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Rosa RL, Berger M, Santi L, Driemeier D, Barros Terraciano P, Campos AR, Guimarães JA, Vainstein MH, Yates JR, Beys-da-Silva WO. Proteomics of Rat Lungs Infected by Cryptococcus gattii Reveals a Potential Warburg-like Effect. J Proteome Res 2019; 18:3885-3895. [PMID: 31502459 DOI: 10.1021/acs.jproteome.9b00326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryptococcus gattii is the causative agent of cryptococcosis infection that can lead to pneumonia and meningitis in immunocompetent individuals. The molecular basis of the pathogenic process and impact on the host biochemistry are poorly understood and remain largely unknown. In this context, a comparative proteomic analysis was performed to investigate the response of the host during an infection caused by C. gattii. Lungs of experimentally infected rats were analyzed by shotgun proteomics to identify differentially expressed proteins induced by C. gattii clinical strain. The proteomic results were characterized using bioinformatic tools, and subsequently, the molecular findings were validated in cell culture and lungs of infected animals. A dramatic change was observed in protein expression triggered by C. gattii infection, especially related to energy metabolism. The main pathways affected include aerobic glycolysis cycle, TCA cycle, and pyrimidine and purine metabolism. Analyses in human lung fibroblast cells confirmed the altered metabolic status found in infected lungs. Thus, it is clear that C. gattii infection triggers important changes in energy metabolism leading to the activation of glycolysis and lactate accumulation in lung cells, culminating in a cancerlike metabolic status known as the Warburg effect. The results presented here provide important insights to better understand C. gattii molecular pathogenesis.
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Affiliation(s)
- Rafael L Rosa
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90040-060 , Brazil.,Centro de Pesquisa Experimental, Laboratório de Bioquímica Farmacológica , Hospital de Clínicas de Porto Alegre (UFRGS) , Porto Alegre , RS 90035-007 , Brazil.,Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90610-000 , Brazil
| | - Markus Berger
- Centro de Pesquisa Experimental, Laboratório de Bioquímica Farmacológica , Hospital de Clínicas de Porto Alegre (UFRGS) , Porto Alegre , RS 90035-007 , Brazil
| | - Lucélia Santi
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90040-060 , Brazil.,Centro de Pesquisa Experimental, Laboratório de Bioquímica Farmacológica , Hospital de Clínicas de Porto Alegre (UFRGS) , Porto Alegre , RS 90035-007 , Brazil.,Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90610-000 , Brazil
| | - David Driemeier
- Departamento de Patologia Clínica Veterinária, Faculdade de Medicina Veterinária , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 91540-000 , Brazil
| | - Paula Barros Terraciano
- Centro de Pesquisa Experimental, Laboratório de Bioquímica Farmacológica , Hospital de Clínicas de Porto Alegre (UFRGS) , Porto Alegre , RS 90035-007 , Brazil
| | - Alexandre R Campos
- Proteomics Core , Sanford Burnham Prebys Medical Discovery Institute , La Jolla , California 92037 , United States
| | - Jorge A Guimarães
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90040-060 , Brazil.,Centro de Pesquisa Experimental, Laboratório de Bioquímica Farmacológica , Hospital de Clínicas de Porto Alegre (UFRGS) , Porto Alegre , RS 90035-007 , Brazil
| | - Marilene H Vainstein
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90040-060 , Brazil
| | - John R Yates
- Departments of Chemical Physiology and Molecular and Cellular Neuroscience , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Walter O Beys-da-Silva
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90040-060 , Brazil.,Centro de Pesquisa Experimental, Laboratório de Bioquímica Farmacológica , Hospital de Clínicas de Porto Alegre (UFRGS) , Porto Alegre , RS 90035-007 , Brazil.,Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , RS 90610-000 , Brazil
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Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E. Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation. Mol Cell Proteomics 2019; 18:909-922. [PMID: 30808727 DOI: 10.1074/mcp.ra119.001316] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/23/2019] [Indexed: 12/15/2022] Open
Abstract
Dendritic cells (DCs) are professional phagocytes that use innate sensing and phagocytosis to internalize and degrade self as well as foreign material, such as pathogenic bacteria, within phagosomes. These intracellular compartments are equipped to generate antigenic peptides that serve as source for antigen presentation to T cells initiating adaptive immune responses. The phagosomal proteome of DCs is only partially studied and is highly dynamic as it changes during phagosome maturation, when phagosomes sequentially interact with endosomes and lysosomes. In addition, the activation status of the phagocyte can modulate the phagosomal composition and is able to shape phagosomal functions.In this study, we determined spatiotemporal changes of the proteome of DC phagosomes during their maturation and compared resting and lipopolysaccharide (LPS)-stimulated bone marrow-derived DCs by label-free, quantitative mass spectrometry. Ovalbumin-coupled latex beads were used as phagocytosis model system and revealed that LPS-treated DCs show decreased recruitment of proteins involved in phagosome maturation, such as subunits of the vacuolar proton ATPase, cathepsin B, D, S, and RAB7. In contrast, those phagosomes were characterized by an increased recruitment of proteins involved in antigen cross-presentation, e.g. different subunits of MHC I molecules, the proteasome and tapasin, confirming the observed increase in cross-presentation efficacy in those cells. Further, several proteins were identified that were not previously associated with phagosomal functions. Hierarchical clustering of phagosomal proteins demonstrated that their acquisition to DC phagosomes is not only dependent on the duration of phagosome maturation but also on the activation state of DCs. Thus, our study provides a comprehensive overview of how DCs alter their phagosome composition in response to LPS, which has profound impact on the initiation of efficient immune responses.
