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Wiggins BG, Wang YF, Burke A, Grunberg N, Vlachaki Walker JM, Dore M, Chahrour C, Pennycook BR, Sanchez-Garrido J, Vernia S, Barr AR, Frankel G, Birdsey GM, Randi AM, Schiering C. Endothelial sensing of AHR ligands regulates intestinal homeostasis. Nature 2023; 621:821-829. [PMID: 37586410 PMCID: PMC10533400 DOI: 10.1038/s41586-023-06508-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Endothelial cells line the blood and lymphatic vasculature, and act as an essential physical barrier, control nutrient transport, facilitate tissue immunosurveillance and coordinate angiogenesis and lymphangiogenesis1,2. In the intestine, dietary and microbial cues are particularly important in the regulation of organ homeostasis. However, whether enteric endothelial cells actively sense and integrate such signals is currently unknown. Here we show that the aryl hydrocarbon receptor (AHR) acts as a critical node for endothelial cell sensing of dietary metabolites in adult mice and human primary endothelial cells. We first established a comprehensive single-cell endothelial atlas of the mouse small intestine, uncovering the cellular complexity and functional heterogeneity of blood and lymphatic endothelial cells. Analyses of AHR-mediated responses at single-cell resolution identified tissue-protective transcriptional signatures and regulatory networks promoting cellular quiescence and vascular normalcy at steady state. Endothelial AHR deficiency in adult mice resulted in dysregulated inflammatory responses and the initiation of proliferative pathways. Furthermore, endothelial sensing of dietary AHR ligands was required for optimal protection against enteric infection. In human endothelial cells, AHR signalling promoted quiescence and restrained activation by inflammatory mediators. Together, our data provide a comprehensive dissection of the effect of environmental sensing across the spectrum of enteric endothelia, demonstrating that endothelial AHR signalling integrates dietary cues to maintain tissue homeostasis by promoting endothelial cell quiescence and vascular normalcy.
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Affiliation(s)
- Benjamin G Wiggins
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
- MRC London Institute of Medical Sciences, London, UK.
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, London, UK
| | - Alice Burke
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - Nil Grunberg
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - Julia M Vlachaki Walker
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - Marian Dore
- MRC London Institute of Medical Sciences, London, UK
| | | | - Betheney R Pennycook
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | | | - Santiago Vernia
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - Alexis R Barr
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - Gad Frankel
- Department of Life Sciences, Imperial College London, London, UK
| | - Graeme M Birdsey
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Anna M Randi
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Chris Schiering
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
- MRC London Institute of Medical Sciences, London, UK.
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2
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David S, Wong JLC, Sanchez-Garrido J, Kwong HS, Low WW, Morecchiato F, Giani T, Rossolini GM, Brett SJ, Clements A, Beis K, Aanensen DM, Frankel G. Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae. PLoS Pathog 2022; 18:e1010334. [PMID: 35816554 PMCID: PMC9302836 DOI: 10.1371/journal.ppat.1010334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/21/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies. Rapidly rising rates of antibiotic resistance among Klebsiella pneumoniae (KP) necessitate a comprehensive understanding of the diversity, spread and clinical impact of resistance mutations. In KP, mutations in outer membrane porins play an important role in mediating resistance to carbapenems, a key class of antibiotics. Here we show that resistance mutations in the extracellular loop 3 (L3) region of the OmpK36 porin are found at high prevalence among clinical genomes and we characterise their diversity and impact on resistance and virulence. They include amino acid insertions of Aspartate (D), Glycine-Aspartate (GD) and Threonine-Aspartate (TD), which act by decreasing the pore size and restricting entry of carbapenems into the bacterial cell. We show that these L3 insertions are associated with large clonal expansions of resistant lineages and impose a fitness cost evident during in vivo competition. Critically, strains harbouring L3 insertions remain susceptible to novel drugs, including beta lactam-beta lactamase inhibitor combinations. This study highlights the importance of monitoring the emergence and spread of strains with OmpK36 L3 insertions for the control of resistant KP infections and provides crucial data for drug development and treatment strategies.
