101
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Verma R, Swift BMC, Handley-Hartill W, Lee JK, Woltmann G, Rees CED, Haldar P. A Novel, High-sensitivity, Bacteriophage-based Assay Identifies Low-level Mycobacterium tuberculosis Bacteremia in Immunocompetent Patients With Active and Incipient Tuberculosis. Clin Infect Dis 2021; 70:933-936. [PMID: 31233122 DOI: 10.1093/cid/ciz548] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
The haematogenous dissemination of Mycobacterium tuberculosis (Mtb) is critical to the pathogenesis of progressive tuberculous infections in animal models. Using a novel, phage-based blood assay, we report the first concordant evidence in well-characterized, immunocompetent human cohorts, demonstrating associations of Mtb bacteremia with progressive phenotypes of latent infection and active pulmonary tuberculosis.
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Affiliation(s)
- Raman Verma
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, Herts
| | | | - Wade Handley-Hartill
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire
| | - Joanne K Lee
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, Herts
| | - Gerrit Woltmann
- Department of Respiratory Medicine, University Hospitals of Leicester National Health Service Trust, Glenfield Hospital, United Kingdom
| | - Catherine E D Rees
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire
| | - Pranabashis Haldar
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, Herts
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102
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Huaman MA, De Cecco CN, Bittencourt MS, Ticona E, Kityo C, Ballena I, Nalukwago S, Nazzinda R, Ticona C, Azañero R, Zhang B, Farquhar C, Hawn TR, Sterling TR, Fichtenbaum CJ, Longenecker CT. Latent Tuberculosis Infection and Subclinical Coronary Atherosclerosis in Peru and Uganda. Clin Infect Dis 2021; 73:e3384-e3390. [PMID: 33388766 DOI: 10.1093/cid/ciaa1934] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Tuberculosis has been linked to an increased risk of atherosclerotic cardiovascular disease (ASCVD). We assessed whether latent tuberculosis infection (LTBI) is associated with subclinical coronary atherosclerosis in two TB-prevalent areas. METHODS We analyzed cross-sectional data from studies conducted in Lima, Peru, and Kampala, Uganda. Individuals ≥40 years old were included. We excluded persons with known history of ASCVD events or active TB. Participants underwent QuantiFERON®-TB (QFT) testing to define LTBI, and computed tomography angiography to examine coronary atherosclerosis. A Coronary Artery Disease-Reporting Data System (CAD-RADS) score ≥3 defined obstructive CAD (plaque causing ≥50% stenosis). RESULTS 113 persons with LTBI and 91 persons without LTBI were included. There were no significant differences between LTBI and non-LTBI participants in terms of age (median [interquartile range]; 56 [51-62] vs. 55 [49-64], p=0.829), male sex (38% vs. 42%; p=0.519), or 10-year ASCVD risk scores (7.1 [3.2-11.7] vs. 6.1 [2.8-10.8]; p=0.533). CAD prevalence (any plaque) was similar between groups (29% vs. 24%; p=0.421). Obstructive CAD was present in 9% of LTBI and 3% of non-LTBI individuals; p=0.095. LTBI was associated with obstructive CAD after adjusting for ASCVD risk score, HIV status, and study site (adjusted odds ratio, 4.96, 95% CI 1.05-23.44; p=0.043). Quantitative QFT TB antigen minus nil interferon-gamma responses were associated with obstructive CAD (adjusted odds ratio, 1.2, 95% CI 1.03-1.41; p=0.022). CONCLUSIONS LTBI was independently associated with an increased likelihood of subclinical obstructive CAD. Our data indicates that LTBI is a non-traditional correlate of ASCVD risk.
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Affiliation(s)
- Moises A Huaman
- Department of Internal Medicine, Division of Infectious Diseases, University of Cincinnati College of Medicine, Ohio, United States of America
| | - Carlo N De Cecco
- Division of Cardiothoracic Imaging, Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, United States of America
| | | | - Eduardo Ticona
- Hospital Nacional Dos de Mayo, Lima, Peru.,Department of Internal Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Cissy Kityo
- Joint Clinical Research Centre, Kampala, Uganda
| | | | | | | | | | | | - Bin Zhang
- Division of Biostatistics and Epidemiology, Cincinnati Children's Medical Center, Ohio, United States of America
| | - Carey Farquhar
- Departments of Medicine and Global Health, University of Washington School of Medicine, Seattle, United States of America
| | - Thomas R Hawn
- Departments of Medicine and Global Health, University of Washington School of Medicine, Seattle, United States of America
| | - Timothy R Sterling
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University School of Medicine, United States of America
| | - Carl J Fichtenbaum
- Department of Internal Medicine, Division of Infectious Diseases, University of Cincinnati College of Medicine, Ohio, United States of America
| | - Chris T Longenecker
- Harrington Heart & Vascular Institute, Case Western Reserve University School of Medicine, Ohio, United States of America
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103
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Irvine EB, Alter G. Understanding the role of antibody glycosylation through the lens of severe viral and bacterial diseases. Glycobiology 2020; 30:241-253. [PMID: 32103252 PMCID: PMC7109349 DOI: 10.1093/glycob/cwaa018] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 01/12/2023] Open
Abstract
Abundant evidence points to a critical role for antibodies in protection and pathology across infectious diseases. While the antibody variable domain facilitates antibody binding and the blockade of infection, the constant domain (Fc) mediates cross talk with the innate immune system. The biological activity of the Fc region is controlled genetically via class switch recombination, resulting in the selection of distinct antibody isotypes and subclasses. However, a second modification is made to all antibodies, via post-translational changes in antibody glycosylation. Studies from autoimmunity and oncology have established the role of immunoglobulin G (IgG) Fc glycosylation as a key regulator of humoral immune activity. However, a growing body of literature, exploring IgG Fc glycosylation through the lens of infectious diseases, points to the role of inflammation in shaping Fc-glycan profiles, the remarkable immune plasticity in antibody glycosylation across pathogen-exposed populations, the canonical and noncanonical functions of glycans and the existence of antigen-specific control over antibody Fc glycosylation. Ultimately, this work provides critical new insights into the functional roles for antibody glycosylation as well as lays the foundation for leveraging antibody glycosylation to drive prevention or control across diseases.
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Affiliation(s)
- Edward B Irvine
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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104
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Sheerin D, Abhimanyu, Wang X, Johnson WE, Coussens A. Systematic evaluation of transcriptomic disease risk and diagnostic biomarker overlap between COVID-19 and tuberculosis: a patient-level meta-analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.11.25.20236646. [PMID: 33269371 PMCID: PMC7709192 DOI: 10.1101/2020.11.25.20236646] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND The novel coronavirus, SARS-CoV-2, has increased the burden on healthcare systems already strained by a high incidence of tuberculosis (TB) as co-infection and dual presentation are occurring in syndemic settings. We aimed to understand the interaction between these diseases by profiling COVID-19 gene expression signatures on RNA-sequencing data from TB-infected individuals. METHODS We performed a systematic review and patient-level meta-analysis by querying PubMed and pre-print servers to derive eligible COVID-19 gene expression signatures from human whole blood (WB), PBMCs or BALF studies. A WB influenza dataset served as a control respiratory disease signature. Three large TB RNA-seq datasets, comprising multiple cohorts from the UK and Africa and consisting of TB patients across the disease spectrum, were chosen to profile these signatures. Putative "COVID-19 risk scores" were generated for each sample in the TB datasets using the TBSignatureProfiler package. Risk was stratified by time to TB diagnosis in progressors and contacts of pulmonary and extra-pulmonary TB. An integrative analysis between TB and COVID-19 single-cell RNA-seq data was performed and a population-level meta-analysis was conducted to identify shared gene ontologies between the diseases and their relative enrichment in COVID-19 disease severity states. RESULTS 35 COVID-19 gene signatures from nine eligible studies comprising 98 samples were profiled on TB RNA-seq data from 1181 samples from 853 individuals. 25 signatures had significantly higher COVID-19 risk in active TB (ATB) compared with latent TB infection (p <0·005), 13 of which were validated in two independent datasets. FCN1 - and SPP1 -expressing macrophages enriched in BALF during severe COVID-19 were identified in circulation during ATB. Shared perturbed ontologies included antigen presentation, epigenetic regulation, platelet activation, and ROS/RNS production were enriched with increasing COVID-19 severity. Finally, we demonstrate that the overlapping transcriptional responses may complicate development of blood-based diagnostic signatures of co-infection. INTERPRETATION Our results identify shared dysregulation of immune responses in COVID-19 and TB as a dual risk posed by co-infection to COVID-19 severity and TB disease progression. These individuals should be followed up for TB in the months subsequent to SARS-CoV-2 diagnosis.
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Affiliation(s)
- Dylan Sheerin
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville 3279, VIC, Australia
| | - Abhimanyu
- Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, 7925, Western Cape, South Africa
| | - Xutao Wang
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biostatistics, Boston University, Boston, MA, USA
| | - W Evan Johnson
- Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biostatistics, Boston University, Boston, MA, USA
| | - Anna Coussens
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville 3279, VIC, Australia
- Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, 7925, Western Cape, South Africa
- Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
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105
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Zafari P, Golpour M, Hafezi N, Bashash D, Esmaeili SA, Tavakolinia N, Rafiei A. Tuberculosis comorbidity with rheumatoid arthritis: Gene signatures, associated biomarkers, and screening. IUBMB Life 2020; 73:26-39. [PMID: 33217772 DOI: 10.1002/iub.2413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
Rheumatoid arthritis (RA) is known to be related to an elevated risk of infections because of its pathobiology and the use of immunosuppressive therapies. Reactivation of latent tuberculosis (TB) infection is a serious issue in patients with RA, especially after receiving anti-TNFs therapy. TNF blocking reinforces the TB granuloma formation and maintenance and the growth of Mycobacterium tuberculosis (Mtb). After intercurrent of TB infection, the standard recommendation is that the treatment with TNF inhibitors to be withheld despite its impressive effect on suppression of inflammation until the infection has resolved. Knowing pathways and mechanisms that are common between two diseases might help to find the mechanistic basis of this comorbidity, as well as provide us a new approach to apply them as therapeutic targets or diagnostic biomarkers. Also, screening for latent TB before initiation of an anti-TNF therapy can minimize complications. This review summarizes the shared gene signature between TB and RA and discusses the biomarkers for early detection of this infection, and screening procedures as well.
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Affiliation(s)
- Parisa Zafari
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Monireh Golpour
- Molecular and Cellular Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Nasim Hafezi
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Naeimeh Tavakolinia
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Rafiei
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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106
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Gauthier M, Agniel D, Thiébaut R, Hejblum BP. dearseq: a variance component score test for RNA-seq differential analysis that effectively controls the false discovery rate. NAR Genom Bioinform 2020; 2:lqaa093. [PMID: 33575637 PMCID: PMC7676475 DOI: 10.1093/nargab/lqaa093] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 12/20/2022] Open
Abstract
RNA-seq studies are growing in size and popularity. We provide evidence that the most commonly used methods for differential expression analysis (DEA) may yield too many false positive results in some situations. We present dearseq, a new method for DEA that controls the false discovery rate (FDR) without making any assumption about the true distribution of RNA-seq data. We show that dearseq controls the FDR while maintaining strong statistical power compared to the most popular methods. We demonstrate this behavior with mathematical proofs, simulations and a real data set from a study of tuberculosis, where our method produces fewer apparent false positives.
