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Yang Y, Mu J, Chen G, Zhan Y, Zhong J, Wei Y, Cheng K, Qin B, You H, Xie P. iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid reveals NELL2 as a potential diagnostic biomarker of tuberculous meningitis. Int J Mol Med 2015; 35:1323-32. [PMID: 25760060 DOI: 10.3892/ijmm.2015.2131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 02/17/2015] [Indexed: 11/06/2022] Open
Abstract
Tuberculous meningitis (TBM) is a serious complication of tuberculosis that affects the central nervous system. As TBM may result in permanent sequelae and death, rapid, accurate diagnostic tests using novel biomarkers are required for the early diagnosis and treatment of TBM. A quantitative proteomic study was therefore performed to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n=12) and healthy controls (n=12). CSF samples were labelled with iTRAQ™ and analyzed by LC-MS/MS. Gene ontology and Pathway analysis were conducted using DAVID bioinformatics resources. Neural epidermal growth factor-like like 2 (NELL2) with the largest fold-change value was selected for validation by western blotting. Proteomic phenotyping revealed over-representation in two inflammation-associated processes, complement and coagulation cascades as well as cell adhesion molecules. Western blotting showed a significant decrease in NELL2 levels in TBM subjects compared to healthy controls. The AUC analysis revealed NELL2 was able to distinguish TBM subjects from healthy controls with 83.3% sensitivity and 75% specificity. In conclusion, the results showed that CSF NELL2 is a potential diagnostic biomarker for TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other intracranial infectious diseases is required for clinical translation.
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Affiliation(s)
- Yongtao Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Jun Mu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Guanghui Chen
- Institute of Neuroscience, Chongqing Medical University, Chongqing, P.R. China
| | - Yuan Zhan
- Institute of Neuroscience, Chongqing Medical University, Chongqing, P.R. China
| | - Jiaju Zhong
- Institute of Neuroscience, Chongqing Medical University, Chongqing, P.R. China
| | - Youdong Wei
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Ke Cheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Bin Qin
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Hongmin You
- Institute of Neuroscience, Chongqing Medical University, Chongqing, P.R. China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
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6
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Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MGB, Rüsch-Gerdes S, Mokrousov I, Aleksic E, Allix-Béguec C, Antierens A, Augustynowicz-Kopeć E, Ballif M, Barletta F, Beck HP, Barry CE, Bonnet M, Borroni E, Campos-Herrero I, Cirillo D, Cox H, Crowe S, Crudu V, Diel R, Drobniewski F, Fauville-Dufaux M, Gagneux S, Ghebremichael S, Hanekom M, Hoffner S, Jiao WW, Kalon S, Kohl TA, Kontsevaya I, Lillebæk T, Maeda S, Nikolayevskyy V, Rasmussen M, Rastogi N, Samper S, Sanchez-Padilla E, Savic B, Shamputa IC, Shen A, Sng LH, Stakenas P, Toit K, Varaine F, Vukovic D, Wahl C, Warren R, Supply P, Niemann S, Wirth T. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 2015; 47:242-9. [PMID: 25599400 PMCID: PMC11044984 DOI: 10.1038/ng.3195] [Citation(s) in RCA: 354] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/19/2014] [Indexed: 01/18/2023]
Abstract
Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.
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Affiliation(s)
- Matthias Merker
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Camille Blin
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Stefano Mona
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Nicolas Duforet-Frebourg
- Université Joseph Fourier, Centre National de la Recherche Scientifique, Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble, France
| | - Sophie Lecher
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Eve Willery
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Michael G B Blum
- Université Joseph Fourier, Centre National de la Recherche Scientifique, Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble, France
| | - Sabine Rüsch-Gerdes
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Eman Aleksic
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | | | - Annick Antierens
- Medical Department, Médecins sans Frontières Switzerland, Geneva, Switzerland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Marie Ballif
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Hans Peter Beck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Clifton E Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | | | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Isolina Campos-Herrero
- Department of Microbiology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Daniela Cirillo
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Helen Cox
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Suzanne Crowe
- 1] Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia. [2] Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia. [3] Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Valeriu Crudu
- National Tuberculosis Reference Laboratory, Phthysiopneumology Institute, Chisinau, Republic of Moldova
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Francis Drobniewski
- 1] Public Health England National Mycobacterial Reference Laboratory and Clinical Tuberculosis and Human Immunodeficiency Virus Group, Queen Mary's School of Medicine and Dentistry, London, UK. [2] Department of Infectious Diseases, Imperial College, London, UK
| | | | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Madeleine Hanekom
- Department of Science and Technology/National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research/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
| | - Sven Hoffner
- Department of Diagnostics and Vaccinology, Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Wei-wei Jiao
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Stobdan Kalon
- US Agency for International Development Quality Health Care Project, Bishkek, Kyrgyzstan
| | - Thomas A Kohl
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Troels Lillebæk
- Statens Serum Institute, International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark
| | - Shinji Maeda
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Vladyslav Nikolayevskyy
- 1] Public Health England National Mycobacterial Reference Laboratory and Clinical Tuberculosis and Human Immunodeficiency Virus Group, Queen Mary's School of Medicine and Dentistry, London, UK. [2] Department of Infectious Diseases, Imperial College, London, UK
| | - Michael Rasmussen
- Statens Serum Institute, International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark
| | - Nalin Rastogi
- World Health Organization Supranational Tuberculosis Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, France
| | - Sofia Samper