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Affiliation(s)
- Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Joshua L. C. Wong
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Hok-Sau Kwong
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, United Kingdom
- Department of Life Sciences, Imperial College London; London, United Kingdom
| | - Wen Wen Low
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Fabio Morecchiato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Stephen J. Brett
- Department of Surgery and Cancer, Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London, London, United Kingdom
| | - Abigail Clements
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Konstantinos Beis
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, United Kingdom
- Department of Life Sciences, Imperial College London; London, United Kingdom
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
- * E-mail:
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3
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Sanchez-Garrido J, Ruano-Gallego D, Choudhary JS, Frankel G. The type III secretion system effector network hypothesis. Trends Microbiol 2022; 30:524-533. [PMID: 34840074 DOI: 10.1016/j.tim.2021.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022]
Abstract
Type III secretion system (T3SS) effectors are key virulence factors that underpin the infection strategy of many clinically important Gram-negative pathogens, including Salmonella enterica, Shigella spp., enteropathogenic and enterohemorrhagic Escherichia coli and their murine equivalent, Citrobacter rodentium. The cellular processes or proteins targeted by the effectors can be common to multiple pathogens or pathogen-specific. The main approach to understanding T3SS-mediated pathogenesis has been to determine the contribution of one effector at a time, with the aim of piecing together individual functions and unveiling infection mechanisms. However, in contrast to this prevailing approach, simultaneous deletion of multiple effectors revealed that they function as an interconnected network in vivo, uncovering effector codependency and context-dependent effector essentiality. This paradigm shift in T3SS biology is at the heart of this opinion article.
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Affiliation(s)
- Julia Sanchez-Garrido
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK.
| | - David Ruano-Gallego
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain.
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Gad Frankel
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
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4
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Ruano-Gallego D, Sanchez-Garrido J, Kozik Z, Núñez-Berrueco E, Cepeda-Molero M, Mullineaux-Sanders C, Naemi Baghshomali Y, Slater SL, Wagner N, Glegola-Madejska I, Roumeliotis TI, Pupko T, Fernández LÁ, Rodríguez-Patón A, Choudhary JS, Frankel G. Type III secretion system effectors form robust and flexible intracellular virulence networks. Science 2021; 371:eabc9531. [PMID: 33707240 DOI: 10.1126/science.abc9531] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 12/15/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022]
Abstract
Infections with many Gram-negative pathogens, including Escherichia coli, Salmonella, Shigella, and Yersinia, rely on type III secretion system (T3SS) effectors. We hypothesized that while hijacking processes within mammalian cells, the effectors operate as a robust network that can tolerate substantial contractions. This was tested in vivo using the mouse pathogen Citrobacter rodentium (encoding 31 effectors). Sequential gene deletions showed that effector essentiality for infection was context dependent and that the network could tolerate 60% contraction while maintaining pathogenicity. Despite inducing very different colonic cytokine profiles (e.g., interleukin-22, interleukin-17, interferon-γ, or granulocyte-macrophage colony-stimulating factor), different networks induced protective immunity. Using data from >100 distinct mutant combinations, we built and trained a machine learning model able to predict colonization outcomes, which were confirmed experimentally. Furthermore, reproducing the human-restricted enteropathogenic E. coli effector repertoire in C. rodentium was not sufficient for efficient colonization, which implicates effector networks in host adaptation. These results unveil the extreme robustness of both T3SS effector networks and host responses.
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Affiliation(s)
- David Ruano-Gallego
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Julia Sanchez-Garrido
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Zuzanna Kozik
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Elena Núñez-Berrueco
- Laboratorio de Inteligencia Artificial, Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Campus de Montegancedo, Boadilla del Monte, Madrid, Spain
| | - Massiel Cepeda-Molero
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | | | - Yasaman Naemi Baghshomali
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Sabrina L Slater
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Izabela Glegola-Madejska
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Luis Ángel Fernández
- Centro Nacional de Biotecnología (CNB-CSIC), Department of Microbial Biotechnology, Madrid, Spain
| | - Alfonso Rodríguez-Patón
- Laboratorio de Inteligencia Artificial, Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Campus de Montegancedo, Boadilla del Monte, Madrid, Spain
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK.
| | - Gad Frankel
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK.
