orcid":"0000-0002-0111-9949","position":0,"is_corresponding":true}],"reference_count":64,"raw_metadata":null,"created_at":"2026-07-19T02:48:34.431522Z","pmid":"40715353","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}