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Affiliation(s)
- Marine Gauthier
- INRIA SISTM, INSERM Bordeaux Population Health Research Center, University of Bordeaux, F-33000 Bordeaux, France
| | | | - Rodolphe Thiébaut
- INRIA SISTM, INSERM Bordeaux Population Health Research Center, University of Bordeaux, F-33000 Bordeaux, France
| | - Boris P Hejblum
- INRIA SISTM, INSERM Bordeaux Population Health Research Center, University of Bordeaux, F-33000 Bordeaux, France
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107
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Type I IFN exacerbates disease in tuberculosis-susceptible mice by inducing neutrophil-mediated lung inflammation and NETosis. Nat Commun 2020; 11:5566. [PMID: 33149141 PMCID: PMC7643080 DOI: 10.1038/s41467-020-19412-6] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is a leading cause of mortality due to infectious disease, but the factors determining disease progression are unclear. Transcriptional signatures associated with type I IFN signalling and neutrophilic inflammation were shown to correlate with disease severity in mouse models of TB. Here we show that similar transcriptional signatures correlate with increased bacterial loads and exacerbate pathology during Mycobacterium tuberculosis infection upon GM-CSF blockade. Loss of GM-CSF signalling or genetic susceptibility to TB (C3HeB/FeJ mice) result in type I IFN-induced neutrophil extracellular trap (NET) formation that promotes bacterial growth and promotes disease severity. Consistently, NETs are present in necrotic lung lesions of TB patients responding poorly to antibiotic therapy, supporting the role of NETs in a late stage of TB pathogenesis. Our findings reveal an important cytokine-based innate immune effector network with a central role in determining the outcome of M. tuberculosis infection. GM-CSF is involved in control over M. tuberculosis infection. Here the authors show that GM-CSF reduces type 1 interferon driven neutrophil recruitment, NETosis and bacterial growth in the lungs of infected mice, and provide evidence that this NETosis occurs in infected humans who are not responsive to antibiotic therapy.
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108
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Lung gene expression signatures suggest pathogenic links and molecular markers for pulmonary tuberculosis, adenocarcinoma and sarcoidosis. Commun Biol 2020; 3:604. [PMID: 33097805 PMCID: PMC7584606 DOI: 10.1038/s42003-020-01318-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022] Open
Abstract
Previous reports have suggested a link between pulmonary tuberculosis (TB), which is caused by Mycobacterium tuberculosis (Mtb), and the development of lung adenocarcinoma (LUAD) and sarcoidosis. Furthermore, these lung diseases share certain clinical similarities that can challenge differential diagnosis in some cases. Here, through comparison of lung transcriptome-derived molecular signatures of TB, LUAD and sarcoidosis patients, we identify certain shared disease-related expression patterns. We also demonstrate that MKI67, an over-expressed gene shared by TB and LUAD, is a key mediator in Mtb-promoted tumor cell proliferation, migration, and invasion. Moreover, we reveal a distinct ossification-related TB lung signature, which may be associated with the activation of the BMP/SMAD/RUNX2 pathway in Mtb-infected macrophages that can restrain mycobacterial survival and promote osteogenic differentiation of mesenchymal stem cells. Taken together, these findings provide novel pathogenic links and potential molecular markers for better understanding and differential diagnosis of pulmonary TB, LUAD and sarcoidosis. Previous work has suggested potential links between Mycobacterium tuberculosis infection and the development of both lung cancer and sarcoidosis, in addition to tuberculosis. Here, Qiyao Chai, Zhe Lu, Zhidong Liu and colleagues report a transcriptomic analysis of lung tissue from tuberculosis, lung adenocarcinoma, and sarcoidosis patients and find that while many disease-linked expression changes are shared between the three diseases, each also has distinct transcriptional signatures that could be useful as molecular markers.
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109
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Sala C, Benjak A, Goletti D, Banu S, Mazza-Stadler J, Jaton K, Busso P, Remm S, Leleu M, Rougemont J, Palmieri F, Cuzzi G, Butera O, Vanini V, Kabir S, Rahman SMM, Nicod L, Cole ST. Multicenter analysis of sputum microbiota in tuberculosis patients. PLoS One 2020; 15:e0240250. [PMID: 33044973 PMCID: PMC7549818 DOI: 10.1371/journal.pone.0240250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
The impact of tuberculosis and of anti-tuberculosis therapy on composition and modification of human lung microbiota has been the object of several investigations. However, no clear outcome has been presented so far and the relationship between M. tuberculosis pulmonary infection and the resident lung microbiota remains vague. In this work we describe the results obtained from a multicenter study of the microbiota of sputum samples from patients with tuberculosis or unrelated lung diseases and healthy donors recruited in Switzerland, Italy and Bangladesh, with the ultimate goal of discovering a microbiota-based biomarker associated with tuberculosis. Bacterial 16S rDNA amplification, high-throughput sequencing and extensive bioinformatic analyses revealed patient-specific flora and high variability in taxon abundance. No common signature could be identified among the individuals enrolled except for minor differences which were not consistent among the different geographical settings. Moreover, anti-tuberculosis therapy did not cause any important variation in microbiota diversity, thus precluding its exploitation as a biomarker for the follow up of tuberculosis patients undergoing treatment.
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Affiliation(s)
- Claudia Sala
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrej Benjak
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Delia Goletti
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | | | | | - Katia Jaton
- Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Philippe Busso
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sille Remm
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marion Leleu
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,BioInformatics Competence Center, UNIL-EPFL, Lausanne, Switzerland
| | - Jacques Rougemont
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Department of Theoretical Physics, University of Geneva, Geneva, Switzerland
| | - Fabrizio Palmieri
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Gilda Cuzzi
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Ornella Butera
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Valentina Vanini
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | | | | | - Laurent Nicod
- Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Stewart T Cole
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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110
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Xia Q, Lee MH, Walsh KF, McAulay K, Bean JM, Fitzgerald DW, Dupnik KM, Johnson WD, Pape JW, Rhee KY, Isa F. Urinary biomarkers of mycobacterial load and treatment response in pulmonary tuberculosis. JCI Insight 2020; 5:136301. [PMID: 32809976 PMCID: PMC7526545 DOI: 10.1172/jci.insight.136301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/06/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUNDControl of the tuberculosis (TB) pandemic remains hindered in part by a lack of simple and accurate measures of treatment efficacy, as current gold standard markers rely on sputum-based assays that are slow and challenging to implement. However, previous work identified urinary N1, N12-diacetylspermine (DiAcSpm), neopterin, hydroxykynurenine, N-acetylhexosamine, ureidopropionic acid, sialic acid, and mass-to-charge ratio (m/z) 241.0903 as potential biomarkers of active pulmonary TB (ATB). Here, we evaluated their ability to serve as biomarkers of TB treatment response and mycobacterial load.METHODSWe analyzed urine samples prospectively collected from 2 cohorts with ATB. A total of 34 study participants from African countries treated with first-line TB therapy rifampin, isoniazid, pyrazinamide, and ethambutol (HRZE) were followed for 1 year, and 35 participants from Haiti treated with either HRZE or an experimental drug were followed for 14 days. Blinded samples were analyzed by untargeted HPLC-coupled high-resolution TOF-mass spectrometry.RESULTSUrinary levels of all 7 molecules significantly decreased by week 26 of successful treatment (P = 0.01 to P < 0.0001) and positively correlated with sputum mycobacterial load (P < 0.0001). Urinary DiAcSpm levels decreased significantly in participants treated with HRZE as early as 14 days (P < 0.0001) but remained unchanged in cases of ineffective therapy (P = 0.14).CONCLUSIONUrinary DiAcSpm, neopterin, hydroxykynurenine, N-acetylhexosamine, ureidopropionic acid, sialic acid, and m/z 241.0903 reductions correlated with successful anti-TB treatment and sputum mycobacterial load. Urinary DiAcSpm levels exhibited reductions capable of differentiating treatment success from failure as early as 2 weeks after the initiation of chemotherapy, advocating its further development as a potentially simple, noninvasive biomarker for assessing treatment response and bacterial load.FUNDINGThis work was supported by the Clinical and Translational Science Center at Weill Cornell College of Medicine (NIH/NCATS 1 UL1 TR002384-02 and KL2TR000458), the Department of Defense (PR170782), the National Institute of Allergy and Infectious Disease grants (NIAID T32AI007613-16, K24 AI098627, and K23 AI131913), the NIH Fogarty International Center grants (R24 TW007988 and TW010062), NIH grant (R01 GM135926), the Abby and Howard P. Milstein Program in Chemical Biology and Translational Medicine, and the Tuberculosis Research Units Networks (TBRU-N, AI111143).
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Affiliation(s)
| | | | | | - Kathrine McAulay
- Center for Global Health
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
| | - James M. Bean
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Daniel W. Fitzgerald
- Center for Global Health
- Department of Medicine, and
- Les Centres GHESKIO, Port-au-Prince, Haiti
| | | | - Warren D. Johnson
- Center for Global Health
- Department of Medicine, and
- Les Centres GHESKIO, Port-au-Prince, Haiti
| | - Jean W. Pape
- Center for Global Health
- Les Centres GHESKIO, Port-au-Prince, Haiti
| | - Kyu Y. Rhee
- Center for Global Health
- Department of Medicine, and
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
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111
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Vestal BE, Moore CM, Wynn E, Saba L, Fingerlin T, Kechris K. MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments. BMC Bioinformatics 2020; 21:375. [PMID: 32859148 PMCID: PMC7455910 DOI: 10.1186/s12859-020-03715-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/18/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND As the barriers to incorporating RNA sequencing (RNA-Seq) into biomedical studies continue to decrease, the complexity and size of RNA-Seq experiments are rapidly growing. Paired, longitudinal, and other correlated designs are becoming commonplace, and these studies offer immense potential for understanding how transcriptional changes within an individual over time differ depending on treatment or environmental conditions. While several methods have been proposed for dealing with repeated measures within RNA-Seq analyses, they are either restricted to handling only paired measurements, can only test for differences between two groups, and/or have issues with maintaining nominal false positive and false discovery rates. In this work, we propose a Bayesian hierarchical negative binomial generalized linear mixed model framework that can flexibly model RNA-Seq counts from studies with arbitrarily many repeated observations, can include covariates, and also maintains nominal false positive and false discovery rates in its posterior inference. RESULTS In simulation studies, we showed that our proposed method (MCMSeq) best combines high statistical power (i.e. sensitivity or recall) with maintenance of nominal false positive and false discovery rates compared the other available strategies, especially at the smaller sample sizes investigated. This behavior was then replicated in an application to real RNA-Seq data where MCMSeq was able to find previously reported genes associated with tuberculosis infection in a cohort with longitudinal measurements. CONCLUSIONS Failing to account for repeated measurements when analyzing RNA-Seq experiments can result in significantly inflated false positive and false discovery rates. Of the methods we investigated, whether they model RNA-Seq counts directly or worked on transformed values, the Bayesian hierarchical model implemented in the mcmseq R package (available at https://github.com/stop-pre16/mcmseq ) best combined sensitivity and nominal error rate control.