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5
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Mylona E, Sanchez-Garrido J, Hoang Thu TN, Dongol S, Karkey A, Baker S, Shenoy AR, Frankel G. Very long O-antigen chains of Salmonella Paratyphi A inhibit inflammasome activation and pyroptotic cell death. Cell Microbiol 2021; 23:e13306. [PMID: 33355403 PMCID: PMC8609438 DOI: 10.1111/cmi.13306] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 11/28/2022]
Abstract
Salmonella Paratyphi A (SPtA) remains one of the leading causes of enteric (typhoid) fever. Yet, despite the recent increased rate of isolation from patients in Asia, our understanding of its pathogenesis is incomplete. Here we investigated inflammasome activation in human macrophages infected with SPtA. We found that SPtA induces GSDMD‐mediated pyroptosis via activation of caspase‐1, caspase‐4 and caspase‐8. Although we observed no cell death in the absence of a functional Salmonella pathogenicity island‐1 (SPI‐1) injectisome, HilA‐mediated overexpression of the SPI‐1 regulon enhances pyroptosis. SPtA expresses FepE, an LPS O‐antigen length regulator, which induces the production of very long O‐antigen chains. Using a ΔfepE mutant we established that the very long O‐antigen chains interfere with bacterial interactions with epithelial cells and impair inflammasome‐mediated macrophage cell death. Salmonella Typhimurium (STm) serovar has a lower FepE expression than SPtA, and triggers higher pyroptosis, conversely, increasing FepE expression in STm reduced pyroptosis. These results suggest that differential expression of FepE results in serovar‐specific inflammasome modulation, which mirrors the pro‐ and anti‐inflammatory strategies employed by STm and SPtA, respectively. Our studies point towards distinct mechanisms of virulence of SPtA, whereby it attenuates inflammasome‐mediated detection through the elaboration of very long LPS O‐polysaccharides.
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Affiliation(s)
- Elli Mylona
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Julia Sanchez-Garrido
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Trang Nguyen Hoang Thu
- Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Avinash R Shenoy
- Department of Infectious Disease, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Gad Frankel
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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6
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Abstract
Nutrients not only act as building blocks but also as signaling molecules. Nutrient-availability promotes cell growth and proliferation and suppresses catabolic processes, such as macroautophagy/autophagy. These effects are mediated by checkpoint kinases such as MTOR (mechanistic target of rapamycin kinase), which is activated by amino acids and growth factors, and AMP-activated protein kinase (AMPK), which is activated by low levels of glucose or ATP. These kinases have wide-ranging activities that can be co-opted by immune cells upon exposure to danger signals, cytokines or pathogens. Here, we discuss recent insight into the regulation and repurposing of nutrient-sensing responses by the innate immune system during infection. Moreover, we examine how natural mutations and pathogen-mediated interventions can alter the balance between anabolic and autophagic pathways leading to a breakdown in tissue homeostasis and/or host defense.Abbreviations: AKT1/PKB: AKT serine/threonine kinase 1; ATG: autophagy related; BECN1: beclin 1; CGAS: cyclic GMP-AMP synthase; EIF2AK4/GCN2: eukaryotic translation initiation factor 2 alpha kinase 4; ER: endoplasmic reticulum; FFAR: free fatty acid receptor; GABARAP: GABA type A receptor-associated protein; IFN: interferon; IL: interleukin; LAP: LC3-associated phagocytosis; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK: mitogen-activated protein kinase; MTOR: mechanistic target of rapamycin kinase; NLR: NOD (nucleotide-binding oligomerization domain) and leucine-rich repeat containing proteins; PI3K, phosphoinositide 3-kinase; PRR: pattern-recognition receptor; PtdIns3K: phosphatidylinositol 3-kinase; RALB: RAS like proto-oncogene B; RHEB: Ras homolog, MTORC1 binding; RIPK1: receptor interacting serine/threonine kinase 1; RRAG: Ras related GTP binding; SQSTM1/p62: sequestosome 1; STING1/TMEM173: stimulator of interferon response cGAMP interactor 1; STK11/LKB1: serine/threonine kinase 11; TBK1: TANK binding kinase 1; TLR: toll like receptor; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; TRIM: tripartite motif protein; ULK1: unc-51 like autophagy activating kinase 1; V-ATPase: vacuolar-type H+-proton-translocating ATPase.