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Affiliation(s)
- Anne-Marie Pauwels
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Anetta Härtlova
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Julien Peltier
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Yasmine Driege
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Griet Baudelet
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Priscille Brodin
- ‖Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Matthias Trost
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rudi Beyaert
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Eik Hoffmann
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium;; ‖Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
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3
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Hoffmann E, Machelart A, Song OR, Brodin P. Proteomics of Mycobacterium Infection: Moving towards a Better Understanding of Pathogen-Driven Immunomodulation. Front Immunol 2018; 9:86. [PMID: 29441067 PMCID: PMC5797607 DOI: 10.3389/fimmu.2018.00086] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/11/2018] [Indexed: 12/11/2022] Open
Abstract
Intracellular bacteria are responsible for many infectious diseases in humans and have developed diverse mechanisms to interfere with host defense pathways. In particular, intracellular vacuoles are an essential niche used by pathogens to alter cellular and organelle functions, which facilitate replication and survival. Mycobacterium tuberculosis (Mtb), the pathogen causing tuberculosis in humans, is not only able to modulate its intraphagosomal fate by blocking phagosome maturation but has also evolved strategies to successfully prevent clearance by immune cells and to establish long-term survival in the host. Mass spectrometry (MS)-based proteomics allows the identification and quantitative analysis of complex protein mixtures and is increasingly employed to investigate host–pathogen interactions. Major challenges are limited availability and purity of pathogen-containing compartments as well as the asymmetric ratio in protein abundance when comparing bacterial and host proteins during the infection. Recent advances in purification techniques and MS technology helped to overcome previous difficulties and enable the detailed proteomic characterization of infected host cells and their pathogen-containing vacuoles. Here, we summarize current findings of the proteomic analysis of Mycobacterium-infected host cells and highlight progress that has been made to study the protein composition of mycobacterial vacuoles. Current investigations focus on the pathogenicity during Mtb infection, which will allow to better understand pathogen-induced changes and immunomodulation of infected host cells. Consequently, future research in this field will have important implications on host response, pathogen survival, and persistence, induced adaptive immunity and metabolic changes of immune cells promoting the development of novel host-directed therapies in tuberculosis.
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Affiliation(s)
- Eik Hoffmann
- CNRS, INSERM, CHU Lille, U1019, UMR8204, Centre d'Infection et d'Immunité de Lille (CIIL), Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Arnaud Machelart
- CNRS, INSERM, CHU Lille, U1019, UMR8204, Centre d'Infection et d'Immunité de Lille (CIIL), Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Ok-Ryul Song
- CNRS, INSERM, CHU Lille, U1019, UMR8204, Centre d'Infection et d'Immunité de Lille (CIIL), Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Priscille Brodin
- CNRS, INSERM, CHU Lille, U1019, UMR8204, Centre d'Infection et d'Immunité de Lille (CIIL), Institut Pasteur de Lille, Université de Lille, Lille, France
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Horvatić A, Kuleš J, Guillemin N, Galan A, Mrljak V, Bhide M. High-throughput proteomics and the fight against pathogens. MOLECULAR BIOSYSTEMS 2017; 12:2373-84. [PMID: 27227577 DOI: 10.1039/c6mb00223d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathogens pose a major threat to human and animal welfare. Understanding the interspecies host-pathogen protein-protein interactions could lead to the development of novel strategies to combat infectious diseases through the rapid development of new therapeutics. The first step in understanding the host-pathogen crosstalk is to identify interacting proteins in order to define crucial hot-spots in the host-pathogen interactome, such as the proposed pharmaceutical targets by means of high-throughput proteomic methodologies. In order to obtain holistic insight into the inter- and intra-species bimolecular interactions, apart from the proteomic approach, sophisticated in silico modeling is used to correlate the obtained large data sets with other omics data and clinical outcomes. Since the main focus in this area has been directed towards human medicine, it is time to extrapolate the existing expertise to a new emerging field: the 'systems veterinary medicine'. Therefore, this review addresses high-throughput mass spectrometry-based technology for monitoring protein-protein interactions in vitro and in vivo and discusses pathogen cultivation, model host cells and available bioinformatic tools employed in vaccine development.
