{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T20:26:51Z","timestamp":1792009611893,"version":"4.4.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1012137","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,4,23]],"date-time":"2024-04-23T00:00:00Z","timestamp":1713830400000}}],"reference-count":81,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2024,4,11]],"date-time":"2024-04-11T00:00:00Z","timestamp":1712793600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100017540","name":"NHLBI Division of Intramural Research","doi-asserted-by":"publisher","award":["5R01HL105427"],"award-info":[{"award-number":["5R01HL105427"]}],"id":[{"id":"10.13039\/100017540","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["2R01AI111914-06A1"],"award-info":[{"award-number":["2R01AI111914-06A1"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["5R01AI134236-04"],"award-info":[{"award-number":["5R01AI134236-04"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["5R01AI123780-03"],"award-info":[{"award-number":["5R01AI123780-03"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017540","name":"NHLBI Division of Intramural Research","doi-asserted-by":"publisher","award":["T32 HL007317-44"],"award-info":[{"award-number":["T32 HL007317-44"]}],"id":[{"id":"10.13039\/100017540","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["2R01AI130454"],"award-info":[{"award-number":["2R01AI130454"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Interleukin-1 (IL-1) signaling is essential for controlling virulent\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    (\n                    <jats:italic>Mtb<\/jats:italic>\n                    ) infection since antagonism of this pathway leads to exacerbated pathology and increased susceptibility. In contrast, the triggering of type I interferon (IFN) signaling is associated with the progression of tuberculosis (TB) disease and linked with negative regulation of IL-1 signaling. However, mice lacking IL-1 signaling can control\n                    <jats:italic>Mtb<\/jats:italic>\n                    infection if infected with an\n                    <jats:italic>Mtb<\/jats:italic>\n                    strain carrying the rifampin-resistance conferring mutation H445Y in its RNA polymerase\n                    <jats:italic>\u03b2<\/jats:italic>\n                    subunit (\n                    <jats:italic>rpoB<\/jats:italic>\n                    -H445Y\n                    <jats:italic>Mtb<\/jats:italic>\n                    ). The mechanisms that govern protection in the absence of IL-1 signaling during\n                    <jats:italic>rpoB<\/jats:italic>\n                    -H445Y\n                    <jats:italic>Mtb<\/jats:italic>\n                    infection are unknown. In this study, we show that in the absence of IL-1 signaling, type I IFN signaling controls\n                    <jats:italic>rpoB<\/jats:italic>\n                    -H445Y\n                    <jats:italic>Mtb<\/jats:italic>\n                    replication, lung pathology, and excessive myeloid cell infiltration. Additionally, type I IFN is produced predominantly by monocytes and recruited macrophages and acts on LysM-expressing cells to drive protection through nitric oxide (NO) production to restrict intracellular\n                    <jats:italic>rpoB<\/jats:italic>\n                    -H445Y\n                    <jats:italic>Mtb<\/jats:italic>\n                    . These findings reveal an unexpected protective role for type I IFN signaling in compensating for deficiencies in IL-1 pathways during\n                    <jats:italic>rpoB<\/jats:italic>\n                    -H445Y\n                    <jats:italic>Mtb<\/jats:italic>\n                    infection.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1012137","type":"journal-article","created":{"date-parts":[[2024,4,11]],"date-time":"2024-04-11T16:19:45Z","timestamp":1712852385000},"page":"e1012137","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["A protective role for type I interferon signaling following infection with Mycobacterium tuberculosis carrying the rifampicin drug resistance-conferring RpoB mutation H445Y"],"prefix":"10.1371","volume":"20","author":[{"given":"Suhas","family":"Bobba","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuldeep S.","family":"Chauhan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadia","family":"Akter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shibali","family":"Das","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekansh","family":"Mittal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barun","family":"Mathema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer A.","family":"Philips","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9545-4982","authenticated-orcid":true,"given":"Shabaana A.","family":"Khader","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,4,11]]},"reference":[{"key":"ppat.1012137.ref001","volume-title":"Global tuberculosis report","year":"2022"},{"key":"ppat.1012137.ref002","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1093\/jac\/dkx506","article-title":"Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care","volume":"73","author":"N Dookie","year":"2018","journal-title":"J Antimicrob Chemother"},{"key":"ppat.1012137.ref003","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1038\/ng.2656","article-title":"Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug resistant tuberculosis","volume":"45","author":"CB Ford","year":"2013","journal-title":"Nat Genet"},{"key":"ppat.1012137.ref004","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/j.jiph.2015.05.003","article-title":"Molecular analysis of rpoB gene mutations in rifampicin resistant Mycobacterium tuberculosis isolates by multiple allele specific polymerase chain reaction in Puducherry, South India.","volume":"8","author":"R Thirumurugan","year":"2015","journal-title":"J Infect Public Health."},{"key":"ppat.1012137.ref005","doi-asserted-by":"crossref","first-page":"463","DOI":"10.4102\/ajlm.v6i2.463","article-title":"Molecular characterisation of rifampicin-resistant Mycobacterium tuberculosis strains from Malawi","volume":"6","author":"T Chikaonda","year":"2017","journal-title":"Afr J Lab Med"},{"key":"ppat.1012137.ref006","doi-asserted-by":"crossref","first-page":"e0198091","DOI":"10.1371\/journal.pone.0198091","article-title":"Prevalence and patterns of rifampicin and isoniazid resistance conferring mutations in Mycobacterium tuberculosis isolates from Uganda","volume":"13","author":"E Kigozi","year":"2018","journal-title":"PLOS ONE"},{"key":"ppat.1012137.ref007","article-title":"Rifampicin drug resistance and host immunity in tuberculosis: more than meets the eye","author":"S Bobba","year":"2023","journal-title":"Trends Immunol"},{"key":"ppat.1012137.ref008","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1084\/jem.20052545","article-title":"Interleukin 12p40 is required for dendritic cell migration and T cell priming after Mycobacterium tuberculosis infection","volume":"203","author":"SA Khader","year":"2006","journal-title":"J Exp Med"},{"key":"ppat.1012137.ref009","first-page":"e01468","article-title":"Lung Epithelial Signaling Mediates Early Vaccine-Induced CD4+ T Cell Activation and Mycobacterium tuberculosis Control.","volume":"0","author":"S Das","year":"2021","journal-title":"mBio"},{"key":"ppat.1012137.ref010","doi-asserted-by":"crossref","first-page":"13894","DOI":"10.1038\/ncomms13894","article-title":"Targeting dendritic cells to accelerate T-cell activation overcomes a bottleneck in tuberculosis vaccine efficacy","volume":"7","author":"KL Griffiths","year":"2016","journal-title":"Nat Commun"},{"key":"ppat.1012137.ref011","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1038\/s41385-018-0071-y","article-title":"A novel role for C-C motif chemokine receptor 2 during infection with hypervirulent Mycobacterium tuberculosis.","volume":"11","author":"MD Dunlap","year":"2018","journal-title":"Mucosal Immunol."},{"key":"ppat.1012137.ref012","first-page":"712","article-title":"CXCR5+ T helper cells mediate protective immunity against tuberculosis","volume":"123","author":"SR Slight","year":"2013","journal-title":"J Clin Invest"},{"key":"ppat.1012137.ref013","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1038\/mi.2014.136","article-title":"Immune requirements for protective Th17 recall responses to Mycobacterium tuberculosis challenge","volume":"8","author":"L Monin","year":"2015","journal-title":"Mucosal Immunol"},{"key":"ppat.1012137.ref014","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.chom.2020.11.013","article-title":"The immune landscape in tuberculosis reveals populations linked to disease and latency","volume":"29","author":"E Esaulova","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ppat.1012137.ref015","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.4049\/jimmunol.1800438","article-title":"Cutting Edge: IL-1R1 Mediates Host Resistance to Mycobacterium tuberculosis by Trans-Protection of Infected Cells","volume":"201","author":"AC Bohrer","year":"2018","journal-title":"J Immunol"},{"key":"ppat.1012137.ref016","first-page":"3326","article-title":"Cutting Edge: Caspase-1 Independent IL-1\u03b2 Production Is Critical for Host Resistance to Mycobacterium tuberculosis and Does Not Require TLR Signaling In Vivo.","volume":"184","author":"KD Mayer-Barber","year":"2010","journal-title":"J Immunol Baltim Md 1950."