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Affiliation(s)
- Julia Sanchez-Garrido
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Avinash R Shenoy
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.,Satellite Group Leader, The Francis Crick Institute, London, UK
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7
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Goddard PJ, Sanchez-Garrido J, Slater SL, Kalyan M, Ruano-Gallego D, Marchès O, Fernández LÁ, Frankel G, Shenoy AR. Enteropathogenic Escherichia coli Stimulates Effector-Driven Rapid Caspase-4 Activation in Human Macrophages. Cell Rep 2020; 27:1008-1017.e6. [PMID: 31018119 PMCID: PMC6486487 DOI: 10.1016/j.celrep.2019.03.100] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/20/2019] [Accepted: 03/27/2019] [Indexed: 12/20/2022] Open
Abstract
Microbial infections can stimulate the assembly of inflammasomes, which activate caspase-1. The gastrointestinal pathogen enteropathogenic Escherichia coli (EPEC) causes localized actin polymerization in host cells. Actin polymerization requires the binding of the bacterial adhesin intimin to Tir, which is delivered to host cells via a type 3 secretion system (T3SS). We show that EPEC induces T3SS-dependent rapid non-canonical NLRP3 inflammasome activation in human macrophages. Notably, caspase-4 activation by EPEC triggers pyroptosis and cytokine processing through the NLRP3-caspase-1 inflammasome. Mechanistically, caspase-4 activation requires the detection of LPS and EPEC-induced actin polymerization, either via Tir tyrosine phosphorylation and the phosphotyrosine-binding adaptor NCK or Tir and the NCK-mimicking effector TccP. An engineered E. coli K12 could reconstitute Tir-intimin signaling, which is necessary and sufficient for inflammasome activation, ruling out the involvement of other virulence factors. Our studies reveal a crosstalk between caspase-4 and caspase-1 that is cooperatively stimulated by LPS and effector-driven actin polymerization. EPEC bacteria expressing virulence genes induce rapid human macrophage pyroptosis Bacterial LPS sensing by caspase-4 activates NLRP3-caspase-1 inflammasomes Actin polymerization driven by Tir-intimin signaling promotes pyroptosis Caspase-1 mediates cytokine processing and gasdermin D cleavage, leading to pyroptosis
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Affiliation(s)
- Philippa J Goddard
- Department of Life Sciences, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK; Department of Medicine, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Julia Sanchez-Garrido
- Department of Medicine, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Sabrina L Slater
- Department of Life Sciences, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Mohini Kalyan
- Department of Medicine, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - David Ruano-Gallego
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Olivier Marchès
- Department of Life Sciences, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Gad Frankel
- Department of Life Sciences, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Avinash R Shenoy
- Department of Medicine, Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK.
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8
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Subbarao S, Sanchez-Garrido J, Krishnan N, Shenoy AR, Robertson BD. Genetic and pharmacological inhibition of inflammasomes reduces the survival of Mycobacterium tuberculosis strains in macrophages. Sci Rep 2020; 10:3709. [PMID: 32111888 PMCID: PMC7048741 DOI: 10.1038/s41598-020-60560-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis infection causes high rates of morbidity and mortality. Host-directed therapy may enhance the immune response, reduce tissue damage and shorten treatment duration. The inflammasome is integral to innate immune responses but over-activation has been described in tuberculosis (TB) pathology and TB-immune reconstitution syndrome. Here we explore how clinical isolates differentially activate the inflammasome and how inflammasome inhibition can lead to enhanced bacterial clearance. Wild-type, Nlrp3−/−/Aim2−/−, Casp1/11−/− and Asc−/− murine bone-marrow derived macrophages (BMDMs) were infected with laboratory strain M. tuberculosis H37Rv or clinical isolates from various lineages. Inflammasome activation and bacterial numbers were measured, and pharmacological inhibition of NLRP3 was achieved using MCC950. Clinical isolates of M. tuberculosis differed in their ability to activate inflammasomes. Beijing isolates had contrasting effects on IL-1β and caspase-1 activation, but all clinical isolates induced lower IL-1β release than H37Rv. Our studies suggest the involvement of NLRP3, AIM2 and an additional unknown sensor in IL-1β maturation. Pharmacological blockade of NLRP3 with MCC950 reduced bacterial survival, and combined treatment with the antimycobacterial drug rifampicin enhanced the effect. Modulating the inflammasome is an attractive adjunct to current anti-mycobacterial therapy that warrants further investigation.