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Affiliation(s)
- Anita Horvatić
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Josipa Kuleš
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Nicolas Guillemin
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Asier Galan
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Vladimir Mrljak
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Mangesh Bhide
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia. and Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia and Institute of Neuroimmunology, Slovakia Academy of Sciences, Bratislava, Slovakia
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5
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Pauwels AM, Trost M, Beyaert R, Hoffmann E. Patterns, Receptors, and Signals: Regulation of Phagosome Maturation. Trends Immunol 2017; 38:407-422. [PMID: 28416446 PMCID: PMC5455985 DOI: 10.1016/j.it.2017.03.006] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/18/2017] [Accepted: 03/21/2017] [Indexed: 12/13/2022]
Abstract
Recognition of microbial pathogens and dead cells and their phagocytic uptake by specialized immune cells are essential to maintain host homeostasis. Phagosomes undergo fusion and fission events with endosomal and lysosomal compartments, a process called ‘phagosome maturation’, which leads to the degradation of the phagosomal content. However, many phagocytic cells also act as antigen-presenting cells and must balance degradation and peptide preservation. Emerging evidence indicates that receptor engagement by phagosomal cargo, as well as inflammatory mediators and cellular activation affect many aspects of phagosome maturation. Unsurprisingly, pathogens have developed strategies to hijack this machinery, thereby interfering with host immunity. Here, we highlight progress in this field, summarize findings on the impact of immune signals, and discuss consequences for pathogen elimination. Self and non-self immune signals are able to delay or accelerate phagosome maturation, and their effects are dependent on the phagocytic cell type, duration of stimulation, and whether the stimulus is particle bound or present in the cellular environment. Acceleration of phagosome maturation enhances pathogen killing, while a delay in phagosome maturation preserves antigenic peptides for presentation to T cells and to initiate adaptive immune responses. Besides its functions in pathogen killing and antigen presentation, the phagosome also functions as a signaling platform and interacts with other cell organelles. Some pathogens are able to arrest phagosome maturation to enhance their intraphagosomal survival and replication or to promote phagosomal escape. The latex bead phagocytosis model system combined with mass spectrometry is a powerful technique to analyze changes in the phagosomal proteome.
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Affiliation(s)
- Anne-Marie Pauwels
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Matthias Trost
- MRC Protein Phosphorylation Unit, University of Dundee, Dundee, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Eik Hoffmann
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Current address: Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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6
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Li P, Wang R, Dong W, Hu L, Zong B, Zhang Y, Wang X, Guo A, Zhang A, Xiang Y, Chen H, Tan C. Comparative Proteomics Analysis of Human Macrophages Infected with Virulent Mycobacterium bovis. Front Cell Infect Microbiol 2017; 7:65. [PMID: 28337427 PMCID: PMC5343028 DOI: 10.3389/fcimb.2017.00065] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/21/2017] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium bovis (M. bovis), the most common pathogens of tuberculosis (TB), is virulent to human and cattle, and transmission between cattle and humans warrants reconsideration concerning food safety and public health. Recently, efforts have begun to analyze cellular proteomic responses induced by Mycobacterium tuberculosis (M. tb). However, the underlying mechanisms by which virulent M. bovis affects human hosts are not fully understood. For the present study, we utilized a global and comparative labeling strategy of isobaric tag for relative and absolute quantitation (iTRAQ) to assess proteomic changes in the human monocyte cell line (THP-1) using a vaccine strain and two virulent strains H37Rv and M. bovis. We measured 2,032 proteins, of which 61 were significantly differentially regulated. Ingenuity Pathway Analysis was employed to investigate the canonical pathways and functional networks involved in the infection. Several pathways, most notably the phagosome maturation pathway and TNF signaling pathway, were differentially affected by virulent strain treatment, including the key proteins CCL20 and ICAM1. Our qRT-PCR results were in accordance with those obtained from iTRAQ. The key enzyme MTHFD2, which is mainly involved in metabolism pathways, as well as LAMTOR2 might be effective upon M. bovis infection. String analysis also suggested that the vacuolar protein VPS26A interacted with TBC1D9B uniquely induced by M. bovis. In this study, we have first demonstrated the application of iTRAQ to compare human protein alterations induced by virulent M. bovis infections, thus providing a conceptual understanding of mycobacteria pathogenesis within the host as well as insight into preventing and controlling TB in human and animal hosts' transmission.
