{"doi":"10.1084/jem.20200650","title":"Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire","abstract":"Tracking how individual naive T cells from a natural TCR repertoire clonally expand, differentiate, and make lineage choices in response to an infection has not previously been possible. Here, using single-cell sequencing technology to identify clones by their unique TCR sequences, we were able to trace the clonal expansion, differentiation trajectory, and lineage commitment of individual virus-specific CD4 T cells during an acute lymphocytic choriomeningitis virus (LCMV) infection. Notably, we found previously unappreciated clonal diversity and cellular heterogeneity among virus-specific helper T cells. Interestingly, although most naive CD4 T cells gave rise to multiple lineages at the clonal level, ∼28% of naive cells exhibited a preferred lineage choice toward either Th1 or TFH cells. Mechanistically, we found that TCR structure, in particular the CDR3 motif of the TCR α chain, skewed lineage decisions toward the TFH cell fate.","journal":"The Journal of Experimental Medicine","year":2020,"id":57860,"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":76,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9378,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":302501,"name":"Moujtaba Y. Kasmani","orcid":"0000-0002-5753-5335","position":1,"is_corresponding":false},{"id":302502,"name":"Ryan Zander","orcid":"0000-0002-7431-8535","position":2,"is_corresponding":false},{"id":302503,"name":"David Schauder","orcid":"0000-0001-7100-8294","position":3,"is_corresponding":false},{"id":302504,"name":"Jeremy P. Snook","orcid":"0000-0002-1396-9254","position":4,"is_corresponding":false},{"id":302505,"name":"Jian Shen","orcid":"0000-0001-8398-2318","position":5,"is_corresponding":false},{"id":303508,"name":"Xiaopeng Wu","orcid":null,"position":6,"is_corresponding":false},{"id":270587,"name":"Robert Burns","orcid":"0000-0001-5334-3486","position":7,"is_corresponding":false},{"id":302506,"name":"Yi-Guang Chen","orcid":"0000-0001-9616-8841","position":8,"is_corresponding":false},{"id":122195,"name":"Chien-Wei Lin","orcid":"0000-0003-4023-7339","position":9,"is_corresponding":false},{"id":52070,"name":"Matthew A. Williams","orcid":"0000-0002-4721-4482","position":10,"is_corresponding":false},{"id":302507,"name":"Weiguo Cui","orcid":"0000-0003-1562-9218","position":11,"is_corresponding":false},{"id":302500,"name":"Achia Khatun","orcid":"0000-0003-0525-4774","position":0,"is_corresponding":true}],"reference_count":59,"raw_metadata":null,"created_at":"2026-07-18T21:06:48.611399Z","pmid":"33201171","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":[]}