},{"key":"ppat.1012137.ref017","first-page":"2540","article-title":"Mycobacterium tuberculosis triggers host type I interferon signaling to regulate IL-1\u03b2 production in human macrophages","volume":"187","author":"A Novikov","year":"2011","journal-title":"J Immunol Baltim Md 1950."},{"key":"ppat.1012137.ref018","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature13489","article-title":"Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk","volume":"511","author":"KD Mayer-Barber","year":"2014","journal-title":"Nature"},{"key":"ppat.1012137.ref019","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1002\/eji.201344219","article-title":"Type I IFN signaling triggers immunopathology in tuberculosis-susceptible mice by modulating lung phagocyte dynamics","volume":"44","author":"A Dorhoi","year":"2014","journal-title":"Eur J Immunol"},{"key":"ppat.1012137.ref020","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/cmi.2016.25","article-title":"Clash of the Cytokine Titans: counter-regulation of interleukin-1 and type I interferon-mediated inflammatory responses","volume":"14","author":"KD Mayer-Barber","year":"2017","journal-title":"Cell Mol Immunol"},{"key":"ppat.1012137.ref021","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1084\/jem.20180325","article-title":"Type I interferons in tuberculosis: Foe and occasionally friend","volume":"215","author":"L Moreira-Teixeira","year":"2018","journal-title":"J Exp Med"},{"key":"ppat.1012137.ref022","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/nature09247","article-title":"An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis","volume":"466","author":"MPR Berry","year":"2010","journal-title":"Nature"},{"key":"ppat.1012137.ref023","doi-asserted-by":"crossref","first-page":"5566","DOI":"10.1038\/s41467-020-19412-6","article-title":"Type I IFN exacerbates disease in tuberculosis-susceptible mice by inducing neutrophil-mediated lung inflammation and NETosis","volume":"11","author":"L Moreira-Teixeira","year":"2020","journal-title":"Nat Commun"},{"key":"ppat.1012137.ref024","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1038\/s41564-018-0245-0","article-title":"Mycobacterium tuberculosis carrying a rifampicin drug resistance mutation reprograms macrophage metabolism through cell wall lipid changes","volume":"3","author":"NC Howard","year":"2018","journal-title":"Nat Microbiol"},{"key":"ppat.1012137.ref025","article-title":"Mycobacterium tuberculosis carrying the rifampicin drug resistance conferring rpoB mutation H445Y is associated with suppressed immunity through type I interferons.","author":"S Bobba","year":"2023","journal-title":"mBio"},{"key":"ppat.1012137.ref026","doi-asserted-by":"crossref","first-page":"135","DOI":"10.33160\/yam.2020.08.001","article-title":"Regulatory Mechanism of SNAP23 in Phagosome Formation and Maturation.","volume":"63","author":"K Hatsuzawa","year":"2020","journal-title":"Yonago Acta Med."},{"key":"ppat.1012137.ref027","doi-asserted-by":"crossref","first-page":"58686","DOI":"10.18632\/oncotarget.17419","article-title":"Calreticulin modulates the intracellular survival of mycobacteria by regulating ER-stress-mediated apoptosis","volume":"8","author":"SH Jo","year":"2017","journal-title":"Oncotarget"},{"key":"ppat.1012137.ref028","doi-asserted-by":"crossref","first-page":"64050","DOI":"10.18632\/oncotarget.19300","article-title":"Sp110 enhances macrophage resistance to Mycobacterium tuberculosis via inducing endoplasmic reticulum stress and inhibiting anti-apoptotic factors","volume":"8","author":"Y Wu","year":"2017","journal-title":"Oncotarget"},{"key":"ppat.1012137.ref029","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1084\/jem.20101664","article-title":"Type I interferon: friend or foe?","volume":"207","author":"G. Trinchieri","year":"2010","journal-title":"J Exp Med"},{"key":"ppat.1012137.ref030","doi-asserted-by":"crossref","first-page":"4895","DOI":"10.1038\/s41467-022-32567-8","article-title":"Temporally restricted activation of IFN\u03b2 signaling underlies response to immune checkpoint therapy in mice.","volume":"13","author":"RM Zemek","year":"2022","journal-title":"Nat Commun"},{"key":"ppat.1012137.ref031","doi-asserted-by":"crossref","first-page":"e1005975","DOI":"10.1371\/journal.ppat.1005975","article-title":"STING-Licensed Macrophages Prime Type I IFN Production by Plasmacytoid Dendritic Cells in the Bone Marrow during Severe Plasmodium yoelii Malaria","volume":"12","author":"E Spaulding","year":"2016","journal-title":"PLOS Pathog"},{"key":"ppat.1012137.ref032","doi-asserted-by":"crossref","first-page":"20416","DOI":"10.1073\/pnas.0808537105","article-title":"Visualization