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Affiliation(s)
- Pei Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Rui Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Wenqi Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Linlin Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Bingbing Zong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Yanyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Yaozu Xiang
- Advanced Institute of Translational Medicine, School of Life Sciences and Technology, Tongji University Shanghai, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
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Abstract
The cause of Crohn’s disease (CD) has posed a conundrum for at least a century. A large body of work coupled with recent technological advances in genome research have at last started to provide some of the answers. Initially this review seeks to explain and to differentiate between bowel inflammation in the primary immunodeficiencies that generally lead to very early onset diffuse bowel inflammation in humans and in animal models, and the real syndrome of CD. In the latter, a trigger, almost certainly enteric infection by one of a multitude of organisms, allows the faeces access to the tissues, at which stage the response of individuals predisposed to CD is abnormal. Direct investigation of patients’ inflammatory response together with genome-wide association studies (GWAS) and DNA sequencing indicate that in CD the failure of acute inflammation and the clearance of bacteria from the tissues, and from within cells, is defective. The retained faecal products result in the characteristic chronic granulomatous inflammation and adaptive immune response. In this review I will examine the contemporary evidence that has led to this understanding, and look for explanations for the recent dramatic increase in the incidence of this disease.
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8
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Abstract
The cause of Crohn's disease (CD) has posed a conundrum for at least a century. A large body of work coupled with recent technological advances in genome research have at last started to provide some of the answers. Initially this review seeks to explain and to differentiate between bowel inflammation in the primary immunodeficiencies that generally lead to very early onset diffuse bowel inflammation in humans and in animal models, and the real syndrome of CD. In the latter, a trigger, almost certainly enteric infection by one of a multitude of organisms, allows the faeces access to the tissues, at which stage the response of individuals predisposed to CD is abnormal. Direct investigation of patients' inflammatory response together with genome-wide association studies (GWAS) and DNA sequencing indicate that in CD the failure of acute inflammation and the clearance of bacteria from the tissues, and from within cells, is defective. The retained faecal products result in the characteristic chronic granulomatous inflammation and adaptive immune response. In this review I will examine the contemporary evidence that has led to this understanding, and look for explanations for the recent dramatic increase in the incidence of this disease.
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9
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Long J, Basu Roy R, Zhang YJ, Antrobus R, Du Y, Smith DL, Weekes MP, Javid B. Plasma Membrane Profiling Reveals Upregulation of ABCA1 by Infected Macrophages Leading to Restriction of Mycobacterial Growth. Front Microbiol 2016; 7:1086. [PMID: 27462310 PMCID: PMC4940386 DOI: 10.3389/fmicb.2016.01086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/29/2016] [Indexed: 01/01/2023] Open
Abstract
The plasma membrane represents a critical interface between the internal and extracellular environments, and harbors multiple proteins key receptors and transporters that play important roles in restriction of intracellular infection. We applied plasma membrane profiling, a technique that combines quantitative mass spectrometry with selective cell surface aminooxy-biotinylation, to Bacille Calmette–Guérin (BCG)-infected THP-1 macrophages. We quantified 559 PM proteins in BCG-infected THP-1 cells. One significantly upregulated cell-surface protein was the cholesterol transporter ABCA1. We showed that ABCA1 was upregulated on the macrophage cell-surface following infection with pathogenic mycobacteria and knockdown of ABCA1 resulted in increased mycobacterial survival within macrophages, suggesting that it may be a novel mycobacterial host-restriction factor.
