{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:51:28Z","timestamp":1787010688477,"version":"build-2736575974"},"posted":{"date-parts":[[2025,10,10]]},"group-title":"Immunology","reference-count":68,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T00:00:00Z","timestamp":1760054400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["AI129980."],"award-info":[{"award-number":["AI129980."]}],"id":[{"id":"https:\/\/ror.org\/001d55x84","id-type":"ROR","asserted-by":"publisher"}]},{"award":["0633005491"],"award-info":[{"award-number":["0633005491"]}],"id":[{"id":"https:\/\/ror.org\/01gavpb45","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Oregon Vetran"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Tuberculosis (TB) is the leading infectious disease killer worldwide and children suffer disproportionately. The ongoing burden of disease, despite widespread vaccination with BCG, highlights the need for novel vaccines. MR1-restricted T (MR1T) cells recognize small molecules, including microbial-derived molecules, presented by the monomorphic MHC class 1- related molecule (MR1). They have both \u201cinnate\u201d effector capacity, allowing them to quickly respond to pathogens including\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  (Mtb), while also having adaptive features (effector memory cell surface phenotype and selective TCR usage). Feasibility of an MR1T cell-based vaccination remains unexplored and critical to this is whether or not MR1T cells possess the capacity for immunological memory. To begin to address this question, peripheral blood mononuclear cells (PBMC) were collected at 9-weeks of age from healthy term- infants in South Africa, who had either received BCG vaccination at birth (n=10) or who had BCG vaccination delayed (n=10). MR1\/5-OP-RU tetramer positive cells were sorted using flow cytometry and single-cell RNA and TCR-seq was performed.\n                  <jats:italic>Ex-vivo<\/jats:italic>\n                  MR1T cells from vaccinated infants demonstrated increased expression of type I interferon response genes consistent with a cytokine mediated response to BCG vaccination. Using the TCR clustering algorithm TCRdist3, similar TCRs were grouped together, revealing a cluster significantly enriched in BCG-vaccinated infants. This cluster exhibited elevated expression of pro- inflammatory and cytotoxic genes, consistent with a recall response to prior vaccination and evidence of possible recognition of Mtb. This work provides the first step in addressing if MR1T cells demonstrate immunological memory, however, further work is needed to understand if these clonal expansions persist and possess the capacity for antigenic recall.\n                <\/jats:p>","DOI":"10.1101\/2025.10.09.681353","type":"posted-content","created":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:05:12Z","timestamp":1760137512000},"source":"Crossref","is-referenced-by-count":2,"title":["BCG Vaccination at Birth Shapes the TCR Usage and Functional Profile of MR1T Cells at 9 Weeks of Age"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5890-2742","authenticated-orcid":false,"given":"Dylan","family":"Kain","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"GW","family":"McElfresh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gwendolyn M.","family":"Swarbrick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Rott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"Boggy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerhard","family":"Walzl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nelita","family":"Du Plessis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Willem","family":"Hanekom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisa","family":"Nemes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muki","family":"Shey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0641-1359","authenticated-orcid":false,"given":"Thomas J.","family":"Scriba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8092-3080","authenticated-orcid":false,"given":"Benjamin N.","family":"Bimber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Lewinsohn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah A.","family":"Lewinsohn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025101405150612000_2025.10.09.681353v1.1","unstructured":"Larson, N . The World\u2019s Biggest Infectious Killer Regains Its Deadly Lead. Science Alerts. Accessed on July 3rd, 