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Affiliation(s)
- Sathyavani Subbarao
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK
| | - Nitya Krishnan
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK.
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Flowers Building, Imperial College London, London, SW7 2AZ, UK.
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9
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Watson JL, Sanchez-Garrido J, Goddard PJ, Torraca V, Mostowy S, Shenoy AR, Clements A. Shigella sonnei O-Antigen Inhibits Internalization, Vacuole Escape, and Inflammasome Activation. mBio 2019; 10:e02654-19. [PMID: 31848280 PMCID: PMC6918081 DOI: 10.1128/mbio.02654-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/11/2019] [Indexed: 12/04/2022] Open
Abstract
Two Shigella species, Shigella flexneri and Shigella sonnei, cause approximately 90% of bacterial dysentery worldwide. While S. flexneri is the dominant species in low-income countries, S. sonnei causes the majority of infections in middle- and high-income countries. S. flexneri is a prototypic cytosolic bacterium; once intracellular, it rapidly escapes the phagocytic vacuole and causes pyroptosis of macrophages, which is important for pathogenesis and bacterial spread. In contrast, little is known about the invasion, vacuole escape, and induction of pyroptosis during S. sonnei infection of macrophages. We demonstrate here that S. sonnei causes substantially less pyroptosis in human primary monocyte-derived macrophages and THP1 cells. This is due to reduced bacterial uptake and lower relative vacuole escape, which results in fewer cytosolic S. sonnei and hence reduced activation of caspase-1 inflammasomes. Mechanistically, the O-antigen (O-Ag), which in S. sonnei is contained in both the lipopolysaccharide and the capsule, was responsible for reduced uptake and the type 3 secretion system (T3SS) was required for vacuole escape. Our findings suggest that S. sonnei has adapted to an extracellular lifestyle by incorporating multiple layers of O-Ag onto its surface compared to other Shigella species.IMPORTANCE Diarrheal disease remains the second leading cause of death in children under five. Shigella remains a significant cause of diarrheal disease with two species, S. flexneri and S. sonnei, causing the majority of infections. S. flexneri are well known to cause cell death in macrophages, which contributes to the inflammatory nature of Shigella diarrhea. Here, we demonstrate that S. sonnei causes less cell death than S. flexneri due to a reduced number of bacteria present in the cell cytosol. We identify the O-Ag polysaccharide which, uniquely among Shigella spp., is present in two forms on the bacterial cell surface as the bacterial factor responsible. Our data indicate that S. sonnei differs from S. flexneri in key aspects of infection and that more attention should be given to characterization of S. sonnei infection.
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Affiliation(s)
- Jayne L Watson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Julia Sanchez-Garrido
- Department of Infectious Disease, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Philippa J Goddard
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Infectious Disease, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Vincenzo Torraca
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Avinash R Shenoy
- Department of Infectious Disease, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Abigail Clements
- Department of Life Sciences, Imperial College London, London, United Kingdom
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10
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Sanchez-Garrido J, Sancho-Shimizu V, Shenoy AR. Regulated proteolysis of p62/SQSTM1 enables differential control of autophagy and nutrient sensing. Sci Signal 2018; 11:11/559/eaat6903. [PMID: 30514811 DOI: 10.1126/scisignal.aat6903] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The multidomain scaffold protein p62 (also called sequestosome-1) is involved in autophagy, antimicrobial immunity, and oncogenesis. Mutations in SQSTM1, which encodes p62, are linked to hereditary inflammatory conditions such as Paget's disease of the bone, frontotemporal dementia (FTD), amyotrophic lateral sclerosis, and distal myopathy with rimmed vacuoles. Here, we report that p62 was proteolytically trimmed by the protease caspase-8 into a stable protein, which we called p62TRM We found that p62TRM, but not full-length p62, was involved in nutrient sensing and homeostasis through the mechanistic target of rapamycin complex 1 (mTORC1). The kinase RIPK1 and caspase-8 controlled p62TRM production and thus promoted mTORC1 signaling. An FTD-linked p62 D329G polymorphism and a rare D329H variant could not be proteolyzed by caspase-8, and these noncleavable variants failed to activate mTORC1, thereby revealing the detrimental effect of these mutations. These findings on the role of p62TRM provide new insights into SQSTM1-linked diseases and mTORC1 signaling.