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Affiliation(s)
- Jing Long
- Collaboration Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University Beijing, China
| | | | | | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge Cambridge, UK
| | - Yuxian Du
- Collaboration Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University Beijing, China
| | - Duncan L Smith
- Cancer Research UK Manchester Institute, University of Manchester Manchester, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge Cambridge, UK
| | - Babak Javid
- Collaboration Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua UniversityBeijing, China; Harvard TH Chan School of Public Health, BostonMA, USA
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10
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Seto S, Tsujimura K, Horii T, Koide Y. Autophagy adaptor protein p62/SQSTM1 and autophagy-related gene Atg5 mediate autophagosome formation in response to Mycobacterium tuberculosis infection in dendritic cells. PLoS One 2013; 8:e86017. [PMID: 24376899 PMCID: PMC3871604 DOI: 10.1371/journal.pone.0086017] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/04/2013] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium tuberculosis is an intracellular pathogen that can survive within phagocytic cells by inhibiting phagolysosome biogenesis. However, host cells can control the intracellular M. tuberculosis burden by the induction of autophagy. The mechanism of autophagosome formation to M. tuberculosis has been well studied in macrophages, but remains unclear in dendritic cells. We therefore characterized autophagosome formation in response to M. tuberculosis infection in dendritic cells. Autophagy marker protein LC3, autophagy adaptor protein p62/SQSTM1 (p62) and ubiquitin co-localized to M. tuberculosis in dendritic cells. Mycobacterial autophagosomes fused with lysosomes during infection, and major histcompatibility complex class II molecules (MHC II) also localized to mycobacterial autophagosomes. The proteins p62 and Atg5 function in the initiation and progression of autophagosome formation to M. tuberculosis, respectively; p62 mediates ubiquitination of M. tuberculosis and Atg5 is involved in the trafficking of degradative vesicles and MHC II to mycobacterial autophagosomes. These results imply that the autophagosome formation to M. tuberculosis in dendritic cells promotes the antigen presentation of mycobacterial peptides to CD4+ T lymphocytes via MHC II.
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Affiliation(s)
- Shintaro Seto
- Department of Infectious Diseases, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
- * E-mail:
| | - Kunio Tsujimura
- Department of Infectious Diseases, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Toshinobu Horii
- Department of Infectious Diseases, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Yukio Koide
- Department of Infectious Diseases, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
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Bakhru P, Sirisaengtaksin N, Soudani E, Mukherjee S, Khan A, Jagannath C. BCG vaccine mediated reduction in the MHC-II expression of macrophages and dendritic cells is reversed by activation of Toll-like receptors 7 and 9. Cell Immunol 2013; 287:53-61. [PMID: 24384074 DOI: 10.1016/j.cellimm.2013.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 11/25/2013] [Accepted: 11/27/2013] [Indexed: 11/25/2022]
Abstract
Tuberculosis is a major cause of death in mankind and BCG vaccine protects against childhood but not adult tuberculosis. BCG avoids lysosomal fusion in macrophages decreasing peptides required for activating CD4 T cells and Th1 immunity while suppressing the expression of MHC-II by antigen presenting cells (APCs). An in vitro model of antigen presentation showed that ligands for TLR-9, 7, 4 and 1/2 increased the ability of APCs to present antigen-85B of BCG to CD4 T cells, which correlated with an increase in MHC-II expression. TLR-activation led to a down-regulation of MARCH1 ubiquitin ligase which prevents the degradation of MHC-II and decreased IL-10 also contributed to an increase in MHC-II. TLR-activation induced up-regulation of MHC-II was inhibited by the blockade of IRAK, NF-kB, and MAPKs. TLR-7 and TLR-9 ligands had the most effective adjuvant like effect on MHC-II of APCs which allowed BCG vaccine mediated activation of CD4 T cells.
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Affiliation(s)
- Pearl Bakhru
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Natalie Sirisaengtaksin
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Emily Soudani
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Seema Mukherjee
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Arshad Khan
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Chinnaswamy Jagannath
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA.
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12
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Abstract
Rab GTPases are at the central node of the machinery that regulates trafficking of organelles, including phagosomes. Thanks to the unique combination of high quality phagosome purification with highly sensitive proteomic studies, the network of Rab proteins that are dynamically associated with phagosomes during the process of maturation of this organelle is relatively well known. Whereas the phagosomal functions of many of the Rab proteins associated with phagosomes are characterized, the role(s) of most of these trafficking regulators remains to be identified. In some cases, even when the function in the context of phagosome biology is described, phagosomal Rab proteins seem to have similar roles. This review summarizes the current knowledge about the identity and function of phagosomal Rab GTPases, with a particular emphasis on new evidence that clarify these seemingly overlapping Rab functions during phagosome maturation.