2024. <https:\/\/www.sciencealert.com\/the-worlds-biggest-infectious-killer-regains-its-deadly-lead>"},{"key":"2025101405150612000_2025.10.09.681353v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/nri.2017.69"},{"issue":"3","key":"2025101405150612000_2025.10.09.681353v1.3","first-page":"278","article-title":"The clinical epidemiology of childhood pulmonary tuberculosis: a critical review of literature from the pre-chemotherapy era","volume":"8","year":"2004","journal-title":"Int J Tuberc Lung Dis"},{"issue":"4","key":"2025101405150612000_2025.10.09.681353v1.4","first-page":"392","article-title":"The natural history of childhood intra-thoracic tuberculosis: a critical review of literature from the prechemotherapy era","volume":"8","year":"2004","journal-title":"Int J Tuberc Lung Dis"},{"issue":"7","key":"2025101405150612000_2025.10.09.681353v1.5","first-page":"732","article-title":"The spectrum of disease in children treated for tuberculosis in a highly endemic area","volume":"10","year":"2006","journal-title":"Int J Tuberc Lung Dis"},{"key":"2025101405150612000_2025.10.09.681353v1.6","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cit790"},{"issue":"1","key":"2025101405150612000_2025.10.09.681353v1.7","first-page":"195","article-title":"Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1","volume":"44","year":"2013","journal-title":"European Journal of Immunology"},{"key":"2025101405150612000_2025.10.09.681353v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/nature01700"},{"key":"2025101405150612000_2025.10.09.681353v1.9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1000054"},{"key":"2025101405150612000_2025.10.09.681353v1.10","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20130958"},{"key":"2025101405150612000_2025.10.09.681353v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4866"},{"key":"2025101405150612000_2025.10.09.681353v1.12","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2011-05-353789"},{"key":"2025101405150612000_2025.10.09.681353v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2014.09.045"},{"key":"2025101405150612000_2025.10.09.681353v1.14","doi-asserted-by":"publisher","DOI":"10.1111\/imm.12461"},{"key":"2025101405150612000_2025.10.09.681353v1.15","doi-asserted-by":"crossref","first-page":"12506","DOI":"10.1038\/ncomms12506","article-title":"Human TRAV1-2-negative MR1-restricted T cells detect S. pyogenes and alternatives to MAIT riboflavin-based antigens","volume":"7","year":"2016","journal-title":"Nature communications"},{"key":"2025101405150612000_2025.10.09.681353v1.16","first-page":"5566995","article-title":"Postnatal Expansion, Maturation, and Functionality of MR1T Cells in Humans","volume":"11","year":"2020","journal-title":"Frontiers in Immunology"},{"key":"2025101405150612000_2025.10.09.681353v1.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2009.08.006"},{"key":"2025101405150612000_2025.10.09.681353v1.18","doi-asserted-by":"publisher","DOI":"10.1002\/eji.200939222"},{"key":"2025101405150612000_2025.10.09.681353v1.19","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20030050"},{"key":"2025101405150612000_2025.10.09.681353v1.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2015.01.014"},{"key":"2025101405150612000_2025.10.09.681353v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.molimm.2010.12.002"},{"key":"2025101405150612000_2025.10.09.681353v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/ni.1890"},{"issue":"1","key":"2025101405150612000_2025.10.09.681353v1.23","first-page":"195","article-title":"The evolution of mechanisms to produce phenotypic heterogeneity in microorganisms","volume":"13","year":"2022","journal-title":"Microorganisms"},{"key":"2025101405150612000_2025.10.09.681353v1.24","doi-asserted-by":"publisher","DOI":"10.1165\/rcmb.2017-0290OC"},{"issue":"9","key":"2025101405150612000_2025.10.09.681353v1.25","doi-asserted-by":"crossref","first-page":"3256","DOI":"10.1128\/IAI.00279-12","article-title":"Polyclonal Mucosa-Associated Invariant T Cells Have Unique Innate Functions in Bacterial Infection","volume":"80","year":"2012","journal-title":"Infection and Immunol"},{"key":"2025101405150612000_2025.10.09.681353v1.26","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s42003-019-0442-2","article-title":"TRAV1-2+ CD8+ T-cells including oligoconal expansions of MAIT cells are enriched in the airways in human tuberculosis","volume":"2","year":"2019","journal-title":"Common