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Mapping scRNA-seq clusters from BAL onto those previously described in peripheral blood facilitated annotation and highlighted differences between tissue resident and circulating immune cells. ScRNA-seq data and functional assays revealed lasting impacts of immune challenge on BAL populations. First, mucosal administration of IL-1β reduced the number of functionally active Treg cells. Second, influenza infection upregulated IFI6 in BAL cells and decreased their susceptibility to virus replication <jats:italic>in vitro</jats:italic>. Our data provide a reference map of porcine BAL cells and reveal lasting immunological consequences of influenza infection and respiratory immunization in a highly relevant large animal model for respiratory virus infection.</jats:p>","journal":"PLOS Pathogens","year":2024,"id":641504,"datarank":0.4335557636844247,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"self_citation_contribution":0.4335557636844247,"citation_network_contribution":0.0,"self_endowment_contribution":0.4335557636844247,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":17,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":884961,"name":"Basudev Paudyal","orcid":"0000-0001-6068-019X","position":1,"is_corresponding":false},{"id":1668010,"name":"Selma Schmidt","orcid":null,"position":2,"is_corresponding":false},{"id":1668011,"name":"Ehsan Sedaghat-Rostami","orcid":null,"position":3,"is_corresponding":false},{"id":1668012,"name":"Soumendu Chakravarti","orcid":null,"position":4,"is_corresponding":false},{"id":1668013,"name":"Sonia Villanueva-Hernández","orcid":null,"position":5,"is_corresponding":false},{"id":1505976,"name":"Katy Moffat","orcid":null,"position":6,"is_corresponding":false},{"id":884958,"name":"Noemi Polo","orcid":"0000-0002-0470-2611","position":7,"is_corresponding":false},{"id":254701,"name":"Nicos Angelopoulos","orcid":"0000-0002-7507-9177","position":8,"is_corresponding":false},{"id":1429154,"name":"Anna Schmidt","orcid":null,"position":9,"is_corresponding":false},{"id":419674,"name":"Matthias Tenbusch","orcid":"0000-0003-3951-9056","position":10,"is_corresponding":false},{"id":884956,"name":"Graham Freimanis","orcid":"0000-0001-8186-2638","position":11,"is_corresponding":false},{"id":1668014,"name":"Wilhelm Gerner","orcid":"0000-0002-2431-5889","position":12,"is_corresponding":false},{"id":342498,"name":"Arianne C. 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Here, we employed single cell RNA-sequencing (scRNA-seq) and flow cytometry to characterize the major leukocyte subsets in bronchoalveolar lavage (BAL), twenty-one days after H1N1pdm09 infection or respiratory immunization with an adenoviral vector vaccine expressing hemagglutinin and nucleoprotein with or without IL-1β. Mapping scRNA-seq clusters from BAL onto those previously described in peripheral blood facilitated annotation and highlighted differences between tissue resident and circulating immune cells. ScRNA-seq data and functional assays revealed lasting impacts of immune challenge on BAL populations. First, mucosal administration of IL-1β reduced the number of functionally active Treg cells. Second, influenza infection upregulated IFI6 in BAL cells and decreased their susceptibility to virus replication <jats:italic>in vitro</jats:italic>. 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