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13
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Chapel A, Kieffer-Jaquinod S, Sagné C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A. An extended proteome map of the lysosomal membrane reveals novel potential transporters. Mol Cell Proteomics 2013; 12:1572-88. [PMID: 23436907 PMCID: PMC3675815 DOI: 10.1074/mcp.m112.021980] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 02/01/2013] [Indexed: 12/22/2022] Open
Abstract
Lysosomes are membrane-bound endocytic organelles that play a major role in degrading cell macromolecules and recycling their building blocks. A comprehensive knowledge of the lysosome function requires an extensive description of its content, an issue partially addressed by previous proteomic analyses. However, the proteins underlying many lysosomal membrane functions, including numerous membrane transporters, remain unidentified. We performed a comparative, semi-quantitative proteomic analysis of rat liver lysosome-enriched and lysosome-nonenriched membranes and used spectral counts to evaluate the relative abundance of proteins. Among a total of 2,385 identified proteins, 734 proteins were significantly enriched in the lysosomal fraction, including 207 proteins already known or predicted as endo-lysosomal and 94 proteins without any known or predicted subcellular localization. The remaining 433 proteins had been previously assigned to other subcellular compartments but may in fact reside on lysosomes either predominantly or as a secondary location. Many membrane-associated complexes implicated in diverse processes such as degradation, membrane trafficking, lysosome biogenesis, lysosome acidification, signaling, and nutrient sensing were enriched in the lysosomal fraction. They were identified to an unprecedented extent as most, if not all, of their subunits were found and retained by our screen. Numerous transporters were also identified, including 46 novel potentially lysosomal proteins. We expressed 12 candidates in HeLa cells and observed that most of them colocalized with the lysosomal marker LAMP1, thus confirming their lysosomal residency. This list of candidate lysosomal proteins substantially increases our knowledge of the lysosomal membrane and provides a basis for further characterization of lysosomal functions.
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Affiliation(s)
- Agnès Chapel
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Sylvie Kieffer-Jaquinod
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Corinne Sagné
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Quentin Verdon
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
- §§Graduate School ED 419, Université Paris-Sud 11, Hôpital Bicêtre, F-94276 Le Kremlin Bicêtre France, and
| | - Corinne Ivaldi
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Mourad Mellal
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jaqueline Thirion
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Michel Jadot
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Christophe Bruley
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jérôme Garin
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Bruno Gasnier
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Agnès Journet
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
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14
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He Y, Li W, Liao G, Xie J. Mycobacterium tuberculosis-Specific Phagosome Proteome and Underlying Signaling Pathways. J Proteome Res 2012; 11:2635-43. [DOI: 10.1021/pr300125t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ying He
- Institute of Modern Biopharmaceuticals,
State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource
of the Three Gorges Area, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Weimin Li
- Beijing Tuberculosis & Thoracic Tumor Research Institute, Tongzhou Qu, Beijing 101149
| | - Guojian Liao
- Institute
of Modern Biopharmaceuticals,
School of Pharmaceutical 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, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
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15
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Li Q. Phagosome proteomics: a powerful tool to assess bacteria-mediated immunomodulation. Bioeng Bugs 2011; 2:194-8. [PMID: 21829091 DOI: 10.4161/bbug.2.4.15563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacteria-mediated immunomodulation has important implications in microbial infection and bacterial vaccines. Intraphagosomal bacteria negotiate survival niches with the intracellular environment by modulating the phagosome composition during invasion. The final phagosome composition determines the fate of the intraphagosomal bacterium or the efficacy of a bacterial vaccine. Therefore, the phagosome proteome is a valuable readout to assess the ability of a natural or genetically engineered bacterial strain to modulate the host immune response. Compared to a preparation of latex-bead-containing phagosomes, the preparation of bacterial phagosomes requires additional measures to ensure comparable purity due to their closer density to some other organelles. This bottleneck can be overcome with delicate preparation protocols, proper experimental designs to facilitate bioinformatics based discrimination against contaminating proteins, and the incorporation of stable-isotope labeled internal standards to correct for contaminating fractions of phagosomal proteins. The rapid progress in the proteomics and bioinformatics fields provides an array of techniques that promise to bring about an unprecedented coverage of both known and as yet undiscovered immunomodulation pathways within bacterial phagosome proteomes. A precise portrait of the bacteria-mediated immunomodulation pathways in phagosomes will likely aid in the intelligent design of bioengineered bacterial vaccine strains for important future biomedical applications.
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Affiliation(s)
- Qingbo Li
- Center for Pharmaceutical Biotechnology and Department of Microbiology and Immunology, University of Illinois, Chicago, USA. ial infectio
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