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Affiliation(s)
- Julia Sanchez-Garrido
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Vanessa Sancho-Shimizu
- Section of Paediatrics, Imperial College London, London W21 PG, UK.,Section of Virology, Imperial College London, London W21 PG, UK
| | - Avinash R Shenoy
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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Eldridge MJG, Sanchez-Garrido J, Hoben GF, Goddard PJ, Shenoy AR. The Atypical Ubiquitin E2 Conjugase UBE2L3 Is an Indirect Caspase-1 Target and Controls IL-1β Secretion by Inflammasomes. Cell Rep 2017; 18:1285-1297. [PMID: 28147281 PMCID: PMC5300903 DOI: 10.1016/j.celrep.2017.01.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 12/12/2016] [Accepted: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
Caspase-1 activation by inflammasome signaling scaffolds initiates inflammation and antimicrobial responses. Caspase-1 proteolytically converts newly induced pro-interleukin 1 beta (IL-1β) into its mature form and directs its secretion, triggering pyroptosis and release of non-substrate alarmins such as interleukin 1 alpha (IL-1α) and HMGB1. While some caspase-1 substrates involved in these events are known, the identities and roles of non-proteolytic targets remain unknown. Here, we use unbiased proteomics to show that the UBE2L3 ubiquitin conjugase is an indirect target of caspase-1. Caspase-1, but not caspase-4, controls pyroptosis- and ubiquitin-independent proteasomal degradation of UBE2L3 upon canonical and non-canonical inflammasome activation by sterile danger signals and bacterial infection. Mechanistically, UBE2L3 acts post-translationally to promote K48-ubiquitylation and turnover of pro-IL-1β and dampen mature-IL-1β production. UBE2L3 depletion increases pro-IL-1β levels and mature-IL-1β secretion by inflammasomes. These findings regarding UBE2L3 as a molecular rheostat have implications for IL-1-driven pathology in hereditary fever syndromes and in autoinflammatory conditions associated with UBE2L3 polymorphisms. Caspase-1 inflammasomes induce loss of UBE2L3 in macrophages and dendritic cells UBE2L3 loss is proteasome-dependent, ubiquitin- and pyroptosis-independent UBE2L3 participates in K48 ubiquitylation and proteasomal turnover of pro-IL-1β UBE2L3 modulates levels of pro-IL-1β available for processing by caspase-1
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Affiliation(s)
- Matthew J G Eldridge
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gil Ferreira Hoben
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Philippa J Goddard
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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12
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Pallett MA, Crepin VF, Serafini N, Habibzay M, Kotik O, Sanchez-Garrido J, Di Santo JP, Shenoy AR, Berger CN, Frankel G. Bacterial virulence factor inhibits caspase-4/11 activation in intestinal epithelial cells. Mucosal Immunol 2017; 10:602-612. [PMID: 27624779 PMCID: PMC5159625 DOI: 10.1038/mi.2016.77] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 08/01/2016] [Indexed: 02/07/2023]
Abstract
The human pathogen enteropathogenic Escherichia coli (EPEC), as well as the mouse pathogen Citrobacter rodentium, colonize the gut mucosa via attaching and effacing lesion formation and cause diarrheal diseases. EPEC and C. rodentium type III secretion system (T3SS) effectors repress innate immune responses and infiltration of immune cells. Inflammatory caspases such as caspase-1 and caspase-4/11 are crucial mediators of host defense and inflammation in the gut via their ability to process cytokines such as interleukin (IL)-1β and IL-18. Here we report that the effector NleF binds the catalytic domain of caspase-4 and inhibits its proteolytic activity. Following infection of intestinal epithelial cells (IECs) EPEC inhibited caspase-4 and IL-18 processing in an NleF-dependent manner. Depletion of caspase-4 in IECs prevented the secretion of mature IL-18 in response to infection with EPECΔnleF. NleF-dependent inhibition of caspase-11 in colons of mice prevented IL-18 secretion and neutrophil influx at early stages of C. rodentium infection. Neither wild-type C. rodentium nor C. rodentiumΔnleF triggered neutrophil infiltration or IL-18 secretion in Cas11 or Casp1/11-deficient mice. Thus, IECs have a key role in modulating early innate immune responses in the gut via a caspase-4/11-IL-18 axis, which is targeted by virulence factors encoded by enteric pathogens.