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Affiliation(s)
- Brian E. Vestal
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St, Denver, 80206 CO USA
| | - Camille M. Moore
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St, Denver, 80206 CO USA
| | - Elizabeth Wynn
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St, Denver, 80206 CO USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO USA
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112
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Scriba TJ, Netea MG, Ginsberg AM. Key recent advances in TB vaccine development and understanding of protective immune responses against Mycobacterium tuberculosis. Semin Immunol 2020; 50:101431. [PMID: 33279383 PMCID: PMC7786643 DOI: 10.1016/j.smim.2020.101431] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/02/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022]
Abstract
Tuberculosis is the leading infectious disease killer globally due to a single pathogen. Despite wide deployment of standard drug regimens, modern diagnostics and a vaccine (bacille Calmette Guerin, BCG), the global tuberculosis epidemic is inadequately controlled. Novel, effective vaccine(s) are a crucial element of the World Health Organization End TB Strategy. TB vaccine research and development has recently been catalysed by several factors, including a revised strategy focused first on preventing pulmonary TB in adolescents and adults who are the main source of transmission, and encouraging evaluations of novel efficacy endpoints. Renewed enthusiasm for TB vaccine research has also been stimulated by recent preclinical and clinical advancements. These include new insights into underlying protective immune responses, including potential roles for 'trained' innate immunity and Th1/Th17 CD4+ (and CD8+) T cells. The field has been further reinvigorated by two positive proof of concept efficacy trials: one evaluating a potential new use of BCG in preventing high risk populations from sustained Mycobacterium tuberculosis infection and the second evaluating a novel, adjuvanted, recombinant protein vaccine candidate (M72/AS01E) for prevention of disease in adults already infected. Fourteen additional candidates are currently in various phases of clinical evaluation and multiple approaches to next generation vaccines are in discovery and preclinical development. The two positive efficacy trials and recent studies in nonhuman primates have enabled the first opportunities to discover candidate vaccine-induced correlates of protection, an effort being undertaken by a broad research consortium.
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Affiliation(s)
- Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, Geert Grooteplein 8, 6525 GA Nijmegen, the Netherlands; Department of Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Germany.
| | - Ann M Ginsberg
- Bill & Melinda Gates Foundation, Division of Global Health, Washington DC, United States.
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113
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Estévez O, Anibarro L, Garet E, Pallares Á, Barcia L, Calviño L, Maueia C, Mussá T, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M, López-Fernández H, Fonseca NA, Reljic R, González-Fernández Á. An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile. Front Immunol 2020; 11:1470. [PMID: 32760401 PMCID: PMC7372107 DOI: 10.3389/fimmu.2020.01470] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
A better understanding of the response against Tuberculosis (TB) infection is required to accurately identify the individuals with an active or a latent TB infection (LTBI) and also those LTBI patients at higher risk of developing active TB. In this work, we have used the information obtained from studying the gene expression profile of active TB patients and their infected –LTBI- or uninfected –NoTBI- contacts, recruited in Spain and Mozambique, to build a class-prediction model that identifies individuals with a TB infection profile. Following this approach, we have identified several genes and metabolic pathways that provide important information of the immune mechanisms triggered against TB infection. As a novelty of our work, a combination of this class-prediction model and the direct measurement of different immunological parameters, was used to identify a subset of LTBI contacts (called TB-like) whose transcriptional and immunological profiles are suggestive of infection with a higher probability of developing active TB. Validation of this novel approach to identifying LTBI individuals with the highest risk of active TB disease merits further longitudinal studies on larger cohorts in TB endemic areas.
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Affiliation(s)
- Olivia Estévez
- CINBIO, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas-Marcosende, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Luis Anibarro
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.,Tuberculosis Unit, Department of Infectious Diseases and Internal Medicine, University Hospital Complex of Pontevedra, Pontevedra, Spain.,Grupo de Estudio de Infecciones por Micobacterias (GEIM), Spanish Society of Infectious Diseases (SEIMC), Madrid, Spain
| | - Elina Garet
- CINBIO, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas-Marcosende, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Ángeles Pallares
- Department of Microbiology, University Hospital Complex of Pontevedra, Pontevedra, Spain
| | - Laura Barcia
- Tuberculosis Unit, Department of Infectious Diseases and Internal Medicine, University Hospital Complex of Pontevedra, Pontevedra, Spain
| | - Laura Calviño
- Tuberculosis Unit, Department of Infectious Diseases and Internal Medicine, University Hospital Complex of Pontevedra, Pontevedra, Spain
| | - Cremildo Maueia
- Departamento de Plataformas Tecnológicas, Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Tufária Mussá
- Departamento de Plataformas Tecnológicas, Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique.,Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Florentino Fdez-Riverola
- CINBIO, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas-Marcosende, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.,ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universitario As Lagoas s/n, Universidad de Vigo, Ourense, Spain
| | - Daniel Glez-Peña
- CINBIO, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas-Marcosende, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.,ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universitario As Lagoas s/n, Universidad de Vigo, Ourense, Spain
| | - Miguel Reboiro-Jato
- CINBIO, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas-Marcosende, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.,ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universitario As Lagoas s/n, Universidad de Vigo, Ourense, Spain
| | - Hugo López-Fernández
- CINBIO, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas-Marcosende, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.,ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universitario As Lagoas s/n, Universidad de Vigo, Ourense, Spain
| | - Nuno A Fonseca
- European Bioinformatics Institute, Cambridge, United Kingdom.,CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal
| | - Rajko Reljic
- St. George's, University of London, London, United Kingdom
| | - África González-Fernández
- CINBIO, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas-Marcosende, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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114
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Alvarez AH, Flores-Valdez MA. Can immunization with Bacillus Calmette-Guérin be improved for prevention or therapy and elimination of chronic Mycobacterium tuberculosis infection? Expert Rev Vaccines 2020; 18:1219-1227. [PMID: 31826664 DOI: 10.1080/14760584.2019.1704263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: Tuberculosis (TB) is one of the most prevalent infectious diseases in the world. Current vaccination with BCG can prevent meningeal and disseminated TB in children. However, success against latent pulmonary TB infection (LTBI) or its reactivation is limited. Evidence suggests that there may be means to improve the efficacy of BCG raising the possibility of developing new vaccine candidates against LTBI.Areas covered: BCG improvements include the use of purified mycobacterial immunogenic proteins, either from an active or dormant state, as well as expressing those proteins from recombinant BCG strains that harvor those specific genes. It also includes boost protein mixtures with synthetic adjuvants or within liposomes, as a way to increase a protective immune response during chronic TB produced in laboratory animal models. References cited were chosen from PubMed searches.Expertopinion: Strategies aiming to improve or boost BCG have been receiving increased attention. With the advent of -omics, it has been possible to dissect several specific stages during mycobacterial infection. Recent experimental models of disease, diagnostic and immunological data obtained from individual M. tuberculosis antigens could introduce promising developments for more effective TB vaccines that may contribute to eliminating the hidden (latent) form of this infectious disease.
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Affiliation(s)
- A H Alvarez
- Biotecnología Médica Farmacéutica (CIATEJ-CONACYT), Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Guadalajara, México
| | - M A Flores-Valdez
- Biotecnología Médica Farmacéutica (CIATEJ-CONACYT), Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Guadalajara, México
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115
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Kwan PKW, Periaswamy B, De Sessions PF, Lin W, Molton JS, Naftalin CM, Naim ANM, Hibberd ML, Paton NI. A blood RNA transcript signature for TB exposure in household contacts. BMC Infect Dis 2020; 20:403. [PMID: 32517725 PMCID: PMC7282166 DOI: 10.1186/s12879-020-05116-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/24/2020] [Indexed: 11/10/2022] Open
Abstract
Background Current tools for diagnosing latent TB infection (LTBI) detect immunological memory of past exposure but are unable to determine whether exposure is recent. We sought to identify a whole-blood transcriptome signature of recent TB exposure. Methods We studied household contacts of TB patients; healthy volunteers without recent history of TB exposure; and patients with active TB. We performed whole-blood RNA sequencing (in all), an interferon gamma release assay (IGRA; in contacts and healthy controls) and PET/MRI lung scans (in contacts only). We evaluated differentially-expressed genes in household contacts (log2 fold change ≥1 versus healthy controls; false-discovery rate < 0.05); compared these to differentially-expressed genes seen in the active TB group; and assessed the association of a composite gene expression score to independent exposure/treatment/immunological variables. Results There were 186 differentially-expressed genes in household contacts (n = 26, age 22–66, 46% male) compared with healthy controls (n = 5, age 29–38, 100% male). Of these genes, 141 (76%) were also differentially expressed in active TB (n = 14, age 27–69, 71% male). The exposure signature included genes from inflammatory response, type I interferon signalling and neutrophil-mediated immunity pathways; and genes such as BATF2 and SCARF1 known to be associated with incipient TB. The composite gene-expression score was higher in IGRA-positive contacts (P = 0.04) but not related to time from exposure, isoniazid prophylaxis, or abnormalities on PET/MRI (all P > 0.19). Conclusions Transcriptomics can detect TB exposure and, with further development, may be an approach of value for epidemiological research and targeting public health interventions.
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Affiliation(s)
- Philip Kam Weng Kwan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 10, 1E Kent Ridge Road, Singapore, 119228, Singapore
| | - Balamurugan Periaswamy
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Paola Florez De Sessions
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wenwei Lin
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 10, 1E Kent Ridge Road, Singapore, 119228, Singapore
| | - James S Molton
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 10, 1E Kent Ridge Road, Singapore, 119228, Singapore
| | - Claire M Naftalin
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 10, 1E Kent Ridge Road, Singapore, 119228, Singapore
| | - Ahmad Nazri Mohamed Naim
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Martin L Hibberd
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,London School of Hygiene & Tropical Medicine, London, UK.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nicholas I Paton
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 10, 1E Kent Ridge Road, Singapore, 119228, Singapore. .,London School of Hygiene & Tropical Medicine, London, UK.
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116
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Penn-Nicholson A, Mbandi SK, Thompson E, Mendelsohn SC, Suliman S, Chegou NN, Malherbe ST, Darboe F, Erasmus M, Hanekom WA, Bilek N, Fisher M, Kaufmann SHE, Winter J, Murphy M, Wood R, Morrow C, Van Rhijn I, Moody B, Murray M, Andrade BB, Sterling TR, Sutherland J, Naidoo K, Padayatchi N, Walzl G, Hatherill M, Zak D, Scriba TJ. RISK6, a 6-gene transcriptomic signature of TB disease risk, diagnosis and treatment response. Sci Rep 2020; 10:8629. [PMID: 32451443 PMCID: PMC7248089 DOI: 10.1038/s41598-020-65043-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 04/27/2020] [Indexed: 11/17/2022] Open
Abstract
Improved tuberculosis diagnostics and tools for monitoring treatment response are urgently needed. We developed a robust and simple, PCR-based host-blood transcriptomic signature, RISK6, for multiple applications: identifying individuals at risk of incident disease, as a screening test for subclinical or clinical tuberculosis, and for monitoring tuberculosis treatment. RISK6 utility was validated by blind prediction using quantitative real-time (qRT) PCR in seven independent cohorts. Prognostic performance significantly exceeded that of previous signatures discovered in the same cohort. Performance for diagnosing subclinical and clinical disease in HIV-uninfected and HIV-infected persons, assessed by area under the receiver-operating characteristic curve, exceeded 85%. As a screening test for tuberculosis, the sensitivity at 90% specificity met or approached the benchmarks set out in World Health Organization target product profiles for non-sputum-based tests. RISK6 scores correlated with lung immunopathology activity, measured by positron emission tomography, and tracked treatment response, demonstrating utility as treatment response biomarker, while predicting treatment failure prior to treatment initiation. Performance of the test in capillary blood samples collected by finger-prick was noninferior to venous blood collected in PAXgene tubes. These results support incorporation of RISK6 into rapid, capillary blood-based point-of-care PCR devices for prospective assessment in field studies.
