{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:45:07Z","timestamp":1792025107822,"version":"4.4.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["R01AI145437"],"award-info":[{"award-number":["R01AI145437"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["R01AI170158"],"award-info":[{"award-number":["R01AI170158"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000061","name":"Fogarty International Center","doi-asserted-by":"publisher","award":["R01NS086312"],"award-info":[{"award-number":["R01NS086312"]}],"id":[{"id":"10.13039\/100000061","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000061","name":"Fogarty International Center","doi-asserted-by":"publisher","award":["D43TW009343"],"award-info":[{"award-number":["D43TW009343"]}],"id":[{"id":"10.13039\/100000061","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UCSF Center for Tuberculosis","award":["R25AI147375"],"award-info":[{"award-number":["R25AI147375"]}]},{"name":"UCSF Center for Tuberculosis","award":["P30AI168440"],"award-info":[{"award-number":["P30AI168440"]}]},{"name":"Westridge Foundation"},{"name":"American Academy of Neurology Clinical Research Training Scholarship","id":[{"id":"https:\/\/ror.org\/00mv9dj85","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["210772\/Z\/18\/Z"],"award-info":[{"award-number":["210772\/Z\/18\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008069","name":"UCSF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008069","id-type":"DOI","asserted-by":"publisher"}]},{"name":"PBBR"},{"name":"RRP IMIA"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["1S10OD028511-01"],"award-info":[{"award-number":["1S10OD028511-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Tuberculous meningitis (TBM) has approximately 50% mortality in people living with HIV. We investigated differences in cerebrospinal fluid (CSF) host immune responses associated with short-term mortality.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We enrolled a prospective cohort of adults with HIV-related TBM in Kampala, Uganda. Metagenomic next-generation sequencing (mNGS) of bulk CSF RNA was used to detect co-infecting or alternate CNS pathogens and refine diagnoses. Host transcriptomic profiles from the refined cohort were compared between 14-day survivors and non-survivors.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Cerebrospinal fluid mNGS reclassified or excluded 14% of participants based on pathogen detection, yielding 110 participants for transcriptomic analysis.Survivors upregulated T-cell receptor signaling (LCK, FYN, LAT), T-cell survival and differentiation (IL7, CD27, IL12RB1), B-cell receptor signaling (CD81, PLCG2, TNFRSF13C), cytotoxic lymphocyte and NK cell genes (KLRD1, ULBP1), TNF signaling, and class I MHC antigen processing pathways, while downregulating neutrophil chemoattractant CXCL1 and classical complement genes C4A and C4B. Unsupervised clustering identified a hypoinflammatory subgroup with significantly elevated mortality.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Short-term TBM survival was associated with upregulation of adaptive immunity alongside TNF signaling and IFN-\u03b3-driven class I MHC antigen processing pathways, with concurrent restraint of complement and neutrophil pathways. This supports investigation of adjunctive targeted agents that preserve protective responses while selectively dampening injurious innate pathways.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/infdis\/jiag313","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T12:29:07Z","timestamp":1781612947000},"page":"e896-e907","source":"Crossref","is-referenced-by-count":0,"title":["Cerebrospinal Fluid Transcriptional Immune Pathways Linked to Survival in HIV-Associated Tuberculous Meningitis"],"prefix":"10.1093","volume":"234","author":[{"given":"Martineau","family":"Louine","sequence":"first","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2930-3043","authenticated-orcid":false,"given":"Ravi","family":"Dandekar","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6275-6001","authenticated-orcid":false,"given":"Sumanth P","family":"Reddy","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3570-5353","authenticated-orcid":false,"given":"Mary C","family":"Karalius","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6408-2330","authenticated-orcid":false,"given":"Greer","family":"Waldrop","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiyin","family":"Wang","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Gakuru","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1335-9787","authenticated-orcid":false,"given":"Sarah","family":"Kimuda","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8820-288X","authenticated-orcid":false,"given":"Timothy","family":"Mugabi","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdu K","family":"Musubire","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0291-651X","authenticated-orcid":false,"given":"Enock","family":"Kagimu","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9601-3006","authenticated-orcid":false,"given":"Mahsa","family":"Abassi","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota , Minneapolis, MN ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mable","family":"Kabahubya","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Darlisha A","family":"Williams","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota , Minneapolis, MN ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0162-4283","authenticated-orcid":false,"given":"Hoang","family":"Van Phan","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4747-3687","authenticated-orcid":false,"given":"Biyue","family":"Dai","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota , Minneapolis, MN ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maham","family":"Zia","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1227-2137","authenticated-orcid":false,"given":"Kelsey C","family":"Zorn","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Fouassier","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chloe","family":"Gerungan","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7171-2169","authenticated-orcid":false,"given":"Pedro S","family":"Marra","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0000-8876","authenticated-orcid":false,"given":"Caleb P","family":"Skipper","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota , Minneapolis, MN ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9431-8938","authenticated-orcid":false,"given":"Nathan C","family":"Bahr","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota , Minneapolis, MN ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6708-4646","authenticated-orcid":false,"given":"Charles R","family":"Langelier","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA ,","place":["USA"]},{"name":"Chan Zuckerberg Biohub San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5070-532X","authenticated-orcid":false,"given":"Fiona V","family":"Cresswell","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]},{"name":"Clinical Research Department, London School of Hygiene and Tropical Medicine , London ,","place":["United Kingdom"]},{"name":"Global Health and Infection Department, Brighton and Sussex Medical School , Brighton ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4715-0060","authenticated-orcid":false,"given":"David R","family":"Boulware","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota , Minneapolis, MN ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David B","family":"Meya","sequence":"additional","affiliation":[{"name":"Infectious Diseases Institute, Makerere University , Kampala ,","place":["Uganda"]},{"name":"Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota , Minneapolis, MN ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8705-5084","authenticated-orcid":false,"given":"Michael R","family":"Wilson","sequence":"additional","affiliation":[{"name":"UCSF Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco , San Francisco, CA ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,18]]},"reference":[{"key":"2026101419594069700_jiag313-B1","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1212\/CON.0000000000001005","article-title":"Neurologic complications of Tuberculosis","volume":"27","author":"Saylor","year":"2021","journal-title":"Continuum"},{"key":"2026101419594069700_jiag313-B2","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1038\/s41590-018-0119-x","article-title":"Tuberculous meningitis: a roadmap for advancing basic and translational research","volume":"19","author":"Jain","year":"2018","journal-title":"Nat Immunol"},{"key":"2026101419594069700_jiag313-B3","doi-asserted-by":"crossref","first-page":"e0243161","DOI":"10.1371\/journal.pone.0243161","article-title":"Metagenomic next generation sequencing for the diagnosis of tuberculosis meningitis: a systematic review and meta-analysis","volume":"15","author":"Yu","year":"2020","journal-title":"PLoS One"},{"key":"2026101419594069700_jiag313-B4","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1038\/s41467-022-29353-x","article-title":"Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics","volume":"13","author":"Ramachandran","year":"2022","journal-title":"Nat Commun"},{"key":"2026101419594069700_jiag313-B5","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/S1473-3099(17)30474-7","article-title":"Diagnostic