{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T07:29:41Z","timestamp":1789111781046,"version":"build-2803163510"},"posted":{"date-parts":[[2025,4,30]]},"group-title":"Infectious Diseases (except HIV\/AIDS)","reference-count":71,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,4,30]],"date-time":"2025-04-30T00:00:00Z","timestamp":1745971200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.medrxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,4,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Early delineation of host immune responses at the moment of\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  (Mtb) exposure and infection is critical to identify individuals at risk of progressing to active tuberculosis (TB). We performed single-cell transcriptional profiling of over 500,000 peripheral blood mononuclear cells from 57 HIV-negative close contacts of TB cases in Brazil, including 25 individuals who developed active disease within two years (progressors) and 32 matched controls who remained disease-free (non-progressors). Cells were stimulated separately with the MTB300 peptide pool or irradiated Mtb (gRV), enabling resolution of antigen-reactive states across adaptive (CD4\u207a T-cells expressing abundant cytokines including IFNG, TNF, and IL17F) and trained-innate lineages, such as NK cells (producing GM-CSF, IFNG, CCL3, CCL4) and monocytes (GM-CSF, IL12B, IL36G). Progressors exhibited early hyper-metabolic CD4\u207a T-cell programs and proliferative NK cell signatures, whereas non-progressors preferentially upregulated complement activation and CCL3\/4-driven chemokine signaling in monocytes. Notably, among progressors, gene expression profiles within antigen-reactive CD4\u207a T-cells and monocytes predicted the timing of progression to active TB. Together, these findings reveal high frequencies and functional diversity of antigen-reactive cells in Mtb-exposed individuals and nominate tractable immune correlates for the rational design of next-generation TB vaccines.\n                <\/jats:p>","DOI":"10.1101\/2025.04.29.25326433","type":"posted-content","created":{"date-parts":[[2025,4,30]],"date-time":"2025-04-30T23:00:10Z","timestamp":1746054010000},"source":"Crossref","is-referenced-by-count":2,"title":["Single-cell immune profiling at time of\n                  <i>M. tuberculosis<\/i>\n                  exposure reveals antigen-reactive programs that predict progression to active disease"],"prefix":"10.64898","author":[{"given":"Jonathan","family":"Pen\u00e3 Avila","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Simmons","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina C.","family":"Figueiredo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan","family":"Turner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcelo","family":"Cordeiro-Santos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeria C.","family":"Rolla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afranio L.","family":"Kristki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rama","family":"Gangula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cynthia","family":"Nochowicz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramesh","family":"Ram","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Bailin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Mallal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvana","family":"Gaudieri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Alves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beatriz Barreto","family":"Barreto-Duarte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Artur T. L.","family":"Queiroz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helder I.","family":"Nakaya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6833-3811","authenticated-orcid":false,"given":"Bruno B.","family":"Andrade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy R.","family":"Sterling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Spyros A.","family":"Kalams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"RePORT-Brazil Consortium","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025050304450439000_2025.04.29.25326433v1.1","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1800993"},{"key":"2025050304450439000_2025.04.29.25326433v1.2","doi-asserted-by":"crossref","unstructured":"Sia, J.K. & Rengarajan, J . Immunology of Mycobacterium tuberculosis Infections. Microbiol Spectr 7 (2019).","DOI":"10.1128\/microbiolspec.GPP3-0022-2018"},{"key":"2025050304450439000_2025.04.29.25326433v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nm.2299"},{"key":"2025050304450439000_2025.04.29.25326433v1.4","doi-asserted-by":"crossref","unstructured":"Mayer-Barber, K.D. & Barber, D.L . Innate and Adaptive Cellular Immune Responses to Mycobacterium tuberculosis Infection. Cold Spring Harbor perspectives in medicine 5 (2015).","DOI":"10.1101\/cshperspect.a018424"},{"key":"2025050304450439000_2025.04.29.25326433v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.06.004."