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Affiliation(s)
- Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ethan Thompson
- Center for Infectious Disease Research, Seattle, WA, USA
| | - Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Sara Suliman
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.,Brigham and Women's Hospital, Division of Rheumatology, Immunity and Inflammation, Harvard Medical School, Boston, USA
| | - Novel N Chegou
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stephanus T Malherbe
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Fatoumatta Darboe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mzwandile Erasmus
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Willem A Hanekom
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Stefan H E Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany.,Hagler Institute for Advanced Study at Texas A&M University, College Station, TX, USA
| | - Jill Winter
- Catalysis Foundation for Health, San Ramon, CA, USA
| | - Melissa Murphy
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Robin Wood
- Desmond Tutu HIV Centre, and Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Carl Morrow
- Desmond Tutu HIV Centre, and Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Ildiko Van Rhijn
- Brigham and Women's Hospital, Division of Rheumatology, Immunity and Inflammation, Harvard Medical School, Boston, USA
| | - Branch Moody
- Brigham and Women's Hospital, Division of Rheumatology, Immunity and Inflammation, Harvard Medical School, Boston, USA
| | - Megan Murray
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bruno B Andrade
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Jayne Sutherland
- Vaccines and Immunity, Medical Research Council Unit, Fajara, The Gambia
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in Africa, Durban, South Africa.,South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in Africa, Durban, South Africa.,South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Gerhard Walzl
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Daniel Zak
- Center for Infectious Disease Research, Seattle, WA, USA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
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Devlin JC, Zwack EE, Tang MS, Li Z, Fenyo D, Torres VJ, Ruggles KV, Loke P. Distinct Features of Human Myeloid Cell Cytokine Response Profiles Identify Neutrophil Activation by Cytokines as a Prognostic Feature during Tuberculosis and Cancer. THE JOURNAL OF IMMUNOLOGY 2020; 204:3389-3399. [PMID: 32350082 DOI: 10.4049/jimmunol.1901133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/13/2020] [Indexed: 12/14/2022]
Abstract
Myeloid cells are a vital component of innate immunity and comprise monocytes, macrophages, dendritic cells, and granulocytes. How myeloid cell lineage affects activation states in response to cytokines remains poorly understood. The cytokine environment and cellular infiltrate during an inflammatory response may contain prognostic features that predict disease outcome. In this study, we analyzed the transcriptional responses of human monocytes, macrophages, dendritic cells, and neutrophils in response to stimulation by IFN-γ, IFN-β, IFN-λ, IL-4, IL-13, and IL-10 cytokines to better understand the heterogeneity of activation states in inflammatory conditions. This generated a myeloid cell-cytokine-specific response matrix that can infer representation of myeloid cells and the cytokine environment they encounter during infection, in tumors and in whole blood. Neutrophils were highly responsive to type 1 and type 2 cytokine stimulation but did not respond to IL-10. We identified transcripts specific to IFN-β stimulation, whereas other IFN signature genes were upregulated by both IFN-γ and IFN-β. When we used our matrix to deconvolute blood profiles from tuberculosis patients, the IFN-β-specific neutrophil signature was reduced in tuberculosis patients with active disease, whereas the shared response to IFN-γ and IFN-β in neutrophils was increased. When applied to glioma patients, transcripts of neutrophils exposed to IL-4/IL-13 and monocyte responses to IFN-γ or IFN-β emerged as opposing predictors of patient survival. Hence, by dissecting how different myeloid cells respond to cytokine activation, we can delineate biological roles for myeloid cells in different cytokine environments during disease processes, especially during infection and tumor progression.
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Affiliation(s)
- Joseph C Devlin
- Sackler Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016.,Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016.,Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016
| | - Erin E Zwack
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016
| | - Mei San Tang
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016
| | - Zhi Li
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016
| | - David Fenyo
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Victor J Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016;
| | - Kelly V Ruggles
- Sackler Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016; .,Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016.,Division of Translational Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016.,Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016; and
| | - P'ng Loke
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016; .,Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
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118
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Ho J, Bokil NJ, Nguyen PTB, Nguyen TA, Liu MY, Hare N, Fox GJ, Saunders BM, Marks GB, Britton WJ. A transcriptional blood signature distinguishes early tuberculosis disease from latent tuberculosis infection and uninfected individuals in a Vietnamese cohort. J Infect 2020; 81:72-80. [PMID: 32330522 DOI: 10.1016/j.jinf.2020.03.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Global tuberculosis (TB) control is restricted by the failure to detect an estimated 3.3 million TB cases annually. In the majority of TB endemic settings, sputum smear microscopy is used to diagnose TB, but this test is insensitive for TB in its early stages. The objective of this study is to establish a concise gene signature that discriminates between individuals with early TB disease, latent TB infection (LTBI) and those without infection. METHODS This is a case control study nested within a cluster-randomised trial of population screening for active TB using Xpert MTB/RIF. Whole blood samples from 303 participants with active TB (97), LTBI (92) and uninfected individuals (114) were subject to transcriptomic analysis of selected target genes based on a systematic review of previous studies. RESULTS Analysis of 82 genes identified a pattern of differentially expressed genes in TB disease. A seven gene signature was identified that distinguished between TB disease and no TB disease with an AUC of 0.86 (95% CI: 0.80-0.91), and between TB disease from LTBI with an AUC of 0.88 (95% CI: 0.82-0.93). CONCLUSION This gene signature accurately distinguishes early TB disease from those without TB disease or infection, in the context of community-wide TB screening. It could be used as a non-sputum based screening tool or triage test to detect prevalent cases of TB in the community.
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Affiliation(s)
- Jennifer Ho
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, Australia; Centenary Institute, The University of Sydney, Sydney, Australia.
| | - Nilesh J Bokil
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Phuong Thi Bich Nguyen
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia
| | - Thu Anh Nguyen
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia
| | - Michael Y Liu
- The ithree Institute, University of Technology Sydney, Sydney, Australia
| | - Nathan Hare
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Greg J Fox
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Bernadette M Saunders
- Centenary Institute, The University of Sydney, Sydney, Australia; School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Guy B Marks
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, Australia
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, Australia; Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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119
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Turner CT, Gupta RK, Tsaliki E, Roe JK, Mondal P, Nyawo GR, Palmer Z, Miller RF, Reeve BW, Theron G, Noursadeghi M. Blood transcriptional biomarkers for active pulmonary tuberculosis in a high-burden setting: a prospective, observational, diagnostic accuracy study. THE LANCET. RESPIRATORY MEDICINE 2020; 8:407-419. [PMID: 32178775 PMCID: PMC7113842 DOI: 10.1016/s2213-2600(19)30469-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND Blood transcriptional signatures are candidates for non-sputum triage or confirmatory tests of tuberculosis. Prospective head-to-head comparisons of their diagnostic accuracy in real-world settings are necessary to assess their clinical use. We aimed to compare the diagnostic accuracy of candidate transcriptional signatures identified by systematic review, in a setting with a high burden of tuberculosis and HIV. METHODS We did a prospective observational study nested within a diagnostic accuracy study of sputum Xpert MTB/RIF (Xpert) and Xpert MTB/RIF Ultra (Ultra) tests for pulmonary tuberculosis. We recruited consecutive symptomatic adults aged 18 years or older self-presenting to a tuberculosis clinic in Cape Town, South Africa. Participants provided blood for RNA sequencing, and sputum samples for liquid culture and molecular testing using Xpert and Ultra. We assessed the diagnostic accuracy of candidate blood transcriptional signatures for active tuberculosis (including those intended to distinguish active tuberculosis from other diseases) identified by systematic review, compared with culture or Xpert MTB/RIF positivity as the standard reference. In our primary analysis, patients with tuberculosis were defined as those with either a positive liquid culture or Xpert result. Patients with missing blood RNA or sputum results were excluded. Our primary objective was to benchmark the diagnostic accuracy of candidate transcriptional signatures against the WHO target product profile (TPP) for a tuberculosis triage test. FINDINGS Between Feb 12, 2016, and July 18, 2017, we obtained paired sputum and RNA sequencing data from 181 participants, 54 (30%) of whom had confirmed pulmonary tuberculosis. Of 27 eligible signatures identified by systematic review, four achieved the highest diagnostic accuracy with similar area under the receiver operating characteristic curves (Sweeney3: 90·6% [95% CI 85·6-95·6]; Kaforou25: 86·9% [80·9-92·9]; Roe3: 86·9% [80·3-93·5]; and BATF2: 86·8% [80·6-93·1]), independent of age, sex, HIV status, previous tuberculosis, or sputum smear result. At test thresholds that gave 70% specificity (the minimum WHO TPP specificity for a triage test), these four signatures achieved sensitivities between 83·3% (95% CI 71·3-91·0) and 90·7% (80·1-96·0). No signature met the optimum criteria, of 95% sensitivity and 80% specificity proposed by WHO for a triage test, or the minimum criteria (of 65% sensitivity and 98% specificity) for a confirmatory test, but all four correctly identified Ultra-positive, culture-negative patients. INTERPRETATION Selected blood transcriptional signatures met the minimum WHO benchmarks for a tuberculosis triage test but not for a confirmatory test. Further development of the signatures is warranted to investigate their possible effects on clinical and health economic outcomes as part of a triage strategy, or when used as add-on confirmatory test in conjunction with the highly sensitive Ultra test for Mycobacterium tuberculosis DNA. FUNDING Royal Society Newton Advanced Fellowship, Wellcome Trust, National Institute of Health Research, and UK Medical Research Council.
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Affiliation(s)
- Carolin T Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Rishi K Gupta
- Institute for Global Health, University College London, London, UK
| | - Evdokia Tsaliki
- Division of Infection and Immunity, University College London, London, UK
| | - Jennifer K Roe
- Division of Infection and Immunity, University College London, London, UK
| | - Prasenjit Mondal
- Division of Infection and Immunity, University College London, London, UK
| | - Georgina R Nyawo
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; and Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Zaida Palmer
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; and Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robert F Miller
- Institute for Global Health, University College London, London, UK
| | - Byron Wp Reeve
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; and Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Grant Theron
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; and Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK.
