{"doi":"10.1101/2021.03.25.436871","title":"Dual TCR-alpha expression on MAIT cells as a potential confounder of TCR interpretation","abstract":"Abstract Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant T cell receptor (TCR) α chain that uses TRAV1-2 joined to TRAJ33/20/12 and recognize metabolites from bacterial riboflavin synthesis bound to the antigen-presenting molecule, MR1. Recently, our attempts to identify alternative MR1-presented antigens led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered antigen specificity is likely to lead to altered affinity for the most potent known antigen, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), we performed bulk TCRα and β chain sequencing, and single cell-based paired TCR sequencing, on T cells that bound the MR1-5-OP-RU tetramer, but with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramer low cells. Whereas we initially interpreted these as diverse MR1-restricted TCRs, single cell TCR sequencing revealed that cells expressing atypical TCRα chains also co-expressed an invariant MAIT TCRα chain. Transfection of each non-TRAV1-2 TCRα chain with the TCRβ chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRα chain expression in human T cells and competition for the endogenous β chain explains the existence of some MR1-5-OP-RU tetramer low T cells. The discovery of simultaneous expression of canonical and non-canonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of antigen specificity.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":220415,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9579,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":499363,"name":"Lars Kjer‐Nielsen","orcid":"0000-0003-3215-2888","position":1,"is_corresponding":false},{"id":483813,"name":"Sarah K. Iwany","orcid":null,"position":2,"is_corresponding":false},{"id":500221,"name":"Kattya López Tamara","orcid":null,"position":3,"is_corresponding":false},{"id":300978,"name":"Liyen Loh","orcid":"0000-0002-1676-0579","position":4,"is_corresponding":false},{"id":819944,"name":"Ludivine Grzelak","orcid":"0000-0002-1298-7565","position":5,"is_corresponding":false},{"id":104934,"name":"Katherine Kedzierska","orcid":"0000-0001-6141-335X","position":6,"is_corresponding":false},{"id":312630,"name":"Tonatiuh A. Ocampo","orcid":"0000-0001-5443-9519","position":7,"is_corresponding":false},{"id":256184,"name":"Alexandra J. Corbett","orcid":"0000-0003-1618-4337","position":8,"is_corresponding":false},{"id":256187,"name":"James McCluskey","orcid":"0000-0002-8597-815X","position":9,"is_corresponding":false},{"id":256186,"name":"Jamie Rossjohn","orcid":"0000-0002-2020-7522","position":10,"is_corresponding":false},{"id":499365,"name":"Segundo R. León","orcid":"0000-0002-5630-5714","position":11,"is_corresponding":false},{"id":376970,"name":"Róger Calderón","orcid":"0000-0001-8932-0489","position":12,"is_corresponding":false},{"id":376976,"name":"Leonid Lecca","orcid":"0000-0003-1363-3985","position":13,"is_corresponding":false},{"id":231936,"name":"Megan Murray","orcid":"0000-0003-0443-1986","position":14,"is_corresponding":false},{"id":312635,"name":"D. Branch Moody","orcid":"0000-0003-2306-3058","position":15,"is_corresponding":false},{"id":252300,"name":"Ildiko Van Rhijn","orcid":"0000-0002-1446-5701","position":16,"is_corresponding":false},{"id":252291,"name":"Sara Suliman","orcid":"0000-0002-5154-576X","position":0,"is_corresponding":true}],"reference_count":78,"raw_metadata":null,"created_at":"2026-07-18T23:53:46.965811Z","pmid":null,"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":[]}