Biol"},{"key":"2025101405150612000_2025.10.09.681353v1.27","doi-asserted-by":"publisher","DOI":"10.1101\/2022.10.12.511825"},{"key":"2025101405150612000_2025.10.09.681353v1.28","doi-asserted-by":"publisher","DOI":"10.1038\/gene.2016.41"},{"issue":"12","key":"2025101405150612000_2025.10.09.681353v1.29","doi-asserted-by":"crossref","first-page":"e20230707","DOI":"10.1084\/jem.20230707","article-title":"CD8+ lymphocytes are critical for early control of tuberculosis in macaques","volume":"220","year":"2023","journal-title":"JEM"},{"key":"2025101405150612000_2025.10.09.681353v1.30","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20140507"},{"issue":"25","key":"2025101405150612000_2025.10.09.681353v1.31","doi-asserted-by":"crossref","first-page":"eaao2556","DOI":"10.1126\/sciimmunol.aao2556","article-title":"MR1 displays the microbial metabolome driving selective MR1-restricted T cell receptor usage","volume":"3","year":"2018","journal-title":"Science Immunology"},{"key":"2025101405150612000_2025.10.09.681353v1.32","doi-asserted-by":"crossref","first-page":"103839","DOI":"10.1016\/j.ebiom.2022.103839","article-title":"Effects of BCG vaccination on donor unrestricted T cells in two prospective cohort studies","volume":"76","year":"2022","journal-title":"eBioMedicine"},{"key":"2025101405150612000_2025.10.09.681353v1.33","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.68605"},{"issue":"5","key":"2025101405150612000_2025.10.09.681353v1.34","doi-asserted-by":"crossref","first-page":"100849","DOI":"10.1016\/j.xgen.2025.100849","article-title":"Enhanced interpretation of immune cell phenotype and function through a rhesus macaque single-cell atlas","volume":"5","year":"2025","journal-title":"Cell Genomics"},{"key":"2025101405150612000_2025.10.09.681353v1.35","doi-asserted-by":"crossref","unstructured":"Kain D , Awad W , McElfresh GW , et al. Human Neonatal MR1T Cells Have Diverse TCR Usage, are Less Cytotoxic and are Unable to Respond to Many Common Childhood Pathogens. BioRxiv. 2025.03.17.643805","DOI":"10.1101\/2025.03.17.643805"},{"key":"2025101405150612000_2025.10.09.681353v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1817-8"},{"key":"2025101405150612000_2025.10.09.681353v1.37","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/s42003-020-01288-3","article-title":"Multidimensional analysis reveal modulation of adaptive and innate immune subsets by tuberculosis vaccines","volume":"3","year":"2020","journal-title":"Communication Biology"},{"key":"2025101405150612000_2025.10.09.681353v1.38","doi-asserted-by":"crossref","first-page":"100313","DOI":"10.1016\/j.eclinm.2020.100313","article-title":"A phase 1b randomized study of the safety and immunological responses to vaccination with H4:IC31, H56:IC31, and BCG revaccination in Mycobacterium tuberculosis-uninfected adolescents in Cape Town, South Africa","volume":"21","year":"2020","journal-title":"eClinicalMedicine"},{"issue":"6","key":"2025101405150612000_2025.10.09.681353v1.39","first-page":"2249","article-title":"An essential role for interferon gamma in resistance to Mycobacterium tuberculosis infection","volume":"176","year":"1993","journal-title":"JEM"},{"issue":"6","key":"2025101405150612000_2025.10.09.681353v1.40","first-page":"571","article-title":"tumor necrosis factor-alpha is required in the protective immune response against Mycobacterium tuberculosis in mice","volume":"2","year":"1995","journal-title":"Immunity"},{"key":"2025101405150612000_2025.10.09.681353v1.41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.1.270"},{"key":"2025101405150612000_2025.10.09.681353v1.42","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20241571"},{"key":"2025101405150612000_2025.10.09.681353v1.43","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00989-2"},{"key":"2025101405150612000_2025.10.09.681353v1.44","doi-asserted-by":"crossref","first-page":"3143","DOI":"10.1038\/ncomms4143","article-title":"Acquisition of innate-like microbial reactivity in mucosal tissues during fetal MAIT-cell development","volume":"5","year":"2014","journal-title":"Nat Comms"},{"key":"2025101405150612000_2025.10.09.681353v1.45","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1900674"},{"key":"2025101405150612000_2025.10.09.681353v1.46","doi-asserted-by":"crossref","first-page":"13579","DOI":"10.1038\/s41598-020-70615-9","article-title":"Artificially induced MAIT cells inhibit M. bovis BCG but not M. tuberculosis during in vivo pulmonary infection","volume":"10","year":"2020","journal-title":"Science