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120
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Gupta RK, Turner CT, Venturini C, Esmail H, Rangaka MX, Copas A, Lipman M, Abubakar I, Noursadeghi M. Concise whole blood transcriptional signatures for incipient tuberculosis: a systematic review and patient-level pooled meta-analysis. THE LANCET. RESPIRATORY MEDICINE 2020; 8:395-406. [PMID: 31958400 PMCID: PMC7113839 DOI: 10.1016/s2213-2600(19)30282-6] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Multiple blood transcriptional signatures have been proposed for identification of active and incipient tuberculosis. We aimed to compare the performance of systematically identified candidate signatures for incipient tuberculosis and to benchmark these against WHO targets. METHODS We did a systematic review and individual participant data meta-analysis. We searched Medline and Embase for candidate whole blood mRNA signatures discovered with the primary objective of diagnosis of active or incipient tuberculosis, compared with controls who were healthy or had latent tuberculosis infection. We tested the performance of eligible signatures in whole blood transcriptomic datasets, in which sampling before tuberculosis diagnosis was done and time to disease was available. Culture-confirmed and clinically or radiologically diagnosed pulmonary or extrapulmonary tuberculosis cases were included. Non-progressor (individuals who remained tuberculosis-free during follow-up) samples with less than 6 months of follow-up from the date of sample collection were excluded, as were participants with prevalent tuberculosis and those who received preventive therapy. Scores were calculated for candidate signatures for each participant in the pooled dataset. Receiver operating characteristic curves, sensitivities, and specificities were examined using prespecified intervals to tuberculosis (<3 months, <6 months, <1 year, and <2 years) from sample collection. This study is registered with PROSPERO, number CRD42019135618. RESULTS We tested 17 candidate mRNA signatures in a pooled dataset from four eligible studies comprising 1126 samples. This dataset included 183 samples from 127 incipient tuberculosis cases in South Africa, Ethiopia, The Gambia, and the UK. Eight signatures (comprising 1-25 transcripts) that predominantly reflect interferon and tumour necrosis factor-inducible gene expression, had equivalent diagnostic accuracy for incipient tuberculosis over a 2-year period with areas under the receiver operating characteristic curves ranging from 0·70 (95% CI 0·64-0·76) to 0·77 (0·71-0·82). The sensitivity of all eight signatures declined with increasing disease-free time interval. Using a threshold derived from two SDs above the mean of uninfected controls to prioritise specificity and positive-predictive value, the eight signatures achieved sensitivities of 24·7-39·9% over 24 months and of 47·1-81·0% over 3 months, with corresponding specificities of more than 90%. Based on pre-test probability of 2%, the eight signatures achieved positive-predictive values ranging from 6·8-9·4% over 24 months and 11·2-14·4% over 3 months. When using biomarker thresholds maximising sensitivity and specificity with equal weighting to both, no signature met the minimum WHO target product profile parameters for incipient tuberculosis biomarkers over a 2-year period. INTERPRETATION Blood transcriptional biomarkers reflect short-term risk of tuberculosis and only exceed WHO benchmarks if applied to 3-6-month intervals. Serial testing among carefully selected target groups might be required for optimal implementation of these biomarkers. FUNDING Wellcome Trust and National Institute for Health Research.
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Affiliation(s)
- Rishi K Gupta
- Institute for Global Health, University College London, London, UK
| | - Carolin T Turner
- Division of Infection & Immunity, University College London, London, UK
| | | | - Hanif Esmail
- Institute for Global Health, University College London, London, UK; Medical Research Council Clinical Trials Unit, University College London, London, UK; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Molebogeng X Rangaka
- Institute for Global Health, University College London, London, UK; Medical Research Council Clinical Trials Unit, University College London, London, UK; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Epidemiology and Biostatistics, School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Andrew Copas
- Institute for Global Health, University College London, London, UK; Medical Research Council Clinical Trials Unit, University College London, London, UK
| | - Marc Lipman
- UCL-TB and UCL Respiratory, University College London, London, UK; Department of Respiratory Medicine, Royal Free London NHS Foundation Trust, London, UK
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection & Immunity, University College London, London, UK.
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Moreira-Teixeira L, Tabone O, Graham CM, Singhania A, Stavropoulos E, Redford PS, Chakravarty P, Priestnall SL, Suarez-Bonnet A, Herbert E, Mayer-Barber KD, Sher A, Fonseca KL, Sousa J, Cá B, Verma R, Haldar P, Saraiva M, O'Garra A. Mouse transcriptome reveals potential signatures of protection and pathogenesis in human tuberculosis. Nat Immunol 2020; 21:464-476. [PMID: 32205882 PMCID: PMC7116040 DOI: 10.1038/s41590-020-0610-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/20/2020] [Indexed: 12/22/2022]
Abstract
Although mouse infection models have been extensively used to study the host response to Mycobacterium tuberculosis, their validity in revealing determinants of human tuberculosis (TB) resistance and disease progression has been heavily debated. Here, we show that the modular transcriptional signature in the blood of susceptible mice infected with a clinical isolate of M. tuberculosis resembles that of active human TB disease, with dominance of a type I interferon response and neutrophil activation and recruitment, together with a loss in B lymphocyte, natural killer and T cell effector responses. In addition, resistant but not susceptible strains of mice show increased lung B cell, natural killer and T cell effector responses in the lung upon infection. Notably, the blood signature of active disease shared by mice and humans is also evident in latent TB progressors before diagnosis, suggesting that these responses both predict and contribute to the pathogenesis of progressive M. tuberculosis infection.
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Affiliation(s)
| | - Olivier Tabone
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | - Christine M Graham
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | - Akul Singhania
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | | | - Paul S Redford
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
- GSK R&D, Medicines Research Centre, Stevenage, UK
| | | | - Simon L Priestnall
- Department of Pathobiology & Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology Team, The Francis Crick Institute, London, UK
| | - Alejandro Suarez-Bonnet
- Department of Pathobiology & Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology Team, The Francis Crick Institute, London, UK
| | - Eleanor Herbert
- Department of Pathobiology & Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology Team, The Francis Crick Institute, London, UK
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kaori L Fonseca
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Programa de Pós-Graduação Ciência para o Desenvolvimento (PGCD), Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Jeremy Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Baltazar Cá
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Programa de Pós-Graduação Ciência para o Desenvolvimento (PGCD), Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Raman Verma
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Pranabashis Haldar
- Department of Respiratory Sciences, National Institute for Health Research Respiratory Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Anne O'Garra
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK.
- National Heart and Lung Institute, Imperial College London, London, UK.
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122
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Cai Y, Dai Y, Wang Y, Yang Q, Guo J, Wei C, Chen W, Huang H, Zhu J, Zhang C, Zheng W, Wen Z, Liu H, Zhang M, Xing S, Jin Q, Feng CG, Chen X. Single-cell transcriptomics of blood reveals a natural killer cell subset depletion in tuberculosis. EBioMedicine 2020; 53:102686. [PMID: 32114394 PMCID: PMC7047188 DOI: 10.1016/j.ebiom.2020.102686] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 12/14/2022] Open
Abstract
Background Tuberculosis (TB) continues to be a critical global health problem, which killed millions of lives each year. Certain circulating cell subsets are thought to differentially modulate the host immune response towards Mycobacterium tuberculosis (Mtb) infection, but the nature and function of these subsets is unclear. Methods Peripheral blood mononuclear cells (PBMC) were isolated from healthy controls (HC), latent tuberculosis infection (LTBI) and active tuberculosis (TB) and then subjected to single-cell RNA sequencing (scRNA-seq) using 10 × Genomics platform. Unsupervised clustering of the cells based on the gene expression profiles using the Seurat package and passed to tSNE for clustering visualization. Flow cytometry was used to validate the subsets identified by scRNA-Seq. Findings Cluster analysis based on differential gene expression revealed both known and novel markers for all main PBMC cell types and delineated 29 cell subsets. By comparing the scRNA-seq datasets from HC, LTBI and TB, we found that infection changes the frequency of immune-cell subsets in TB. Specifically, we observed gradual depletion of a natural killer (NK) cell subset (CD3-CD7+GZMB+) from HC, to LTBI and TB. We further verified that the depletion of CD3-CD7+GZMB+ subset in TB and found an increase in this subset frequency after anti-TB treatment. Finally, we confirmed that changes in this subset frequency can distinguish patients with TB from LTBI and HC. Interpretation We propose that the frequency of CD3-CD7+GZMB+ in peripheral blood could be used as a novel biomarker for distinguishing TB from LTBI and HC. Fund The study was supported by Natural Science Foundation of China (81770013, 81525016, 81772145, 81871255 and 91942315), National Science and Technology Major Project (2017ZX10201301), Science and Technology Project of Shenzhen (JCYJ20170412101048337) and Guangdong Provincial Key Laboratory of Regional Immunity and Diseases (2019B030301009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Yi Cai
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Youchao Dai
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China; Research Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510000, China
| | - Yejun Wang
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Qianqing Yang
- Guangdong Key Lab for Diagnosis &Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518000, China
| | - Jiubiao Guo
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Cailing Wei
- Guangdong Key Lab for Diagnosis &Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518000, China
| | - Weixin Chen
- Guangdong Key Lab for Diagnosis &Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518000, China
| | - Huanping Huang
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Jialou Zhu
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Chi Zhang
- Shenzhen University General Hospital, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Weidong Zheng
- Shenzhen University General Hospital, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Zhihua Wen
- Yuebei Second People's Hospital, Shaoguan 512000, China
| | - Haiying Liu
- The MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Mingxia Zhang
- Guangdong Key Lab for Diagnosis &Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518000, China
| | - Shaojun Xing
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
| | - Qi Jin
- The MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Carl G Feng
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China; Department of Infectious Diseases and Immunology, Sydney Medical School, the University of Sydney, Sydney, NSW 2006, Australia
| | - Xinchun Chen
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China.
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Infect and Inject: How Mycobacterium tuberculosis Exploits Its Major Virulence-Associated Type VII Secretion System, ESX-1. Microbiol Spectr 2020; 7. [PMID: 31172908 PMCID: PMC6698389 DOI: 10.1128/microbiolspec.bai-0024-2019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium tuberculosis is an ancient master of the art of causing human disease. One important weapon within its fully loaded arsenal is the type VII secretion system. M. tuberculosis has five of them: ESAT-6 secretion systems (ESX) 1 to 5. ESX-1 has long been recognized as a major cause of attenuation of the FDA-licensed vaccine Mycobacterium bovis BCG, but its importance in disease progression and transmission has recently been elucidated in more detail. This review summarizes the recent advances in (i) the understanding of the ESX-1 structure and components, (ii) our knowledge of ESX-1's role in hijacking macrophage function to set a path for infection and dissemination, and (iii) the development of interventions that utilize ESX-1 for diagnosis, drug interventions, host-directed therapies, and vaccines.
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Fonseca KL, Maceiras AR, Matos R, Simoes-Costa L, Sousa J, Cá B, Barros L, Fernandes AI, Mereiter S, Reis R, Gomes J, Tapia G, Rodríguez-Martínez P, Martín-Céspedes M, Vashakidze S, Gogishvili S, Nikolaishvili K, Appelberg R, Gärtner F, Rodrigues PNS, Vilaplana C, Reis CA, Magalhães A, Saraiva M. Deficiency in the glycosyltransferase Gcnt1 increases susceptibility to tuberculosis through a mechanism involving neutrophils. Mucosal Immunol 2020; 13:836-848. [PMID: 32203062 PMCID: PMC7434595 DOI: 10.1038/s41385-020-0277-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 02/12/2020] [Indexed: 02/04/2023]
Abstract
Modulation of immunity and disease by glycans is increasingly recognized. However, how host glycosylation shapes and is shaped by tuberculosis remains poorly understood. We show that deficiency in the glucosaminyl (N-acetyl) transferase 1 (Gcnt1), a key enzyme for core-2 O-glycans biosynthesis, drives susceptibility to Mycobacterium tuberculosis infection. The increased susceptibility of Gcnt1 deficient mice was characterized by extensive lung immune pathology, mechanistically related to neutrophils. Uninfected Gcnt1 deficient mice presented bone marrow, blood and lung neutrophilia, which further increased with infection. Blood neutrophilia required Gcnt1 deficiency in the hematopoietic compartment, relating with enhanced granulopoiesis, but normal cellular egress from the bone marrow. Interestingly, for the blood neutrophilia to translate into susceptibility to M. tuberculosis infection, Gnct1 deficiency in the stroma was also necessary. Complete Gcnt1 deficiency associated with increased lung expression of the neutrophil chemoattractant CXCL2. Lastly, we demonstrate that the transcript levels of various glycosyltransferase-encoding genes were altered in whole blood of active tuberculosis patients and that sialyl Lewis x, a glycan widely present in human neutrophils, was detected in the lung of tuberculosis patients. Our findings reveal a previously unappreciated link between Gcnt1, neutrophilia and susceptibility to M. tuberculosis infection, uncovering new players balancing the immune response in tuberculosis.