accuracy of Xpert MTB\/RIF ultra for tuberculous meningitis in HIV-infected adults: a prospective cohort study","volume":"18","author":"Bahr","year":"2018","journal-title":"Lancet Infect Dis"},{"key":"2026101419594069700_jiag313-B6","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.5588\/ijtld.15.0253","article-title":"Improved diagnostic sensitivity for tuberculous meningitis with Xpert(\u00ae) MTB\/RIF of centrifuged CSF","volume":"19","author":"Bahr","year":"2015","journal-title":"Int J Tuberc Lung Dis"},{"key":"2026101419594069700_jiag313-B7","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1002\/JLB.MR0318-102R","article-title":"The pathogenesis of tuberculous meningitis","volume":"105","author":"Davis","year":"2019","journal-title":"J Leukoc Biol"},{"key":"2026101419594069700_jiag313-B8","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1056\/NEJMoa2216218","article-title":"Adjunctive dexamethasone for tuberculous meningitis in HIV-positive adults","volume":"389","author":"Donovan","year":"2023","journal-title":"N Engl J Med"},{"key":"2026101419594069700_jiag313-B9","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.1056\/NEJMoa040573","article-title":"Dexamethasone for the treatment of tuberculous meningitis in adolescents and adults","volume":"351","author":"Thwaites","year":"2004","journal-title":"N Engl J Med"},{"key":"2026101419594069700_jiag313-B10","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1016\/S1473-3099(10)70138-9","article-title":"Tuberculous meningitis: a uniform case definition for use in clinical research","volume":"10","author":"Marais","year":"2010","journal-title":"Lancet Infect Dis"},{"key":"2026101419594069700_jiag313-B11","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1016\/S1473-3099(19)30550-X","article-title":"Xpert MTB\/RIF ultra for the diagnosis of HIV-associated tuberculous meningitis: a prospective validation study","volume":"20","author":"Cresswell","year":"2020","journal-title":"Lancet Infect Dis"},{"key":"2026101419594069700_jiag313-B12","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1534\/g3.113.005967","article-title":"PRICE: software for the targeted assembly of components of (meta) genomic sequence data","volume":"3","author":"Ruby","year":"2013","journal-title":"G3 (Bethesda)"},{"key":"2026101419594069700_jiag313-B13","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-Seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2026101419594069700_jiag313-B14","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1038\/s41467-017-02554-5","article-title":"A general and flexible method for signal extraction from single-cell RNA-Seq data","volume":"9","author":"Risso","year":"2018","journal-title":"Nat Commun"},{"key":"2026101419594069700_jiag313-B15","doi-asserted-by":"crossref","first-page":"12433","DOI":"10.1038\/s41598-024-62437-w","article-title":"A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros","volume":"14","author":"Abegaz","year":"2024","journal-title":"Sci Rep"},{"key":"2026101419594069700_jiag313-B16","first-page":"111","article-title":"A primer on model selection using the akaike information criterion","volume":"5","author":"Portet","year":"2020","journal-title":"Infect Dis Model"},{"key":"2026101419594069700_jiag313-B17","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2026101419594069700_jiag313-B18","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/bioinformatics\/btt703","article-title":"Causal analysis approaches in ingenuity pathway analysis","volume":"30","author":"Kr\u00e4mer","year":"2014","journal-title":"Bioinformatics"},{"key":"2026101419594069700_jiag313-B19","doi-asserted-by":"crossref","first-page":"872832","DOI":"10.3389\/fimmu.2022.872832","article-title":"High-throughput sequencing unravels the cell heterogeneity of cerebrospinal fluid in the bacterial meningitis of children","volume":"13","author":"Xiao","year":"2022","journal-title":"Front Immunol"},{"key":"2026101419594069700_jiag313-B20","doi-asserted-by":"crossref","first-page":"RP92344","DOI":"10.7554\/eLife.92344","article-title":"Whole blood transcriptional profiles and the pathogenesis of tuberculous meningitis","volume":"13","author":"Hai","year":"2024","journal-title":"eLife"},{"key":"2026101419594069700_jiag313-B21","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1182\/blood.2020009246","article-title":"The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury","volume":"137","author":"Zinter","year":"2021","journal-title":"Blood"},{"key":"2026101419594069700_jiag313-B22","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/nri3084","article-title":"Towards a systems understanding of MHC class