of IFN\u03b2 production by plasmacytoid versus conventional dendritic cells under specific stimulation conditions in vivo","volume":"105","author":"S Scheu","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1012137.ref033","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1007\/978-1-4939-7837-3_24","article-title":"Cre Driver Mice Targeting Macrophages.","volume":"1784","author":"J Shi","year":"2018","journal-title":"Methods Mol Biol Clifton NJ"},{"key":"ppat.1012137.ref034","doi-asserted-by":"crossref","first-page":"e20200887","DOI":"10.1084\/jem.20200887","article-title":"Type I interferon signaling mediates Mycobacterium tuberculosis\u2013induced macrophage death","volume":"218","author":"L Zhang","year":"2020","journal-title":"J Exp Med"},{"key":"ppat.1012137.ref035","doi-asserted-by":"crossref","first-page":"6205","DOI":"10.4049\/jimmunol.1200255","article-title":"Dynamic Roles of Type I and Type II IFNs in Early Infection with Mycobacterium tuberculosis","volume":"188","author":"L Desvignes","year":"2012","journal-title":"J Immunol"},{"key":"ppat.1012137.ref036","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nri3787","article-title":"Type I interferons in infectious disease","volume":"15","author":"F McNab","year":"2015","journal-title":"Nat Rev Immunol"},{"key":"ppat.1012137.ref037","doi-asserted-by":"crossref","first-page":"2128","DOI":"10.1038\/s41564-019-0578-3","article-title":"Type I interferon-driven susceptibility to Mycobacterium tuberculosis is mediated by interleukin-1 receptor antagonist IL-1Ra.","volume":"4","author":"DX Ji","year":"2019","journal-title":"Nat Microbiol."},{"key":"ppat.1012137.ref038","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1016\/S0140-6736(15)01316-1","article-title":"A prospective blood RNA signature for tuberculosis disease risk","volume":"387","author":"DE Zak","year":"2016","journal-title":"Lancet Lond Engl"},{"key":"ppat.1012137.ref039","doi-asserted-by":"crossref","first-page":"2308","DOI":"10.1038\/s41467-018-04579-w","article-title":"A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection","volume":"9","author":"A Singhania","year":"2018","journal-title":"Nat Commun"},{"key":"ppat.1012137.ref040","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":"K Mayer-Barber","year":"2011","journal-title":"Immunity"},{"key":"ppat.1012137.ref041","doi-asserted-by":"crossref","first-page":"5752","DOI":"10.1073\/pnas.091096998","article-title":"Virulence of a Mycobacterium tuberculosis clinical isolate in mice is determined by failure to induce Th1 type immunity and is associated with induction of IFN-\u03b1\/\u03b2","volume":"98","author":"C Manca","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1012137.ref042","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1172\/JCI40817","article-title":"Intranasal Poly-IC treatment exacerbates tuberculosis in mice through the pulmonary recruitment of a pathogen-permissive monocyte\/macrophage population","volume":"120","author":"LRV Antonelli","year":"2010","journal-title":"J Clin Invest"},{"key":"ppat.1012137.ref043","doi-asserted-by":"crossref","first-page":"2348","DOI":"10.4049\/jimmunol.1801303","article-title":"Mycobacterium tuberculosis Inhibits Autocrine Type I IFN Signaling to Increase Intracellular Survival","volume":"202","author":"DA Banks","year":"2019","journal-title":"J Immunol"},{"key":"ppat.1012137.ref044","doi-asserted-by":"crossref","first-page":"109195","DOI":"10.1016\/j.celrep.2021.109195","article-title":"Type I interferon decreases macrophage energy metabolism during mycobacterial infection","volume":"35","author":"GS Olson","year":"2021","journal-title":"Cell Rep"},{"key":"ppat.1012137.ref045","article-title":"Early cellular mechanisms of type I interferon-driven susceptibility to tuberculosis","author":"DI Kotov","year":"2023","journal-title":"Cell"},{"key":"ppat.1012137.ref046","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.immuni.2018.12.027","article-title":"Plasmacytoid Dendritic Cells: Development, Regulation, and Function.","volume":"50","author":"B. Reizis","year":"2019","journal-title":"Immunity"},{"key":"ppat.1012137.ref047","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.coviro.2011.10.026","article-title":"Type I interferons: diversity of sources, production pathways and effects on immune responses.","volume":"1","author":"M Swiecki","year":"2011","journal-title":"Curr Opin Virol"},{"key":"ppat.1012137.ref048","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1084\/jem.20172020","article-title":"Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny","volume":"215","author":"L Huang","year":"2018","journal-title":"J