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Affiliation(s)
- Kaori L. Fonseca
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal ,grid.418346.c0000 0001 2191 3202Programa de Pós-Graduação Ciência para o Desenvolvimento (PGCD), Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Rita Matos
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Luisa Simoes-Costa
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Jeremy Sousa
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Baltazar Cá
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Leandro Barros
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Ana Isabel Fernandes
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Stefan Mereiter
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Ricardo Reis
- CDP-Centro de Diagnóstico Pneumológico do Porto, Porto, Portugal
| | - Joana Gomes
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Gustavo Tapia
- grid.411438.b0000 0004 1767 6330UAB—Pathology Department, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Paula Rodríguez-Martínez
- grid.411438.b0000 0004 1767 6330UAB—Pathology Department, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Montse Martín-Céspedes
- grid.411438.b0000 0004 1767 6330UAB—Pathology Department, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Sergo Vashakidze
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Shota Gogishvili
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Keti Nikolaishvili
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Rui Appelberg
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Fátima Gärtner
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Pedro N. S. Rodrigues
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Cristina Vilaplana
- UAB—Experimental Tuberculosis Unit. Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias. Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Barcelona, Spain
| | - Celso A. Reis
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226FMUP—Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Ana Magalhães
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Margarida Saraiva
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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125
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Lee SC, Tang MS, Easton AV, Devlin JC, Chua LL, Cho I, Moy FM, Khang TF, Lim YAL, Loke P. Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures. PLoS Pathog 2019; 15:e1008066. [PMID: 31841569 PMCID: PMC6913942 DOI: 10.1371/journal.ppat.1008066] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/03/2019] [Indexed: 12/24/2022] Open
Abstract
Helminth infection and dietary intake can affect the intestinal microbiota, as well as the immune system. Here we analyzed the relationship between fecal microbiota and blood profiles of indigenous Malaysians, referred to locally as Orang Asli, in comparison to urban participants from the capital city of Malaysia, Kuala Lumpur. We found that helminth infections had a larger effect on gut microbial composition than did dietary intake or blood profiles. Trichuris trichiura infection intensity also had the strongest association with blood transcriptional profiles. By characterizing paired longitudinal samples collected before and after deworming treatment, we determined that changes in serum zinc and iron levels among the Orang Asli were driven by changes in helminth infection status, independent of dietary metal intake. Serum zinc and iron levels were associated with changes in the abundance of several microbial taxa. Hence, there is considerable interplay between helminths, micronutrients and the microbiota on the regulation of immune responses in humans.
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Affiliation(s)
- Soo Ching Lee
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Centre of Excellence for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (SCL); (YALL); (PL)
| | - Mei San Tang
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Alice V. Easton
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Joseph Cooper Devlin
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Ling Ling Chua
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
- Department of Paediatrics, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Ilseung Cho
- Department of Medicine, Division of Gastroenterology, New York University School of Medicine, New York, New York, United States of America
| | - Foong Ming Moy
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tsung Fei Khang
- University of Malaya Centre for Data Analytics, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Mathematical Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yvonne A. L. Lim
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Centre of Excellence for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (SCL); (YALL); (PL)
| | - P’ng Loke
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
- * E-mail: (SCL); (YALL); (PL)
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126
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Wang J, Hussain T, Zhang K, Liao Y, Yao J, Song Y, Sabir N, Cheng G, Dong H, Li M, Ni J, Mangi MH, Zhao D, Zhou X. Inhibition of type I interferon signaling abrogates early Mycobacterium bovis infection. BMC Infect Dis 2019; 19:1031. [PMID: 31801478 PMCID: PMC6894119 DOI: 10.1186/s12879-019-4654-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022] Open
Abstract
Background Mycobacterium bovis (M. bovis) is the principal causative agent of bovine tuberculosis; however, it may also cause serious infection in human being. Type I IFN is a key factor in reducing viral multiplication and modulating host immune response against viral infection. However, the regulatory pathways of Type I IFN signaling during M. bovis infection are not yet fully explored. Here, we investigate the role of Type I IFN signaling in the pathogenesis of M. bovis infection in mice. Methods C57BL/6 mice were treated with IFNAR1-blocking antibody or Isotype control 24 h before M. bovis infection. After 21 and 84 days of infection, mice were sacrificed and the role of Type I IFN signaling in the pathogenesis of M. bovis was investigated. ELISA and qRT-PCR were performed to detect the expression of Type I IFNs and related genes. Lung lesions induced by M. bovis were assessed by histopathological examination. Viable bacterial count was determined by CFU assay. Results We observed an abundant expression of Type I IFNs in the serum and lung tissues of M. bovis infected mice. In vivo blockade of Type I IFN signaling reduced the recruitment of neutrophils to the lung tissue, mediated the activation of macrophages leading to an increased pro-inflammatory profile and regulated the inflammatory cytokine production. However, no impact was observed on T cell activation and recruitment in the early acute phase of infection. Additionally, blocking of type I IFN signaling reduced bacterial burden in the infected mice as compared to untreated infected mice. Conclusions Altogether, our results reveal that Type I IFN mediates a balance between M. bovis-mediated inflammatory reaction and host defense mechanism. Thus, modulating Type I IFN signaling could be exploited as a therapeutic strategy against a large repertoire of inflammatory disorders including tuberculosis.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China
| | - Tariq Hussain
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kai Zhang
- School of Agriculture, Ningxia University, Ningxia, China
| | - Yi Liao
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiao Yao
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yinjuan Song
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Naveed Sabir
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guangyu Cheng
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Haodi Dong
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Miaoxuan Li
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiamin Ni
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Mazhar Hussain Mangi
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Deming Zhao
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiangmei Zhou
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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Ji DX, Yamashiro LH, Chen KJ, Mukaida N, Kramnik I, Darwin KH, Vance RE. Type I interferon-driven susceptibility to Mycobacterium tuberculosis is mediated by IL-1Ra. Nat Microbiol 2019; 4:2128-2135. [PMID: 31611644 PMCID: PMC6879852 DOI: 10.1038/s41564-019-0578-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
The bacterium Mycobacterium tuberculosis (Mtb) causes tuberculosis and is responsible for more human mortality than any other single pathogen1. Progression to active disease occurs in only a fraction of infected individuals and is predicted by an elevated type I interferon (IFN) response2-7. Whether or how IFNs mediate susceptibility to Mtb has been difficult to study due to a lack of suitable mouse models6-11. Here, we examined B6.Sst1S congenic mice that carry the 'susceptible' allele of the Sst1 locus that results in exacerbated Mtb disease12-14. We found that enhanced production of type I IFNs was responsible for the susceptibility of B6.Sst1S mice to Mtb. Type I IFNs affect the expression of hundreds of genes, several of which have previously been implicated in susceptibility to bacterial infections6,7,15-18. Nevertheless, we found that heterozygous deficiency in just a single IFN target gene, Il1rn, which encodes interleukin-1 receptor antagonist (IL-1Ra), is sufficient to reverse IFN-driven susceptibility to Mtb in B6.Sst1S mice. In addition, antibody-mediated neutralization of IL-1Ra provided therapeutic benefit to Mtb-infected B6.Sst1S mice. Our results illustrate the value of the B6.Sst1S mouse to model IFN-driven susceptibility to Mtb, and demonstrate that IL-1Ra is an important mediator of type I IFN-driven susceptibility to Mtb infections in vivo.
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Affiliation(s)
- Daisy X Ji
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Livia H Yamashiro
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Katherine J Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Naofumi Mukaida
- Division of Molecular Bioregulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Igor Kramnik
- The National Emerging Infectious Diseases Laboratory, Department of Medicine (Pulmonary Center), and Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Russell E Vance
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Cancer Research Laboratory, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
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128
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Abstract
Tuberculosis (TB) is the leading killer among all infectious diseases worldwide despite extensive use of the Mycobacterium bovis bacille Calmette-Guérin (BCG) vaccine. A safer and more effective vaccine than BCG is urgently required. More than a dozen TB vaccine candidates are under active evaluation in clinical trials aimed to prevent infection, disease, and recurrence. After decades of extensive research, renewed promise of an effective vaccine against this ancient airborne disease has recently emerged. In two innovative phase 2b vaccine clinical trials, one for the prevention of Mycobacterium tuberculosis infection in healthy adolescents and another for the prevention of TB disease in M. tuberculosis-infected adults, efficacy signals were observed. These breakthroughs, based on the greatly expanded knowledge of the M. tuberculosis infection spectrum, immunology of TB, and vaccine platforms, have reinvigorated the TB vaccine field. Here, we review our current understanding of natural immunity to TB, limitations in BCG immunity that are guiding vaccinologists to design novel TB vaccine candidates and concepts, and the desired attributes of a modern TB vaccine. We provide an overview of the progress of TB vaccine candidates in clinical evaluation, perspectives on the challenges faced by current vaccine concepts, and potential avenues to build on recent successes and accelerate the TB vaccine research-and-development trajectory.
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129
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Llibre A, Bilek N, Bondet V, Darboe F, Mbandi SK, Penn-Nicholson A, Hatherill M, Rozenberg F, Scriba TJ, Duffy D. Plasma Type I IFN Protein Concentrations in Human Tuberculosis. Front Cell Infect Microbiol 2019; 9:296. [PMID: 31508378 PMCID: PMC6713931 DOI: 10.3389/fcimb.2019.00296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/31/2019] [Indexed: 12/02/2022] Open
Abstract
Tuberculosis (TB) remains one of the leading causes of mortality worldwide, and a lack of understanding of basic disease pathogenesis is hampering development of new vaccines and treatments. Multiple studies have previously established a role for type I interferon (IFN) in TB disease. Type I IFNs are critical immune mediators for host responses to viral infection, yet their specific influence in bacterial infection remains unclear. As IFN-stimulated genes (ISGs) can have both stimulatory and inhibitory effects on immune function, clarifying the role of type I interferon in TB remains an important question. The quantification of interferon proteins in the circulation of patients has been restricted until the recent development of digital ELISA. To test the hypothesis that patients with active TB disease have elevated circulating type I IFN we quantified plasma IFNα and β proteins with Simoa digital ELISA in patients with active disease and asymptomatic M. tuberculosis infection. Strikingly no differences were observed between these two groups, while plasma from acute influenza infection revealed significantly higher plasma levels of both IFNα and IFNβ proteins. These results suggest a discordance between ISG mRNA expression by blood leukocytes and circulating type I IFN in TB.