- Instituto de Investigación Sanitaria Aragón, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | | | - Branislava Savic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Isdore Chola Shamputa
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Adong Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Li-Hwei Sng
- Central Tuberculosis Laboratory, Department of Pathology, Singapore General Hospital, Singapore
| | - Petras Stakenas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Kadri Toit
- Tartu University Hospital United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | - Dragana Vukovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Robin Warren
- Department of Science and Technology/National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research/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
| | - Philip Supply
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France. [5] Genoscreen, Lille, France
| | - Stefan Niemann
- 1] Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany. [2] German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Thierry Wirth
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
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7
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Li W, Fan X, Long Q, Xie L, Xie J. Mycobacterium tuberculosis effectors involved in host-pathogen interaction revealed by a multiple scales integrative pipeline. INFECTION GENETICS AND EVOLUTION 2015; 32:1-11. [PMID: 25709069 DOI: 10.1016/j.meegid.2015.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/02/2015] [Accepted: 02/14/2015] [Indexed: 01/04/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter host immunity. Proteins are one important player in the host-pathogen interaction. A comprehensive list of such proteins will benefit our understanding of pathogenesis of Mtb. METHODS A genome-scale dataset was created from different sources of published data: global gene expression studies in disease models; genome-wide insertional mutagenesis defining gene essentiality under different conditions; genes lost in clinical isolates; subcellular localization analysis and non-homology analysis. Using data mining and meta-analysis, expressed proteins critical for intracellular survival of Mtb are first identified, followed by subcellular localization analysis, finally filtering a series of subtractive channel of analysis to find out promising drug target candidates. RESULTS The analysis found 54 potential candidates essential for the intracellular survival of the pathogen and non-homologous to host or gut flora, and might be promising drug targets. CONCLUSION Based on our meta-analysis and bioinformatics analysis, 54 hits were found from Mtb around 4000 open reading frames. These hits can be good candidates for further experimental investigation.
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Affiliation(s)
- Wu Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Shandong 250022, China
| | - Quanxin Long
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; The Second Affiliated Hospital and the Key Laboratory of Molecular Biology of Infectious Diseases of the Ministry of Education, Chongqing Medical University, 1 Medical Road, Yuzhong District, Chongqing 400016, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.
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12
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Abdullah Z, Geiger S, Nino-Castro A, Böttcher JP, Muraliv E, Gaidt M, Schildberg FA, Riethausen K, Flossdorf J, Krebs W, Chakraborty T, Kurts C, Schultze JL, Knolle PA, Klotz L. Lack of PPARγ in myeloid cells confers resistance to Listeria monocytogenes infection. PLoS One 2012; 7:e37349. [PMID: 22629382 PMCID: PMC3357414 DOI: 10.1371/journal.pone.0037349] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 04/18/2012] [Indexed: 12/24/2022] Open
Abstract
The peroxisomal proliferator-activated receptor γ (PPARγ) is a nuclear receptor that controls inflammation and immunity. Innate immune defense against bacterial infection appears to be compromised by PPARγ. The relevance of PPARγ in myeloid cells, that organize anti-bacterial immunity, for the outcome of immune responses against intracellular bacteria such as Listeria monocytogenes in vivo is unknown. We found that Listeria monocytogenes infection of macrophages rapidly led to increased expression of PPARγ. This prompted us to investigate whether PPARγ in myeloid cells influences innate immunity against Listeria monocytogenes infection by using transgenic mice with myeloid-cell specific ablation of PPARγ (LysMCre×PPARγ(flox/flox)). Loss of PPARγ in myeloid cells results in enhanced innate immune defense against Listeria monocytogenes infection both, in vitro and in vivo. This increased resistance against infection was characterized by augmented levels of bactericidal factors and inflammatory cytokines: ROS, NO, IFNγ TNF IL-6 and IL-12. Moreover, myeloid cell-specific loss of PPARγ enhanced chemokine and adhesion molecule expression leading to improved recruitment of inflammatory Ly6C(hi) monocytes to sites of infection. Importantly, increased resistance against Listeria infection in the absence of PPARγ was not accompanied by enhanced immunopathology. Our results elucidate a yet unknown regulatory network in myeloid cells that is governed by PPARγ and restrains both listeriocidal activity and recruitment of inflammatory monocytes during Listeria infection, which may contribute to bacterial immune escape. Pharmacological interference with PPARγ activity in myeloid cells might represent a novel strategy to overcome intracellular bacterial infection.
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Affiliation(s)
- Zeinab Abdullah
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Sergej Geiger
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Andrea Nino-Castro
- Genomics & Immunoregulation, LIMES Institute, Universität Bonn, Bonn, Germany
| | - Jan P. Böttcher
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Eugenia Muraliv
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Moritz Gaidt
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Frank A. Schildberg
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Kati Riethausen
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Juliane Flossdorf
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Wolfgang Krebs
- Genomics & Immunoregulation, LIMES Institute, Universität Bonn, Bonn, Germany
| | - Trinad Chakraborty
- Institute for Medical Microbiology, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Christian Kurts
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Joachim L. Schultze
- Genomics & Immunoregulation, LIMES Institute, Universität Bonn, Bonn, Germany
| | - Percy A. Knolle
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
| | - Luisa Klotz
- Institutes of Molecular Medicine and Experimental Immunology, Universität Bonn, Bonn, Germany
- Clinic for Neurology – Inflammatory Disorders of the Nervous System and Neuro-oncology, Universität Münster, Münster, Germany
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