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Affiliation(s)
- Mitchell A. Pallett
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK
| | - Valerie F. Crepin
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK
| | - Nicolas Serafini
- Innate Immunity Unit, Institut Pasteur, Paris, France,Inserm U668, Paris, France
| | - Maryam Habibzay
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK
| | - Olga Kotik
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK
| | - Julia Sanchez-Garrido
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK
| | - James P. Di Santo
- Innate Immunity Unit, Institut Pasteur, Paris, France,Inserm U668, Paris, France
| | - Avinash R. Shenoy
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK
| | - Cedric N. Berger
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK
| | - Gad Frankel
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, UK,Corresponding author, Gad Frankel, MRC CMBI, Flowers Building, Imperial College, London, SW7 2AZ,
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13
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Eleftheriadou I, Dieringer M, Poh XY, Sanchez-Garrido J, Gao Y, Sgourou A, Simmons LE, Mazarakis ND. Selective transduction of astrocytic and neuronal CNS subpopulations by lentiviral vectors pseudotyped with Chikungunya virus envelope. Biomaterials 2017; 123:1-14. [PMID: 28152379 DOI: 10.1016/j.biomaterials.2017.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 12/15/2022]
Abstract
Lentiviral vectors are gene delivery vehicles that integrate into the host genome of dividing and non-dividing mammalian cells facilitating long-term transgene expression. Lentiviral vector versatility is greatly increased by incorporating heterologous viral envelope proteins onto the vector particles instead of the native envelope, conferring on these pseudotyped vectors a modified tropism and host range specificity. We investigated the pseudotyping efficiency of HIV-1 based lentiviral vectors with alphaviral envelope proteins from the Chikungunya Virus (CHIKV-G) and Sindbis Virus (SINV-G). Following vector production optimisation, titres for the CHIKV-G pseudotype were comparable to the VSV-G pseudotype but those for the SINV-G pseudotype were significantly lower. High titre CHIKV-G pseudotyped vector efficiently transduced various human and mouse neural cell lines and normal human astrocytes (NHA) in vitro. Although transduction was broad, tropism for NHAs was observed. In vivo stereotaxic delivery in striatum, thalamus and hippocampus respectively in the adult rat brain revealed localised transduction restricted to striatal astrocytes and hippocampal dentate granule neurons. Transduction of different subtypes of granule neurons from precursor to post-mitotic stages of differentiation was evident in the sub-granular zone and dentate granule cell layer. No significant inflammatory response was observed, but comparable to that of VSV-G pseudotyped lentiviral vectors. Robust long-term expression followed for three months post-transduction along with absence of neuroinflammation, coupled to the selective and unique neuron/glial tropism indicates that these vectors could be useful for modelling and gene therapy studies in the CNS.
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Affiliation(s)
- Ioanna Eleftheriadou
- Gene Therapy, Centre for Neuroinflammation & Neurodegeneration, Division of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Michael Dieringer
- Gene Therapy, Centre for Neuroinflammation & Neurodegeneration, Division of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Xuan Ying Poh
- Gene Therapy, Centre for Neuroinflammation & Neurodegeneration, Division of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Julia Sanchez-Garrido
- Gene Therapy, Centre for Neuroinflammation & Neurodegeneration, Division of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Yunan Gao
- Gene Therapy, Centre for Neuroinflammation & Neurodegeneration, Division of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Argyro Sgourou
- Laboratory of Biology, Hellenic Open University, Tsamadou 13-15, 26222 Patra, Greece
| | - Laura E Simmons
- Gene Therapy, Centre for Neuroinflammation & Neurodegeneration, Division of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Nicholas D Mazarakis
- Gene Therapy, Centre for Neuroinflammation & Neurodegeneration, Division of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom.
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