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Affiliation(s)
- Alba Llibre
- Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, Paris, France.,INSERM U1223, Institut Pasteur, Paris, France
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Vincent Bondet
- Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, Paris, France.,INSERM U1223, Institut Pasteur, Paris, France
| | - Fatoumatta Darboe
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Flore Rozenberg
- Université Paris Descartes & AP-HP, Groupe Hospitalier Universitaire Paris Centre, Service de Virologie, Paris, France
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Darragh Duffy
- Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, Paris, France.,INSERM U1223, Institut Pasteur, Paris, France
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130
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Rohlwink UK, Figaji A, Wilkinson KA, Horswell S, Sesay AK, Deffur A, Enslin N, Solomons R, Van Toorn R, Eley B, Levin M, Wilkinson RJ, Lai RPJ. Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity. Nat Commun 2019; 10:3767. [PMID: 31434901 PMCID: PMC6704154 DOI: 10.1038/s41467-019-11783-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022] Open
Abstract
Tuberculous meningitis (TBM) is the most severe form of TB with high rates of mortality and morbidity. Here we conduct RNA-sequencing on whole blood as well as on ventricular and lumbar cerebrospinal fluid (CSF) of pediatric patients treated for TBM. Differential transcript expression of TBM cases are compared with healthy controls in whole blood and with non-TB cerebral infection controls in CSF. Whole blood RNA-Seq analysis demonstrates a distinct immune response pattern in TBM, with significant increase in both canonical and non-canonical inflammasome activation and decrease in T-cell activation. In ventricular CSF, a significant enrichment associated with neuronal excitotoxicity and cerebral damage is detected in TBM. Finally, compartmental comparison in TBM indicates that the ventricular profile represents brain injury whereas the lumbar profile represents protein translation and cytokine signaling. Together, transcriptomic analysis shows that disease processes differ between the periphery and the central nervous system, and within brain compartments. Tuberculosis meningitis (TBM) is a severe form of TB with limited treatment options. Here, the authors perform RNA sequencing on whole blood and on ventricular and lumbar cerebrospinal fluid (CSF) samples from pediatric patients treated for TBM to characterize the immune response and tissue damage.
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Affiliation(s)
- Ursula K Rohlwink
- Neuroscience Institute, Division of Neurosurgery, University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anthony Figaji
- Neuroscience Institute, Division of Neurosurgery, University of Cape Town, Cape Town, South Africa
| | - Katalin A Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Abdul K Sesay
- The Francis Crick Institute, London, NW1 1AT, UK.,Genomics Core, MRC Unit The Gambia at LSHTM, Serrekunda, The Gambia
| | - Armin Deffur
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Nico Enslin
- Neuroscience Institute, Division of Neurosurgery, University of Cape Town, Cape Town, South Africa
| | - Regan Solomons
- Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - Ronald Van Toorn
- Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Michael Levin
- Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,The Francis Crick Institute, London, NW1 1AT, UK.,Department of Medicine, University of Cape Town, Cape Town, South Africa.,Department of Infectious Disease, Imperial College London, London, W2 1PG, UK
| | - Rachel P J Lai
- The Francis Crick Institute, London, NW1 1AT, UK. .,Department of Infectious Disease, Imperial College London, London, W2 1PG, UK.
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131
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Host-Based Diagnostics for Acute Respiratory Infections. Clin Ther 2019; 41:1923-1938. [PMID: 31353133 DOI: 10.1016/j.clinthera.2019.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE The inappropriate use of antimicrobials, especially in acute respiratory infections (ARIs), is largely driven by difficulty distinguishing bacterial, viral, and noninfectious etiologies of illness. A new frontier in infectious disease diagnostics looks to the host response for disease classification. This article examines how host response-based diagnostics for ARIs are being used in clinical practice, as well as new developments in the research pipeline. METHODS A limited search was conducted of the relevant literature, with emphasis placed on literature published in the last 5 years (2014-2019). FINDINGS Advances are being made in all areas of host response-based diagnostics for ARIs. Specifically, there has been significant progress made in single protein biomarkers, as well as in various "omics" fields (including proteomics, metabolomics, and transcriptomics) and wearable technologies. There are many potential applications of a host response-based approach; a few key examples include the ability to discriminate bacterial and viral disease, presymptomatic diagnosis of infection, and pathogen-specific host response diagnostics, including modeling disease progression. IMPLICATIONS As biomarker measurement technologies continue to improve, host response-based diagnostics will increasingly be translated to clinically available platforms that can generate a holistic characterization of an individual's health. This knowledge, in the hands of both patient and provider, can improve care for the individual patient and help fight rising rates of antibiotic resistance.
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132
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Bossel Ben-Moshe N, Hen-Avivi S, Levitin N, Yehezkel D, Oosting M, Joosten LAB, Netea MG, Avraham R. Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells. Nat Commun 2019; 10:3266. [PMID: 31332193 PMCID: PMC6646406 DOI: 10.1038/s41467-019-11257-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 07/03/2019] [Indexed: 12/20/2022] Open
Abstract
Complex interactions between different host immune cell types can determine the outcome of pathogen infections. Advances in single cell RNA-sequencing (scRNA-seq) allow probing of these immune interactions, such as cell-type compositions, which are then interpreted by deconvolution algorithms using bulk RNA-seq measurements. However, not all aspects of immune surveillance are represented by current algorithms. Here, using scRNA-seq of human peripheral blood cells infected with Salmonella, we develop a deconvolution algorithm for inferring cell-type specific infection responses from bulk measurements. We apply our dynamic deconvolution algorithm to a cohort of healthy individuals challenged ex vivo with Salmonella, and to three cohorts of tuberculosis patients during different stages of disease. We reveal cell-type specific immune responses associated not only with ex vivo infection phenotype but also with clinical disease stage. We propose that our approach provides a predictive power to identify risk for disease, and human infection outcomes. Complex interactions between different host immune cell types can determine the outcome of pathogen infections. Here, Avraham and colleagues present a deconvolution algorithm that uses single-cell RNA and bulk RNA sequencing measurements of pathogen-infected cells to predict disease risk outcomes.
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Affiliation(s)
- Noa Bossel Ben-Moshe
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Shelly Hen-Avivi
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Natalia Levitin
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Dror Yehezkel
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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133
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De Maio F, Squeglia F, Goletti D, Delogu G. The Mycobacterial HBHA Protein: A Promising Biomarker for Tuberculosis. Curr Med Chem 2019; 26:2051-2060. [PMID: 30378481 DOI: 10.2174/0929867325666181029165805] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/01/2018] [Accepted: 10/18/2018] [Indexed: 02/06/2023]
Abstract
A major goal in tuberculosis (TB) research is the identification, among the subjects infected with Mycobacterium tuberculosis (Mtb), of those with active TB, or at higher risk of developing active disease, from the latently infected subjects. The classical heterogeneity of Mtb infection and TB disease is a major obstacle toward the identification of reliable biomarkers that can stratify Mtb infected subjects based on disease risk. The heparin-binding haemagglutinin (HBHA) is a mycobacterial surface antigen that is implicated in tuberculosis (TB) pathogenesis. The host immune response against HBHA varies depending on the TB status and several studies are supporting the role of HBHA as a useful biomarker of TB.
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Affiliation(s)
- Flavio De Maio
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Milano, Italy.,Fondazione Policlinico Universitario A. Gemelli- IRCCS, Rome, Italy
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Napoli, Italy
| | - Delia Goletti
- Translational Research Unit, Department of Epidemiology and Preclinical Research, "L. Spallanzani" National Institute for Infectious Diseases (INMI) IRCCCS, Rome, Italy
| | - Giovanni Delogu
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Milano, Italy.,Fondazione Policlinico Universitario A. Gemelli- IRCCS, Rome, Italy
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134
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Barral-Arca R, Pardo-Seco J, Bello X, Martinón-Torres F, Salas A. Ancestry patterns inferred from massive RNA-seq data. RNA (NEW YORK, N.Y.) 2019; 25:857-868. [PMID: 31010885 PMCID: PMC6573782 DOI: 10.1261/rna.070052.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/16/2019] [Indexed: 05/24/2023]
Abstract
There is a growing body of evidence suggesting that patterns of gene expression vary within and between human populations. However, the impact of this variation in human diseases has been poorly explored, in part owing to the lack of a standardized protocol to estimate biogeographical ancestry from gene expression studies. Here we examine several studies that provide new solid evidence indicating that the ancestral background of individuals impacts gene expression patterns. Next, we test a procedure to infer genetic ancestry from RNA-seq data in 25 data sets where information on ethnicity was reported. Genome data of reference continental populations retrieved from The 1000 Genomes Project were used for comparisons. Remarkably, only eight out of 25 data sets passed FastQC default filters. We demonstrate that, for these eight population sets, the ancestral background of donors could be inferred very efficiently, even in data sets including samples with complex patterns of admixture (e.g., American-admixed populations). For most of the gene expression data sets of suboptimal quality, ancestral inference yielded odd patterns. The present study thus brings a cautionary note for gene expression studies highlighting the importance to control for the potential confounding effect of ancestral genetic background.
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Affiliation(s)
- Ruth Barral-Arca
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Xabi Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
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135
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Singhania A, Graham CM, Gabryšová L, Moreira-Teixeira L, Stavropoulos E, Pitt JM, Chakravarty P, Warnatsch A, Branchett WJ, Conejero L, Lin JW, Davidson S, Wilson MS, Bancroft G, Langhorne J, Frickel E, Sesay AK, Priestnall SL, Herbert E, Ioannou M, Wang Q, Humphreys IR, Dodd J, Openshaw PJM, Mayer-Barber KD, Jankovic D, Sher A, Lloyd CM, Baldwin N, Chaussabel D, Papayannopoulos V, Wack A, Banchereau JF, Pascual VM, O'Garra A. Transcriptional profiling unveils type I and II interferon networks in blood and tissues across diseases. Nat Commun 2019; 10:2887. [PMID: 31253760 PMCID: PMC6599044 DOI: 10.1038/s41467-019-10601-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
Understanding how immune challenges elicit different responses is critical for diagnosing and deciphering immune regulation. Using a modular strategy to interpret the complex transcriptional host response in mouse models of infection and inflammation, we show a breadth of immune responses in the lung. Lung immune signatures are dominated by either IFN-γ and IFN-inducible, IL-17-induced neutrophil- or allergy-associated gene expression. Type I IFN and IFN-γ-inducible, but not IL-17- or allergy-associated signatures, are preserved in the blood. While IL-17-associated genes identified in lung are detected in blood, the allergy signature is only detectable in blood CD4+ effector cells. Type I IFN-inducible genes are abrogated in the absence of IFN-γ signaling and decrease in the absence of IFNAR signaling, both independently contributing to the regulation of granulocyte responses and pathology during Toxoplasma gondii infection. Our framework provides an ideal tool for comparative analyses of transcriptional signatures contributing to protection or pathogenesis in disease.
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Affiliation(s)
- Akul Singhania
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, NW1 1AT, UK
| | - Christine M Graham
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, NW1 1AT, UK
| | - Leona Gabryšová
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, NW1 1AT, UK
| | - Lúcia Moreira-Teixeira
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, NW1 1AT, UK
| | - Evangelos Stavropoulos
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, NW1 1AT, UK
| | - Jonathan M Pitt
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Annika Warnatsch
- Antimicrobial Defence Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - William J Branchett
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Laura Conejero
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jing-Wen Lin
- Malaria Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sophia Davidson
- Immunoregulation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Mark S Wilson
- Helminth Immunology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Gregory Bancroft
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jean Langhorne
- Malaria Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Eva Frickel
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Abdul K Sesay
- Advanced Sequencing Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon L Priestnall
- Department of Pathobiology & Population Sciences, Royal Veterinary College, London, AL9 7TA, UK
| | - Eleanor Herbert
- Department of Pathobiology & Population Sciences, Royal Veterinary College, London, AL9 7TA, UK
| | - Marianna Ioannou
- Antimicrobial Defence Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Qian Wang
- Antimicrobial Defence Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ian R Humphreys
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - Jonathan Dodd
- Respiratory Infection Section, National Heart and Lung Institute, Imperial College London, London, W2 1PG, UK
| | - Peter J M Openshaw
- Respiratory Infection Section, National Heart and Lung Institute, Imperial College London, London, W2 1PG, UK
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dragana Jankovic
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Clare M Lloyd
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Nicole Baldwin
- Baylor Institute for Immunology Research, Dallas, TX, 75204, USA
| | - Damien Chaussabel
- Systems Biology and Immunology Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | | | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Virginia M Pascual
- Drukier Institute for Children's Health, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Anne O'Garra
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, NW1 1AT, UK.