Reports"},{"key":"2025101405150612000_2025.10.09.681353v1.47","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1302799110"},{"key":"2025101405150612000_2025.10.09.681353v1.48","doi-asserted-by":"crossref","first-page":"2097","DOI":"10.3389\/fimmu.2020.02097","article-title":"MAIT Cells Display a Specific Response to Type 1 IFN Underlying the Adjuvant Effect of TLR7\/8 Ligands","volume":"11","year":"2020","journal-title":"Frontiers in Immunology"},{"key":"2025101405150612000_2025.10.09.681353v1.49","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20230037"},{"key":"2025101405150612000_2025.10.09.681353v1.50","doi-asserted-by":"crossref","first-page":"101096","DOI":"10.1016\/j.xcrm.2023.101096","article-title":"Blood transcriptional correlates of BCG-induces protection against tuberculosis in rhesus macaques","volume":"4","year":"2023","journal-title":"Cell Reports Medicine"},{"key":"2025101405150612000_2025.10.09.681353v1.51","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41385-020-0332-4","article-title":"MAIT cell-directed therapy of Mycobacterium tuberculosis infection","volume":"14","year":"2021","journal-title":"Mucosal Immunology"},{"key":"2025101405150612000_2025.10.09.681353v1.52","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1038\/s41385-021-00425-3","article-title":"Functional inactivation of pulmonary MAIT cells following 5-OPRU treatment of non-human primates","volume":"14","year":"2021","journal-title":"Mucosal Immunology"},{"issue":"102","key":"2025101405150612000_2025.10.09.681353v1.53","doi-asserted-by":"crossref","first-page":"eadp9841","DOI":"10.1126\/sciimmunol.adp9841","article-title":"MAIT cell plasticity enables functional adaptation that drives antibacterial immune protection","volume":"9","year":"2024","journal-title":"Science Immunology"},{"key":"2025101405150612000_2025.10.09.681353v1.54","doi-asserted-by":"publisher","DOI":"10.1126\/science.aax6624"},{"key":"2025101405150612000_2025.10.09.681353v1.55","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20140484"},{"issue":"9","key":"2025101405150612000_2025.10.09.681353v1.56","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1111\/imcb.12370","article-title":"The MAIT TCR\u03b2 chain contributed to discrimination of microbial ligand","volume":"98","year":"2020","journal-title":"Immunol Cell Biol"},{"key":"2025101405150612000_2025.10.09.681353v1.57","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1705759114"},{"key":"2025101405150612000_2025.10.09.681353v1.58","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.32532"},{"key":"2025101405150612000_2025.10.09.681353v1.59","doi-asserted-by":"publisher","DOI":"10.1038\/nature13160"},{"key":"2025101405150612000_2025.10.09.681353v1.60","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-1935-5"},{"key":"2025101405150612000_2025.10.09.681353v1.61","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac213"},{"issue":"2907","key":"2025101405150612000_2025.10.09.681353v1.62","first-page":"1","article-title":"Nuclei multiplexing with barcoded antibodies for single- nucleus genomics","volume":"10","year":"2019","journal-title":"Nature Communications"},{"issue":"4","key":"2025101405150612000_2025.10.09.681353v1.63","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors","volume":"8","year":"2019","journal-title":"Cell Syst"},{"key":"2025101405150612000_2025.10.09.681353v1.64","unstructured":"Seurat 4.3.0. Seurat \u2013 Guided Clustering Tutorial. Accessed June 30th, 2024 <https:\/\/satijalab.org\/seurat\/articles\/pbmc3k_tutorial.html>"},{"key":"2025101405150612000_2025.10.09.681353v1.65","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00989-2"},{"issue":"9","key":"2025101405150612000_2025.10.09.681353v1.66","first-page":"1","article-title":"and Zeileis A. kernlab \u2013 An S2 Package for Kernel Methods in R","volume":"11","year":"2024","journal-title":"Journal of Statistical Software"},{"key":"2025101405150612000_2025.10.09.681353v1.67","doi-asserted-by":"crossref","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","year":"2019","journal-title":"Scientific Reports"},{"key":"2025101405150612000_2025.10.09.681353v1.68","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1000407"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.10.09.681353","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:46:46Z","timestamp":1768470406000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.10.09.681353"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,10]]},"references-count":68,"URL":"https:\/\/doi.org\/10.1101\/2025.10.09.681353","relation":{},"subject":[],"published":{"date-parts":[[2025,10,10]]},"subtype":"preprint"}}