},{"key":"2025050304450439000_2025.04.29.25326433v1.6","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.175.7.4611"},{"key":"2025050304450439000_2025.04.29.25326433v1.7","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.0902587"},{"key":"2025050304450439000_2025.04.29.25326433v1.8","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1111\/j.1365-2567.2005.02259.x","article-title":"NK cell activity in tuberculosis is associated with impaired CD11a and ICAM-1 expression: a regulatory role of monocytes in NK activation","volume":"116","year":"2005","journal-title":"Immunology"},{"key":"2025050304450439000_2025.04.29.25326433v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/mi.2016.105"},{"key":"2025050304450439000_2025.04.29.25326433v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2019.02.015"},{"key":"2025050304450439000_2025.04.29.25326433v1.11","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199201233260404"},{"key":"2025050304450439000_2025.04.29.25326433v1.12","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa011110"},{"key":"2025050304450439000_2025.04.29.25326433v1.13","unstructured":"Mazurek, G.H. et al. Updated guidelines for using Interferon Gamma Release Assays to detect Mycobacterium tuberculosis infection - United States, 2010. MMWR Recomm Rep 59, 1-25 (2010)."},{"key":"2025050304450439000_2025.04.29.25326433v1.14","doi-asserted-by":"crossref","unstructured":"Barreto-Duarte, B. et al. Increased Frequency of Memory CD4+ T-Cell Responses in Individuals With Previously Treated Extrapulmonary Tuberculosis. Frontiers in immunology 11 (2020).","DOI":"10.3389\/fimmu.2020.605338"},{"key":"2025050304450439000_2025.04.29.25326433v1.15","doi-asserted-by":"publisher","DOI":"10.1002\/1615-9861(200104)1:4<574::AID-PROT574>3.0.CO;2-8"},{"key":"2025050304450439000_2025.04.29.25326433v1.16","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1128\/iai.63.4.1491-1497.1995","article-title":"Human T-cell responses to secreted antigen fractions of Mycobacterium tuberculosis","volume":"63","year":"1995","journal-title":"Infection and immunity"},{"key":"2025050304450439000_2025.04.29.25326433v1.17","doi-asserted-by":"crossref","unstructured":"Arlehamn, C.S. et al. Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP10, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ). J Immunol 188, 5020-5031 (2012).","DOI":"10.4049\/jimmunol.1103556"},{"key":"2025050304450439000_2025.04.29.25326433v1.18","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1128\/CDLI.6.4.606-609.1999","article-title":"Cellular immune responses to ESAT-6 discriminate between patients with pulmonary disease due to Mycobacterium avium complex and those with pulmonary disease due to Mycobacterium tuberculosis","volume":"6","year":"1999","journal-title":"Clin Diagn Lab Immunol"},{"key":"2025050304450439000_2025.04.29.25326433v1.19","doi-asserted-by":"publisher","DOI":"10.1086\/314640"},{"key":"2025050304450439000_2025.04.29.25326433v1.20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.1.270"},{"key":"2025050304450439000_2025.04.29.25326433v1.21","doi-asserted-by":"publisher","DOI":"10.1086\/318081"},{"key":"2025050304450439000_2025.04.29.25326433v1.22","doi-asserted-by":"publisher","DOI":"10.1164\/ajrccm.163.4.2009100"},{"key":"2025050304450439000_2025.04.29.25326433v1.23","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.167.9.5217"},{"key":"2025050304450439000_2025.04.29.25326433v1.24","doi-asserted-by":"crossref","unstructured":"Ubolyam, S. et al. Performance of a simple flow cytometric assay in diagnosing active tuberculosis. Tuberculosis 126, 102017 (2021).","DOI":"10.1016\/j.tube.2020.102017"},{"key":"2025050304450439000_2025.04.29.25326433v1.25","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/s00430-018-00576-4","article-title":"Diagnostic performance in active TB of QFT-Plus assay and co-expression of CD25\/CD134 in response to new antigens of Mycobacterium tuberculosis","volume":"208","year":"2019","journal-title":"Med Microbiol Immunol"},{"key":"2025050304450439000_2025.04.29.25326433v1.26","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1401151"},{"key":"2025050304450439000_2025.04.29.25326433v1.27","doi-asserted-by":"crossref","unstructured":"Cai, Y. et al. Single-cell transcriptomics of blood reveals a natural killer cell subset depletion in tuberculosis. EBioMedicine 53, 102686 (2020).","DOI":"10.1016\/j.ebiom.2020.102686"},{"key":"2025050304450439000_2025.04.29.25326433v1.28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005760"},{"key":"2025050304450439000_2025.04.29.25326433v1.29","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.ijid.2020.11.140","article-title":"Novel stepwise approach to assess representativeness of a large multicenter observational cohort of tuberculosis patients: The example of RePORT Brazil","volume":"103","year":"2021","journal-title":"Int J Infect Dis"},{"key":"2025050304450439000_2025.04.29.25326433v1.30","doi-asserted-by":"crossref","unstructured":"Buttner, M. , Ostner, J. , Muller, C.L. , Theis, F.J. & Schubert, B . scCODA is a Bayesian model for compositional single-cell data analysis. Nature communications 12, 6876 (2021).","DOI":"10.1038\/s41467-021-27150-6"},{"key":"2025050304450439000_2025.04.29.25326433v1.31","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.172.1.130"},{"key":"2025050304450439000_2025.04.29.25326433v1.32","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.176.4.2610"},{"key":"2025050304450439000_2025.04.29.25326433v1.33","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.180.3.1729"},{"key":"2025050304450439000_2025.04.29.25326433v1.34","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2009-04-215491"},{"key":"2025050304450439000_2025.04.29.25326433v1.35","doi-asserted-by":"crossref","first-page":"e51329","DOI":"10.15252\/embr.202051329","article-title":"Phosphodiesterase 4A confers resistance to PGE2-mediated suppression in CD25(+) \/CD54(+) NK cells","volume":"22","year":"2021","journal-title":"EMBO Rep"},{"key":"2025050304450439000_2025.04.29.25326433v1.36","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2016-02-698027"},{"key":"2025050304450439000_2025.04.29.25326433v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/nri3803"},{"key":"2025050304450439000_2025.04.29.25326433v1.38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003130"},{"key":"2025050304450439000_2025.04.29.25326433v1.39","doi-asserted-by":"publisher","DOI":"10.1038\/ni1467"},{"key":"2025050304450439000_2025.04.29.25326433v1.40","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201243090"},{"key":"2025050304450439000_2025.04.29.25326433v1.41","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(94)90372-7"},{"key":"2025050304450439000_2025.04.29.25326433v1.42","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(01)00237-9"},{"key":"2025050304450439000_2025.04.29.25326433v1.43","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.170.10.5210"},{"key":"2025050304450439000_2025.04.29.25326433v1.44","doi-asserted-by":"crossref","first-page":"e277","DOI":"10.1371\/journal.pmed.0030277","article-title":"Mycobacterium tuberculosis induces interleukin-32 production through a caspase-1\/IL-18\/interferon-gamma-dependent mechanism","volume":"3","year":"2006","journal-title":"PLoS medicine"},{"key":"2025050304450439000_2025.04.29.25326433v1.45","doi-asserted-by":"publisher","DOI":"10.1016\/S1074-7613(04)00380-2"},{"key":"2025050304450439000_2025.04.29.25326433v1.46","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0712381105"},{"key":"2025050304450439000_2025.04.29.25326433v1.47","doi-asserted-by":"crossref","unstructured":"Netea, M.G. et al. Trained immunity: A program of innate immune memory in health and disease. Science 352, aaf1098 (2016).","DOI":"10.1126\/science.aaf1098"},{"key":"2025050304450439000_2025.04.29.25326433v1.48","doi-asserted-by":"publisher","DOI":"10.1172\/JCI128877"},{"key":"2025050304450439000_2025.04.29.25326433v1.49","doi-asserted-by":"crossref","unstructured":"Bailin, S.S. et al. Changes in subcutaneous white adipose tissue cellular composition and molecular programs underlie glucose intolerance in persons with HIV. Frontiers in immunology 14, 1152003 (2023).","DOI":"10.3389\/fimmu.2023.1152003"},{"key":"2025050304450439000_2025.04.29.25326433v1.50","unstructured":"Zheng, G.X. et al. Massively parallel digital transcriptional profiling of single cells. Nature communications 8, 14049 (2017)."},{"key":"2025050304450439000_2025.04.29.25326433v1.51","doi-asserted-by":"crossref","unstructured":"Alves, E. et al. Underrepresentation of activating KIR gene expression in single-cell RNA-seq data is due to KIR gene misassignment. European journal of immunology, e2350590 (2023).","DOI":"10.1002\/eji.202350590"},{"key":"2025050304450439000_2025.04.29.25326433v1.52","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/s41592-020-0820-1","article-title":"Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes","volume":"17","year":"2020","journal-title":"Nature methods"},{"key":"2025050304450439000_2025.04.29.25326433v1.53","doi-asserted-by":"crossref","unstructured":"Dill-McFarland, K.A. et al. Genome-wide association study in Brazil identifies genetic susceptibility to tuberculosis with single-cell gene expression effects. medRxiv (2025).","DOI":"10.1101\/2025.03.13.25323932"},{"key":"2025050304450439000_2025.04.29.25326433v1.54","doi-asserted-by":"crossref","unstructured":"Neavin, D. et al. Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods. Genome Biol 25, 94 (2024).","DOI":"10.1186\/s13059-024-03224-8"},{"key":"2025050304450439000_2025.04.29.25326433v1.55","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2020.05.010","article-title":"Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning","volume":"11","year":"2020","journal-title":"Cell Systems"},{"key":"2025050304450439000_2025.04.29.25326433v1.56","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01206-w"},{"key":"2025050304450439000_2025.04.29.25326433v1.57","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01733-8"},{"key":"2025050304450439000_2025.04.29.25326433v1.58","doi-asserted-by":"crossref","unstructured":"Linderman, G.C. , Zhao, J. & Kluger, Y . Zero-preserving imputation of scRNA-seq data using low-rank approximation. bioRxiv, 397588 (2018).","DOI":"10.1101\/397588"},{"key":"2025050304450439000_2025.04.29.25326433v1.59","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","year":"2019","journal-title":"Nature methods"},{"key":"2025050304450439000_2025.04.29.25326433v1.60","doi-asserted-by":"crossref","unstructured":"Traag, V.A. , Waltman, L. & van Eck, N.J . From Louvain to Leiden: guaranteeing well-connected communities. Scientific reports 9, 5233 (2019).","DOI":"10.1038\/s41598-019-41695-z"},{"key":"2025050304450439000_2025.04.29.25326433v1.61","doi-asserted-by":"crossref","unstructured":"Healy, J. & McInnes, L. Uniform manifold approximation and projection. Nature Reviews Methods Primers 4, 82 (2024).","DOI":"10.1038\/s43586-024-00363-x"},{"key":"2025050304450439000_2025.04.29.25326433v1.62","doi-asserted-by":"publisher","DOI":"10.1038\/S41587-023-01767-Y"},{"key":"2025050304450439000_2025.04.29.25326433v1.63","doi-asserted-by":"crossref","unstructured":"Chen, Y. , Chen, L. , Lun, Aaron T.L. , Baldoni, Pedro L. & Smyth, Gordon K . edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Research 53 (2025).","DOI":"10.1093\/nar\/gkaf018"},{"key":"2025050304450439000_2025.04.29.25326433v1.64","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007"},{"key":"2025050304450439000_2025.04.29.25326433v1.65","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks461"},{"key":"2025050304450439000_2025.04.29.25326433v1.66","unstructured":"Korotkevich, G. et al. Fast gene set enrichment analysis. bioRxiv, 060012 (2021)."},{"key":"2025050304450439000_2025.04.29.25326433v1.67","doi-asserted-by":"crossref","unstructured":"Milacic, M. et al. The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research 52, D672-D678 (2023).","DOI":"10.1093\/nar\/gkad1025"},{"key":"2025050304450439000_2025.04.29.25326433v1.68","doi-asserted-by":"crossref","unstructured":"Ulgen, E. , Ozisik, O. & Sezerman, O.U . pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front Genet 10, 858 (2019).","DOI":"10.3389\/fgene.2019.00858"},{"key":"2025050304450439000_2025.04.29.25326433v1.69","first-page":"D638","article-title":"The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","year":"2022","journal-title":"Nucleic Acids Research"},{"key":"2025050304450439000_2025.04.29.25326433v1.70","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.10602726"},{"key":"2025050304450439000_2025.04.29.25326433v1.71","doi-asserted-by":"crossref","unstructured":"Mule, M.P. , Martins, A.J. & Tsang, J.S . Normalizing and denoising protein expression data from droplet-based single cell profiling. Nature communications 13, 2099 (2022).","DOI":"10.1038\/s41467-022-29356-8"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.04.29.25326433","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T20:34:53Z","timestamp":1768509293000},"score":1,"resource":{"primary":{"URL":"http:\/\/medrxiv.org\/lookup\/doi\/10.1101\/2025.04.29.25326433"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,30]]},"references-count":71,"URL":"https:\/\/doi.org\/10.1101\/2025.04.29.25326433","relation":{"has-review":[{"id-type":"doi","id":"10.1162\/2e3983f5.5432efa9","asserted-by":"object"},{"id-type":"doi","id":"10.1162\/2e3983f5.40f57c94","asserted-by":"object"},{"id-type":"doi","id":"10.1162\/2e3983f5.f42c862b","asserted-by":"object"},{"id-type":"doi","id":"10.1162\/2e3983f5.935143a9","asserted-by":"object"},{"id-type":"doi","id":"10.1162\/2e3983f5.9d8d6096","asserted-by":"object"}]},"subject":[],"published":{"date-parts":[[2025,4,30]]},"subtype":"preprint"}}