Exp Med"},{"key":"ppat.1012137.ref049","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/978-1-4939-6581-6_23","article-title":"Mycobacterium tuberculosis: Readouts of bacterial fitness and the environment within the phagosome","volume":"1519","author":"S Tan","year":"2017","journal-title":"Methods Mol Biol Clifton NJ"},{"key":"ppat.1012137.ref050","doi-asserted-by":"crossref","first-page":"107523","DOI":"10.1016\/j.celrep.2020.107523","article-title":"CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues.","volume":"31","author":"CR Stoltzfus","year":"2020","journal-title":"Cell Rep"},{"key":"ppat.1012137.ref051","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1038\/s41467-019-09816-4","article-title":"Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma","volume":"10","author":"B Carow","year":"2019","journal-title":"Nat Commun"},{"key":"ppat.1012137.ref052","doi-asserted-by":"crossref","first-page":"e20221392","DOI":"10.1084\/jem.20221392","article-title":"Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosis","volume":"220","author":"AJ Sawyer","year":"2023","journal-title":"J Exp Med"},{"key":"ppat.1012137.ref053","doi-asserted-by":"crossref","first-page":"5001","DOI":"10.4049\/jimmunol.178.8.5001","article-title":"Protective Role of Macrophages in Noninflammatory Lung Injury Caused by Selective Ablation of Alveolar Epithelial Type II Cells1","volume":"178","author":"Y Miyake","year":"2007","journal-title":"J Immunol"},{"key":"ppat.1012137.ref054","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.3389\/fimmu.2017.01618","article-title":"Promoter Specificity and Efficacy in Conditional and Inducible Transgenic Targeting of Lung Macrophages.","volume":"8","author":"AL McCubbrey","year":"2017","journal-title":"Front Immunol"},{"key":"ppat.1012137.ref055","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.jim.2014.05.009","article-title":"Comparative analysis of the efficiency and specificity of myeloid-Cre deleting strains using ROSA-EYFP reporter mice","volume":"408","author":"CL Abram","year":"2014","journal-title":"J Immunol Methods"},{"key":"ppat.1012137.ref056","first-page":"270","article-title":"IFN-\u03b3 from CD4 T cells is essential for host survival and enhances CD8 T cell function during Mycobacterium tuberculosis infection","volume":"190","author":"AM Green","year":"2013","journal-title":"J Immunol Baltim Md 1950."},{"key":"ppat.1012137.ref057","first-page":"2965","article-title":"Control of Mycobacterium tuberculosis infection by a subset of lung parenchyma homing CD4 T cells.","volume":"192","author":"S Sakai","year":"2014","journal-title":"J Immunol Baltim Md 1950."},{"key":"ppat.1012137.ref058","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1080\/08941930600985710","article-title":"Regulation of Nitric Oxide Synthesis in Wounds by IFN-\u03b3 Depends on TNF-\u03b1.","volume":"19","author":"M Sch\u00e4ffer","year":"2006","journal-title":"J Invest Surg"},{"key":"ppat.1012137.ref059","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.celrep.2019.12.033","article-title":"Dual RNA-Seq of Mtb-Infected Macrophages In Vivo Reveals Ontologically Distinct Host-Pathogen Interactions.","volume":"30","author":"D Pisu","year":"2020","journal-title":"Cell Rep"},{"key":"ppat.1012137.ref060","doi-asserted-by":"crossref","first-page":"27326","DOI":"10.1038\/srep27326","article-title":"Macrophage-mediated inflammatory response decreases mycobacterial survival in mouse MSCs by augmenting NO production.","volume":"6","author":"K Yang","year":"2016","journal-title":"Sci Rep"},{"key":"ppat.1012137.ref061","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/S0962-8479(97)90005-8","article-title":"Mycobacterium tuberculosis (MTB)- stimulated production of nitric oxide by human alveolar macrophages and relationship of nitric oxide production to growth inhibition of MTB.","volume":"78","author":"EA Rich","year":"1997","journal-title":"Tuber Lung Dis"},{"key":"ppat.1012137.ref062","doi-asserted-by":"crossref","first-page":"3644","DOI":"10.1128\/iai.65.9.3644-3647.1997","article-title":"Mechanism of nitric oxide-dependent killing of Mycobacterium bovis BCG in human alveolar macrophages","volume":"65","author":"Y Nozaki","year":"1997","journal-title":"Infect Immun"},{"key":"ppat.1012137.ref063","doi-asserted-by":"crossref","first-page":"100192","DOI":"10.1016\/j.crmeth.2022.100192","article-title":"An integrated toolbox to profile macrophage immunometabolism","volume":"2","author":"SGS Verberk","year":"2022","journal-title":"Cell Rep Methods"},{"key":"ppat.1012137.ref064","doi-asserted-by":"crossref","first-page":"5243","DOI":"10.1073\/pnas.94.10.5243","article-title":"Identification of nitric oxide