{"doi":"10.1101/2025.05.08.652962","title":"Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma","abstract":"Abstract Background T cells play a central role in host protection against respiratory pathogens, but a maladaptive T cell response can lead to pulmonary diseases. Defining the biology of protective versus pathogenic T cell responses in the lungs of humans will be critical to nominate novel approaches to improve respiratory health. Previous studies have examined T cells from the lungs captured via bronchoalveolar lavage (BAL), endobronchial brushings, or biopsies. However, whether these different approaches are capturing distinct T cell phenotypes and/or clonotypes remains unclear. Objective To evaluate and compare the transcriptional signatures of T cells isolated via BAL versus endobronchial brushings in healthy controls (HCs) and allergic asthmatics (AAs). Methods Flexible bronchoscopy was performed to obtain BAL and endobronchial brushings from 3 HC and 3 AA subjects. CD3+ T cells were sorted and single cell RNA- and T cell receptor (TCR)-sequencing was performed using the 10X Chromium platform. Unbiased clustering, differential gene expression analysis and TCR repertoire analysis was performed. Results Unbiased clustering analysis allowed us to define 7 CD8 and 6 CD4 T cell subsets. The most significant difference in T cell subsets abundance between AAs and HCs was the enrichment of CD4 T helper type 2 (Th2) cells when comparing endobronchial brush samples (OR=26.2, P=0.002), but not when examining BAL (OR=1.7, P=0.46), indicating differences in the T cell subsets captured from the BAL versus airway mucosa specimen processing. In further support of this observation, comparing the BAL and brush T cells across all subjects revealed an up-regulation of resident-memory T cell markers (i.e. ITGAE, CD69 ) in brush T cells versus BAL T cells in both CD4 and CD8 lineages. In contrast, BAL CD8 and CD4 T cells exhibited an enriched type I and II interferon signatures compared to brush T cells. Lastly, TCR repertoire analysis revealed that brush T cells contained dramatically expanded TCR clones. Expanded T cell clones from the brush expressed high levels of resident-memory markers, suggesting the airway mucosa is enriched for T RM cells with unique TCR specificity. Conclusions Sampling T cells via BAL versus airway brushings yielded distinct T cell phenotypes and clonotypes with important implications for future research in lung immunology.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":565960,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9526,"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":89090,"name":"Neal P. Smith","orcid":"0000-0003-1394-3158","position":1,"is_corresponding":false},{"id":1469459,"name":"Amandine Selle","orcid":"0000-0002-9057-8580","position":2,"is_corresponding":false},{"id":1371559,"name":"Roya Best","orcid":null,"position":3,"is_corresponding":false},{"id":1162077,"name":"Sidney Martin","orcid":null,"position":4,"is_corresponding":false},{"id":1469830,"name":"Elizabeth Tuttle","orcid":null,"position":5,"is_corresponding":false},{"id":531485,"name":"Morris Ling","orcid":"0000-0002-9657-8960","position":6,"is_corresponding":false},{"id":227570,"name":"Benjamin D. Medoff","orcid":"0000-0002-2558-0449","position":7,"is_corresponding":false},{"id":14837,"name":"Alexandra–Chloé Villani","orcid":"0000-0001-7461-0408","position":8,"is_corresponding":false},{"id":256462,"name":"Andrew D. Luster","orcid":"0000-0001-9679-7912","position":9,"is_corresponding":false},{"id":268518,"name":"Rod A. Rahimi","orcid":"0000-0002-7929-2899","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-19T02:56:32.546082Z","pmid":"40462898","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":[]}