{"doi":"10.1101/2024.08.17.608295","title":"Tissue determinants of the human T cell receptor repertoire.","abstract":"98% of T cells reside in tissues, yet nearly all human T cell analyses are performed from peripheral blood. We single-cell sequenced 5.7 million T cells from ten donors' autologous blood and tonsils and sought to answer key questions about T cell receptor biology previously unanswerable by smaller-scale experiments. We identified distinct clonal expansions and distributions in blood compared to tonsils, with surprisingly low (1-7%) clonal sharing. These few shared clones exhibited divergent phenotypes across bodily sites. Analysis of antigen-specific CD8 T cells revealed location as a main determinant of frequency, phenotype, and immunodominance. Finally, diversity estimates from the tissue recalibrates current repertoire diversity estimates, and we provide a refined estimate of whole-body repertoire. Given the tissue-restricted nature of T cell phenotypes, functions, differentiation, and clonality revealed by this dataset, we conclude that tissue analyses are crucial for accurate repertoire analysis and monitoring changes after perturbing therapies.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":486306,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9288,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":887295,"name":"James Henderson","orcid":"0000-0003-3714-4799","position":1,"is_corresponding":false},{"id":1021085,"name":"Elizabeth Levendosky","orcid":"0000-0001-6230-1851","position":2,"is_corresponding":false},{"id":1330093,"name":"Sankalan Bhattacharyya","orcid":null,"position":3,"is_corresponding":false},{"id":678623,"name":"Jenna M. Kastenschmidt","orcid":"0000-0002-0067-5142","position":4,"is_corresponding":false},{"id":1021083,"name":"Andrew M. Sorn","orcid":"0000-0001-8660-1533","position":5,"is_corresponding":false},{"id":1021084,"name":"Mahina Tabassum Mitul","orcid":"0000-0002-5344-6810","position":6,"is_corresponding":false},{"id":1021875,"name":"Aviv I. Benchorin","orcid":null,"position":7,"is_corresponding":false},{"id":1330094,"name":"Kyle Batucal","orcid":null,"position":8,"is_corresponding":false},{"id":380224,"name":"Allyssa L. Daugherty","orcid":"0000-0001-8428-0422","position":9,"is_corresponding":false},{"id":249350,"name":"Samuel J. H. Murphy","orcid":"0000-0002-5694-3572","position":10,"is_corresponding":false},{"id":1329702,"name":"Chandrani Thakur","orcid":"0000-0003-2833-0610","position":11,"is_corresponding":false},{"id":1021087,"name":"Douglas K. Trask","orcid":"0000-0003-0550-442X","position":12,"is_corresponding":false},{"id":1021086,"name":"Gurpreet S. Ahuja","orcid":"0000-0002-3196-0819","position":13,"is_corresponding":false},{"id":1023938,"name":"Annie Moisan","orcid":"0000-0002-4944-4548","position":14,"is_corresponding":false},{"id":991131,"name":"Andreas Mayer","orcid":"0000-0002-6643-7622","position":15,"is_corresponding":false},{"id":818398,"name":"Naresha Saligrama","orcid":"0000-0003-2526-7150","position":16,"is_corresponding":false},{"id":228597,"name":"Lisa E. Wagar","orcid":"0000-0001-5980-3586","position":17,"is_corresponding":false},{"id":501722,"name":"Suhas Sureshchandra","orcid":"0000-0002-4141-8564","position":0,"is_corresponding":true}],"reference_count":87,"raw_metadata":null,"created_at":"2026-07-19T02:07:57.049469Z","pmid":"39229002","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":[]}