I and MHC class II antigen presentation","volume":"11","author":"Neefjes","year":"2011","journal-title":"Nat Rev Immunol"},{"key":"2026101419594069700_jiag313-B23","doi-asserted-by":"publisher","author":"Barnacle","DOI":"10.64898\/2026.03.10.710544"},{"key":"2026101419594069700_jiag313-B24","doi-asserted-by":"crossref","first-page":"2894","DOI":"10.1093\/jimmun\/vkaf186","article-title":"Single-cell profiling of blood and cerebrospinal fluid in tuberculous meningitis","volume":"214","author":"Tram","year":"2025","journal-title":"J Immunol"},{"key":"2026101419594069700_jiag313-B25","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/80868","article-title":"Interleukin-7 mediates the homeostasis of na\u00efve and memory CD8 T cells in vivo","volume":"1","author":"Schluns","year":"2000","journal-title":"Nat Immunol"},{"key":"2026101419594069700_jiag313-B26","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/80877","article-title":"CD27 is required for generation and long-term maintenance of T cell immunity","volume":"1","author":"Hendriks","year":"2000","journal-title":"Nat Immunol"},{"key":"2026101419594069700_jiag313-B27","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41435-018-0023-2","article-title":"Human IL12RB1 expression is allele-biased and produces a novel IL12 response regulator","volume":"20","author":"Reeme","year":"2019","journal-title":"Genes Immun"},{"key":"2026101419594069700_jiag313-B28","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.tube.2016.08.001","article-title":"Antibodies and tuberculosis","volume":"101","author":"Jacobs","year":"2016","journal-title":"Tuberculosis (Edinb)"},{"key":"2026101419594069700_jiag313-B29","doi-asserted-by":"publisher","first-page":"954936","DOI":"10.3389\/fimmu.2022.954936","article-title":"Role of B cells as antigen presenting cells","volume":"13","author":"Rastogi","year":"2022","journal-title":"Front Immunol"},{"key":"2026101419594069700_jiag313-B30","doi-asserted-by":"crossref","first-page":"5517856","DOI":"10.1155\/2021\/5517856","article-title":"Phenotype of peripheral NK cells in latent, active, and meningeal Tuberculosis","volume":"2021","author":"Chore\u00f1o-Parra","year":"2021","journal-title":"J Immunol Res"},{"key":"2026101419594069700_jiag313-B31","doi-asserted-by":"crossref","first-page":"e70063","DOI":"10.1371\/journal.pone.0070063","article-title":"Modulation of NKG2D expression in human CD8+ T cells corresponding with Tuberculosis drug cure","volume":"8","author":"Hassan","year":"2013","journal-title":"PLoS One"},{"key":"2026101419594069700_jiag313-B32","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1111\/cei.13565","article-title":"Immunological basis of early clearance of Mycobacterium tuberculosis infection: the role of natural killer cells","volume":"204","author":"Abebe","year":"2021","journal-title":"Clin Exp Immunol"},{"key":"2026101419594069700_jiag313-B33","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.cytogfr.2010.10.004","article-title":"IL-17 and Th17 cells in tuberculosis","volume":"21","author":"Torrado","year":"2010","journal-title":"Cytokine Growth Factor Rev"},{"key":"2026101419594069700_jiag313-B34","doi-asserted-by":"crossref","DOI":"10.1172\/JCI175264","article-title":"Immune mechanisms of granuloma formation in sarcoidosis and tuberculosis","volume":"134","author":"Weeratunga","year":"2024","journal-title":"J Clin Invest"},{"key":"2026101419594069700_jiag313-B35","doi-asserted-by":"crossref","first-page":"17023","DOI":"10.1038\/sigtrans.2017.23","article-title":"NF-\u03baB signaling in inflammation","volume":"2","author":"Liu","year":"2017","journal-title":"Sig Transduct Target Ther"},{"key":"2026101419594069700_jiag313-B36","doi-asserted-by":"crossref","first-page":"e012567","DOI":"10.1136\/bmjopen-2016-012567","article-title":"Risk of tuberculosis in patients treated with TNF-\u03b1 antagonists: a systematic review and meta-analysis of randomised controlled trials","volume":"7","author":"Zhang","year":"2017","journal-title":"BMJ Open"},{"key":"2026101419594069700_jiag313-B37","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1016\/j.immuni.2011.12.002","article-title":"Innate and adaptive interferons suppress IL-1\u03b1 and IL-1\u03b2 production by distinct pulmonary myeloid subsets during Mycobacterium tuberculosis infection","volume":"35","author":"Mayer-Barber","year":"2011","journal-title":"Immunity"},{"key":"2026101419594069700_jiag313-B38","doi-asserted-by":"crossref","first-page":"e1441","DOI":"10.1002\/wrna.1441","article-title":"The GAIT translational control system","volume":"9","author":"Arif","year":"2018","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2026101419594069700_jiag313-B39","doi-asserted-by":"crossref","first-page":"2559","DOI":"10.4049\/jimmunol.1100963","article-title":"IFN-induced