synthase as a protective locus against\u2009tuberculosis","volume":"94","author":"JD MacMicking","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1012137.ref065","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.vetmic.2019.04.019","article-title":"Interleukin 1 alpha (IL-1\u03b1) restricts Brucella abortus 544 survival through promoting lysosomal-mediated killing and NO production in macrophages.","volume":"232","author":"HT Hop","year":"2019","journal-title":"Vet Microbiol"},{"key":"ppat.1012137.ref066","doi-asserted-by":"crossref","first-page":"14248","DOI":"10.1074\/jbc.M116.716704","article-title":"Rifampin Resistance Mutations Are Associated with Broad Chemical Remodeling of Mycobacterium tuberculosis","volume":"291","author":"N Lahiri","year":"2016","journal-title":"J Biol Chem"},{"key":"ppat.1012137.ref067","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00148-17","article-title":"The Cell Wall Lipid PDIM Contributes to Phagosomal Escape and Host Cell Exit of Mycobacterium tuberculosis.","volume":"8","author":"J Quigley","year":"2017","journal-title":"mBio"},{"key":"ppat.1012137.ref068","doi-asserted-by":"crossref","first-page":"e1006363","DOI":"10.1371\/journal.ppat.1006363","article-title":"Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence","volume":"13","author":"AK Barczak","year":"2017","journal-title":"PLOS Pathog"},{"key":"ppat.1012137.ref069","doi-asserted-by":"crossref","DOI":"10.1111\/cmi.12726","article-title":"ESX-1 and phthiocerol dimycocerosates of Mycobacterium tuberculosis act in concert to cause phagosomal rupture and host cell apoptosis","volume":"19","author":"J Augenstreich","year":"2017","journal-title":"Cell Microbiol"},{"key":"ppat.1012137.ref070","doi-asserted-by":"crossref","first-page":"e136937","DOI":"10.1172\/jci.insight.136937","article-title":"Mycobacterium tuberculosis cords within lymphatic endothelial cells to evade host immunity","volume":"5","author":"TR Lerner","year":"2020","journal-title":"JCI Insight"},{"key":"ppat.1012137.ref071","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/ni1449","article-title":"IL-23 and IL-17 in the establishment of protective pulmonary CD4+ T cell responses after vaccination and during Mycobacterium tuberculosis challenge","volume":"8","author":"SA Khader","year":"2007","journal-title":"Nat Immunol"},{"key":"ppat.1012137.ref072","doi-asserted-by":"crossref","first-page":"3098","DOI":"10.1172\/JCI130546","article-title":"S100A8\/A9 regulates CD11b expression and neutrophil recruitment during chronic tuberculosis","volume":"130","author":"NR Scott","journal-title":"J Clin Invest"},{"key":"ppat.1012137.ref073","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkz114","article-title":"The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads","volume":"47","author":"Y Liao","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"ppat.1012137.ref074","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":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"ppat.1012137.ref075","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B Methodol."},{"key":"ppat.1012137.ref076","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1039\/C5MB00663E","article-title":"ReactomePA: an R\/Bioconductor package for reactome pathway analysis and visualization.","volume":"12","author":"G Yu","year":"2016","journal-title":"Mol Biosyst"},{"key":"ppat.1012137.ref077","first-page":"060012","article-title":"Fast gene set enrichment analysis","author":"G Korotkevich","year":"2021","journal-title":"bioRxiv"},{"key":"ppat.1012137.ref078","author":"H Wickham","year":"2022","journal-title":"Simple, Consistent Wrappers for Common String Operations."},{"key":"ppat.1012137.ref079","author":"R. Kolde","year":"2019","journal-title":"pheatmap: Pretty Heatmaps"},{"key":"ppat.1012137.ref080","author":"H. Wickham","year":"2016"},{"key":"ppat.1012137.ref081","author":"M. Carlson","year":"2019","journal-title":"org.Hs.eg.db"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1012137","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,4,23]],"date-time":"2024-04-23T00:00:00Z","timestamp":1713830400000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1012137","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,23]],"date-time":"2024-04-23T13:59:13Z","timestamp":1713880753000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1012137"}},"subtitle":[],"editor":[{"given":"Padmini","family":"Salgame","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,4,11]]},"references-count":81,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2024,4,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1012137","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,11]]}}}