{"doi":"10.1101/2025.05.06.652535","title":"Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis","abstract":"Abstract Assigning antigen specificity to T cell receptor (TCR) sequences is challenging due to the TCR repertoire’s diversity and the complexity of TCR:antigen recognition. We developed the P eptide- D riven I dentification of TCR s (PDI-TCR) assay that combines in vitro expansion of cells with peptide pools, bulk TCR sequencing, and statistical analysis to identify antigen-specific TCRs from human blood. A key feature of PDI-TCR is the ability to distinguish true antigen-specific TCR clonotypes from TCRs associated with unspecific bystander activation by comparing responses to non-overlapping peptide pools. We applied PDI-TCR to Tuberculosis (TB) patients, sampling blood at diagnosis and throughout treatment, and Mycobacterium tuberculosis (Mtb)-sensitized healthy individuals (IGRA+). We identified hundreds of Mtb-specific TCRs, as well as unspecific TCRs, and characterized their phenotype in each cohort by single-cell RNA sequencing ex vivo . Mtb-specific T cells were highly diverse, with short-lived effector phenotypes only present in TB at diagnosis, while memory phenotypes were maintained through treatment. In contrast, unspecific expanded T cells were more clonally restricted, had a cytotoxic phenotype, and were maintained throughout treatment. This showcases PDI-TCR as a powerful tool for identifying antigen-specific TCRs, which enables direct ex vivo identification and monitoring of antigen-specific T cells.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":557845,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9411,"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":1199451,"name":"Raphael Trevizani","orcid":"0000-0002-9029-5329","position":1,"is_corresponding":false},{"id":881263,"name":"Leila Y. Chihab","orcid":null,"position":2,"is_corresponding":false},{"id":639465,"name":"Ashu Chawla","orcid":null,"position":3,"is_corresponding":false},{"id":914167,"name":"Kai Fung","orcid":"0000-0001-6817-1541","position":4,"is_corresponding":false},{"id":19878,"name":"Jason Greenbaum","orcid":"0000-0002-1381-0390","position":5,"is_corresponding":false},{"id":811337,"name":"Kendall Kearns","orcid":"0000-0002-4633-4554","position":6,"is_corresponding":false},{"id":342843,"name":"Aruna Dharshan De Silva","orcid":"0000-0001-5291-9543","position":7,"is_corresponding":false},{"id":1442359,"name":"Wathsala Gunasinghe","orcid":"0000-0001-7861-5652","position":8,"is_corresponding":false},{"id":1043515,"name":"Judy Perera","orcid":null,"position":9,"is_corresponding":false},{"id":1458323,"name":"Hansani Gunasekera","orcid":null,"position":10,"is_corresponding":false},{"id":1442833,"name":"Darsha D. Senevirathne","orcid":null,"position":11,"is_corresponding":false},{"id":252307,"name":"Thomas J. Scriba","orcid":"0000-0002-0641-1359","position":12,"is_corresponding":false},{"id":55670,"name":"Alessandro Sette","orcid":"0000-0001-7013-2250","position":13,"is_corresponding":false},{"id":230241,"name":"Cecilia S. Lindestam Arlehamn","orcid":"0000-0001-7302-8002","position":14,"is_corresponding":false},{"id":471661,"name":"Julie G. Burel","orcid":"0000-0003-1692-2758","position":15,"is_corresponding":false},{"id":34766,"name":"Bjoern Peters","orcid":"0000-0002-8457-6693","position":16,"is_corresponding":false},{"id":919503,"name":"Rashmi Tippalagama","orcid":"0000-0001-6157-8592","position":0,"is_corresponding":true}],"reference_count":54,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:55:21.727661Z","pmid":"40654739","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":[]}