TPR protein IFIT3 potentiates antiviral signaling by bridging MAVS and TBK1","volume":"187","author":"Liu","year":"2011","journal-title":"J Immunol"},{"key":"2026101419594069700_jiag313-B40","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/j.0105-2896.2005.00308.x","article-title":"Interferon-gamma, the functional plasticity of the ubiquitin-proteasome system, and MHC class I antigen processing","volume":"207","author":"Strehl","year":"2005","journal-title":"Immunol Rev"},{"key":"2026101419594069700_jiag313-B41","doi-asserted-by":"crossref","first-page":"16840","DOI":"10.1038\/s41598-018-35393-5","article-title":"Deciphering the molecular basis of mycobacteria and lipoglycan recognition by the C-type lectin dectin-2","volume":"8","author":"Decout","year":"2018","journal-title":"Sci Rep"},{"key":"2026101419594069700_jiag313-B42","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1038\/s41420-023-01524-9","article-title":"The role of CXCL family members in different diseases","volume":"9","author":"Zhou","year":"2023","journal-title":"Cell Death Discov"},{"key":"2026101419594069700_jiag313-B43","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/cr.2009.139","article-title":"Complement and its role in innate and adaptive immune responses","volume":"20","author":"Dunkelberger","year":"2010","journal-title":"Cell Res"},{"key":"2026101419594069700_jiag313-B44","first-page":"677","article-title":"Inflammasome activation underlying central nervous system deterioration in HIV-associated Tuberculosis","volume":"215","author":"Marais","year":"2017","journal-title":"J Infect Dis"},{"key":"2026101419594069700_jiag313-B45","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1093\/infdis\/jiag032","article-title":"Cerebrospinal fluid hypo-inflammation drives mortality in HIV-associated tuberculous meningitis","volume":"233","author":"Wilt","year":"2026","journal-title":"J Infect Dis"},{"key":"2026101419594069700_jiag313-B46","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.medj.2020.11.003","article-title":"Tuberculosis endotypes to guide stratified host-directed therapy","volume":"2","author":"DiNardo","year":"2021","journal-title":"Med"},{"key":"2026101419594069700_jiag313-B47","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.medj.2022.07.001","article-title":"Interleukin-1 receptor antagonist anakinra as treatment for paradoxical responses in HIV-negative tuberculosis patients: a case series","volume":"3","author":"van Arkel","year":"2022","journal-title":"Med"},{"key":"2026101419594069700_jiag313-B48","doi-asserted-by":"crossref","first-page":"226","DOI":"10.3988\/jcn.2023.0290","article-title":"Infliximab for intractable paradoxical reaction in culture-negative Tuberculosis meningitis","volume":"20","author":"Kim","year":"2024","journal-title":"J Clin Neurol"},{"key":"2026101419594069700_jiag313-B49","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1186\/s12889-024-19683-4","article-title":"Prevalence, incidence, and case fatality of tuberculous meningitis in adults living with HIV: a systematic review and meta-analysis","volume":"24","author":"Chen","year":"2024","journal-title":"BMC Public Health"},{"key":"2026101419594069700_jiag313-B50","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.1093\/cid\/ciab527","article-title":"Male sex is associated with worse microbiological and clinical outcomes following Tuberculosis treatment: a retrospective cohort study, a systematic review of the literature, and meta-analysis","volume":"73","author":"Chidambaram","year":"2021","journal-title":"Clin Infect Dis"}],"container-title":["The Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jid\/advance-article-pdf\/doi\/10.1093\/infdis\/jiag313\/68548725\/jiag313.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jid\/article-pdf\/234\/4\/e896\/68548725\/jiag313.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jid\/article-pdf\/234\/4\/e896\/68548725\/jiag313.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T23:59:53Z","timestamp":1792022393000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jid\/article\/234\/4\/e896\/8711066"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,18]]},"references-count":50,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,6,18]]},"published-print":{"date-parts":[[2026,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/infdis\/jiag313","relation":{},"ISSN":["0022-1899","1537-6613"],"issn-type":[{"value":"0022-1899","type":"print"},{"value":"1537-6613","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10,15]]},"published":{"date-parts":[[2026,6,18]]}}}