- National Heart and Lung Institute, Imperial College London, London, W2 1PG, UK.
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136
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Changes in inflammatory protein and lipid mediator profiles persist after antitubercular treatment of pulmonary and extrapulmonary tuberculosis: A prospective cohort study. Cytokine 2019; 123:154759. [PMID: 31226436 DOI: 10.1016/j.cyto.2019.154759] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 05/20/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The identification of meaningful biomarkers of tuberculosis (TB) has potential to improve diagnosis, disease staging and prediction of treatment outcomes. It has been shown that active pulmonary TB (PTB) is associated with qualitative and quantitative changes in systemic immune profile, suggesting a chronic inflammatory imbalance. Here we characterized the profile of PTB and extrapulmonary TB (EPTB) in a prospective cohort study. METHODS We measured a panel of 27 inflammatory cytokines, soluble receptors, and lipid mediators in peripheral blood from patients with PTB or EPTB from a prospective clinical study in China. Multidimensional analyses were performed to describe associations between plasma levels of biomarkers and different TB disease presentation profiles. RESULTS Mycobacterium tuberculosis infection induced changes in both the expression and correlation profiles of plasma mediators of inflammation in patients with PTB compared to those with EPTB. Increases in mycobacterial loads in sputum smears were associated with rises in concentrations of several molecules involved in TB pathogenesis, such as IL-1β, IFN-α, IL-10 and PGF2α. Moreover, PTB patients presenting with severe disease exhibited a distinct inflammatory profile hallmarked by heightened levels of TNF-α, IL-1β, IL17, IL-18 and IL-27. Interestingly, while antitubercular treatment (ATT) resulted in early changes of plasma concentrations of markers in PTB, changes were delayed in EPTB patients. Exploratory analyses of the molecular degree of perturbation (MDP) of the inflammatory mediators before and during ATT suggested the occurrence of infection and/or treatment-induced long lasting "inflammatory imprinting" of biomarker profiles in TB. At 24 weeks post ATT commencement, markers underlying the observed increases in MDP scores were IL-27 in PTB and IL-1β in EPTB patients. CONCLUSION Our findings describe systemic and durable changes in the concentrations of inflammatory cytokines and lipid mediators in both PTB and EPTB and emphasize the role of M. tuberculosis bacterial burden and site of disease in modulating patient immune biomarkers.
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137
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Abstract
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.
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Affiliation(s)
- Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Steven A Miller
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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138
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Crow MK, Ronnblom L. Type I interferons in host defence and inflammatory diseases. Lupus Sci Med 2019; 6:e000336. [PMID: 31205729 PMCID: PMC6541752 DOI: 10.1136/lupus-2019-000336] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022]
Abstract
Type I interferons (IFN) can have dual and opposing roles in immunity, with effects that are beneficial or detrimental to the individual depending on whether IFN pathway activation is transient or sustained. Determinants of IFN production and its functional consequences include the nature of the microbial or nucleic acid stimulus, the type of nucleic acid sensor involved in inducing IFN, the predominant subtype of type I IFN produced and the immune ecology of the tissue at the time of IFN expression. When dysregulated, the type I IFN system drives many autoimmune and non-autoimmune inflammatory diseases, including SLE and the tissue inflammation associated with chronic infection. The type I IFN system may also contribute to outcomes for patients affected by solid cancers or myocardial infarction. Significantly more research is needed to discern the mechanisms of induction and response to type I IFNs across these diseases, and patient endophenotyping may help determine whether the cytokine is acting as 'friend' or 'foe', within a particular patient, and at the time of treatment. This review summarises key concepts and discussions from the second International Summit on Interferons in Inflammatory Diseases, during which expert clinicians and scientists evaluated the evidence for the role of type I IFNs in autoimmune and other inflammatory diseases.
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Affiliation(s)
- Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, Weill Cornell Medical College, New York City, New York, USA
| | - Lars Ronnblom
- Section of Rheumatology, Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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139
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Yu J, Peterson DR, Baran AM, Bhattacharya S, Wylie TN, Falsey AR, Mariani TJ, Storch GA. Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection. J Infect Dis 2019; 219:1151-1161. [PMID: 30339221 PMCID: PMC6420164 DOI: 10.1093/infdis/jiy608] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Recently there has been a growing interest in the potential for host transcriptomic analysis to augment the diagnosis of infectious diseases. METHODS We compared nasal and blood samples for evaluation of the host transcriptomic response in children with acute respiratory syncytial virus (RSV) infection, symptomatic non-RSV respiratory virus infection, asymptomatic rhinovirus infection, and virus-negative asymptomatic controls. We used nested leave-one-pair-out cross-validation and supervised principal components analysis to define small sets of genes whose expression patterns accurately classified subjects. We validated gene classification scores using an external data set. RESULTS Despite lower quality of nasal RNA, the number of genes detected by microarray in each sample type was equivalent. Nasal gene expression signal derived mainly from epithelial cells but also included a variable leukocyte contribution. The number of genes with increased expression in virus-infected children was comparable in nasal and blood samples, while nasal samples also had decreased expression of many genes associated with ciliary function and assembly. Nasal gene expression signatures were as good or better for discriminating between symptomatic, asymptomatic, and uninfected children. CONCLSUSIONS Our results support the use of nasal samples to augment pathogen-based tests to diagnose viral respiratory infection.
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Affiliation(s)
- Jinsheng Yu
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Ann R Falsey
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
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140
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Sousa J, Saraiva M. Paradigm changing evidence that alter tuberculosis perception and detection: Focus on latency. INFECTION GENETICS AND EVOLUTION 2018; 72:78-85. [PMID: 30576838 DOI: 10.1016/j.meegid.2018.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 12/23/2022]
Abstract
Tuberculosis remains a devastating disease to Mankind, ranking as the ninth cause of death worldwide. Eliminating tuberculosis as proven much more difficult than once anticipated. In addition to the delay in diagnosis and drug resistance problems that compromise the efficacy of treatment, the enormous reservoir of latently infected individuals continuously feeds the epidemics. However, targeting latency with prophylactic antibiotic administration is not possible at the populational level. Together, these issues call for a better understanding of latency, as well as for a more precise identification of individuals at high risk of reactivation. For this, recent paradigm changing evidence need to be taken into account, most notably, the existence of a tuberculosis spectrum; the genetic diversity of both humans and tuberculosis-causing bacteria; and the changes in the human population that interfere with tuberculosis. Here we discuss latency in the light of these variables and how that understanding can move forward tuberculosis research and elimination.
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Affiliation(s)
- Jeremy Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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141
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Satti I, McShane H. Current approaches toward identifying a correlate of immune protection from tuberculosis. Expert Rev Vaccines 2018; 18:43-59. [PMID: 30466332 DOI: 10.1080/14760584.2019.1552140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Mycobacterium tuberculosis kills more people than any other pathogen. Vaccination is the most cost-effective control measure for any infectious disease. Development of an effective vaccine against tuberculosis is hindered by the uncertain predictive value of preclinical animal models, incomplete understanding of protective immunity and lack of validated immune correlates of protection (COP). AREAS COVERED Here we review what is known about protective immunity against M.tb, the preclinical and clinical cohorts that can be utilized to identify COP, and COP that have been identified to date. EXPERT COMMENTARY The identification of COP would allow the rational design and development of vaccine candidates which can then be optimized and prioritized based on the induction of these immune responses. Once validated in field efficacy trials, such COP could potentially facilitate the development and licensure of vaccines, in combination with human efficacy data. The identification and validation of COP would represent a very significant advance in TB vaccine development. Every opportunity to collect samples and cohorts on which to cross-validate pre-existing COP and identify novel COP should be exploited. Furthermore, global cooperation and collaboration on such samples will ensure that the utility of such precious samples is fully exploited.
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Affiliation(s)
- Iman Satti
- a Jenner Institute, Nuffield Department of Medicine , University of Oxford , Oxford , UK
| | - Helen McShane
- a Jenner Institute, Nuffield Department of Medicine , University of Oxford , Oxford , UK
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142
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Singhania A, Wilkinson RJ, Rodrigue M, Haldar P, O'Garra A. The value of transcriptomics in advancing knowledge of the immune response and diagnosis in tuberculosis. Nat Immunol 2018; 19:1159-1168. [PMID: 30333612 PMCID: PMC6554194 DOI: 10.1038/s41590-018-0225-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/28/2018] [Indexed: 01/06/2023]
Abstract
Blood transcriptomics analysis of tuberculosis has revealed an interferon-inducible gene signature that diminishes in expression after successful treatment; this promises improved diagnostics and treatment monitoring, which are essential for the eradication of tuberculosis. Sensitive radiography revealing lung abnormalities and blood transcriptomics have demonstrated heterogeneity in patients with active tuberculosis and exposed asymptomatic people with latent tuberculosis, suggestive of a continuum of infection and immune states. Here we describe the immune response to infection with Mycobacterium tuberculosis revealed through the use of transcriptomics, as well as differences among clinical phenotypes of infection that might provide information on temporal changes in host immunity associated with evolving infection. We also review the diverse blood transcriptional signatures, composed of small sets of genes, that have been proposed for the diagnosis of tuberculosis and the identification of at-risk asymptomatic people and suggest novel approaches for the development of such biomarkers for clinical use.
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Affiliation(s)
- Akul Singhania
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK
| | - Robert J Wilkinson
- Laboratory of Tuberculosis, The Francis Crick Institute, London, UK
- Department of Medicine, Imperial College London, London, UK
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, 7925, Cape Town, Republic of South Africa
| | - Marc Rodrigue
- Medical Diagnostic Discovery Department, bioMerieux SA, Marcy l'Etoile, France
| | - Pranabashis Haldar
- Respiratory Biomedical Research Centre, Institute for Lung Health, Department of Infection Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Anne O'Garra
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, UK.
- National Heart and Lung Institute, Imperial College London, London, UK.
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143
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Moreira-Teixeira L, Mayer-Barber K, Sher A, O'Garra A. Type I interferons in tuberculosis: Foe and occasionally friend. J Exp Med 2018; 215:1273-1285. [PMID: 29666166 PMCID: PMC5940272 DOI: 10.1084/jem.20180325] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis remains one of the leading causes of mortality worldwide, and, despite its clinical significance, there are still significant gaps in our understanding of pathogenic and protective mechanisms triggered by Mycobacterium tuberculosis infection. Type I interferons (IFN) regulate a broad family of genes that either stimulate or inhibit immune function, having both host-protective and detrimental effects, and exhibit well-characterized antiviral activity. Transcriptional studies have uncovered a potential deleterious role for type I IFN in active tuberculosis. Since then, additional studies in human tuberculosis and experimental mouse models of M. tuberculosis infection support the concept that type I IFN promotes both bacterial expansion and disease pathogenesis. More recently, studies in a different setting have suggested a putative protective role for type I IFN. In this study, we discuss the mechanistic and contextual factors that determine the detrimental versus beneficial outcomes of type I IFN induction during M. tuberculosis infection, from human disease to experimental mouse models of tuberculosis.
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Affiliation(s)
- Lúcia Moreira-Teixeira
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, England, UK
| | - Katrin Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Anne O'Garra
- Laboratory of Immunoregulation and Infection, The Francis Crick Institute, London, England, UK
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, England, UK
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