Imperial College London

DrThomasClarke

Faculty of MedicineDepartment of Medicine

Research Fellow
 
 
 
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Contact

 

+44 (0)20 7594 2074thomas.clarke

 
 
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Location

 

5.40CFlowers buildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

17 results found

Brown RL, Clarke TB, 2017, The regulation of host defences to infection by the microbiota, IMMUNOLOGY, Vol: 150, Pages: 1-6, ISSN: 0019-2805

JOURNAL ARTICLE

Brown RL, Sequeira RP, Clarke TB, 2017, The microbiota protects against respiratory infection via GM-CSF signaling., Nat Commun, Vol: 8

The microbiota promotes resistance to respiratory infection, but the mechanistic basis for this is poorly defined. Here, we identify members of the microbiota that protect against respiratory infection by the major human pathogens Streptococcus pneumoniae and Klebsiella pneumoniae. We show that the microbiota enhances respiratory defenses via granulocyte-macrophage colony-stimulating factor (GM-CSF) signaling, which stimulates pathogen killing and clearance by alveolar macrophages through extracellular signal-regulated kinase signaling. Increased pulmonary GM-CSF production in response to infection is primed by the microbiota through interleukin-17A. By combining models of commensal colonization in antibiotic-treated and germ-free mice, using cultured commensals from the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla, we found that potent Nod-like receptor-stimulating bacteria in the upper airway (Staphylococcus aureus and Staphylococcus epidermidis) and intestinal microbiota (Lactobacillus reuteri, Enterococcus faecalis, Lactobacillus crispatus and Clostridium orbiscindens) promote resistance to lung infection through Nod2 and GM-CSF. Our data reveal the identity, location, and properties of bacteria within the microbiota that regulate lung immunity, and delineate the host signaling axis they activate to protect against respiratory infection.

JOURNAL ARTICLE

Dominguez-Huettinger E, Boon NJ, Clarke TB, Tanaka RJet al., 2017, Mathematical Modeling of Streptococcus pneumoniae Colonization, Invasive Infection and Treatment, FRONTIERS IN PHYSIOLOGY, Vol: 8, ISSN: 1664-042X

JOURNAL ARTICLE

Pader V, Hakim S, Painter KL, Wigneshweraraj S, Clarke TB, Edwards AMet al., 2017, Staphylococcus aureus inactivates daptomycin by releasing membrane phospholipids, NATURE MICROBIOLOGY, Vol: 2, ISSN: 2058-5276

JOURNAL ARTICLE

Hergott CB, Roche AM, Tamashiro E, Clarke TB, Bailey AG, Laughlin A, Bushman FD, Weiser JNet al., 2016, Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis, BLOOD, Vol: 127, Pages: 2460-2471, ISSN: 0006-4971

JOURNAL ARTICLE

Clarke TB, 2014, Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands, INFECTION AND IMMUNITY, Vol: 82, Pages: 4596-4606, ISSN: 0019-9567

JOURNAL ARTICLE

Clarke TB, 2014, Microbial Programming of Systemic Innate Immunity and Resistance to Infection, PLOS PATHOGENS, Vol: 10, ISSN: 1553-7366

JOURNAL ARTICLE

Dominguez-Huttinger E, Clarke TB, Tanaka RJ, 2014, Mathematical modelling of host pathogen interactions at mucosal surfaces reveals the dual role of the epithelial barrier in determining the outcome of infectious processes, IMMUNOLOGY, Vol: 143, Pages: 150-150, ISSN: 0019-2805

JOURNAL ARTICLE

Clarke TB, Francella N, Huegel A, Weiser JNet al., 2011, Invasive bacterial pathogens exploit TLR-mediated downregulation of tight junction components to facilitate translocation across the epithelium., Cell Host Microbe, Vol: 9, Pages: 404-414

Streptococcus pneumoniae and Haemophilus influenzae are members of the normal human nasal microbiota with the ability to cause invasive infections. Bacterial invasion requires translocation across the epithelium; however, mechanistic understanding of this process is limited. Examining the epithelial response to murine colonization by S. pneumoniae and H. influenzae, we observed the TLR-dependent downregulation of claudins 7 and 10, tight junction components key to the maintenance of epithelial barrier integrity. When modeled in vitro, claudin downregulation was preceded by upregulation of SNAIL1, a transcriptional repressor of tight junction components, and these phenomena required p38 MAPK and TGF-β signaling. Consequently, downregulation of SNAIL1 expression inhibited bacterial translocation across the epithelium. Furthermore, disruption of epithelial barrier integrity by claudin 7 inhibition in vitro or TLR stimulation in vivo promoted bacterial translocation. These data support a general mechanism for epithelial opening exploited by invasive pathogens to facilitate movement across the epithelium to initiate disease.

JOURNAL ARTICLE

Clarke TB, Weiser JN, 2011, Intracellular sensors of extracellular bacteria., Immunol Rev, Vol: 243, Pages: 9-25

Initial recognition of bacteria by the innate immune system is thought to occur primarily by germline-encoded pattern recognition receptors (PRRs). These receptors are present in multiple compartments of host cells and are thus capable of surveying both the intracellular and extracellular milieu for bacteria. It has generally been presumed that the cellular location of these receptors dictates what type of bacteria they respond to: extracellular bacteria being recognized by cell surface receptors, such as certain Toll-like receptors, and bacteria that are capable of breaching the plasma membrane and entering the cytoplasm, being sensed by cytoplasmic receptors, including the Nod-like receptors (NLRs). Increasingly, it is becoming apparent that this is a false dichotomy and that extracellular bacteria can be sensed by cytoplasmic PRRs and this is crucial for controlling the levels of these bacteria. In this review, we discuss the role of two NLRs, Nod1 and Nod2, in the recognition of and response to extracellular bacteria.

JOURNAL ARTICLE

Clarke TB, Davis KM, Lysenko ES, Zhou AY, Yu Y, Weiser JNet al., 2010, Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity., Nat Med, Vol: 16, Pages: 228-231

Humans are colonized by a large and diverse bacterial flora (the microbiota) essential for the development of the gut immune system. A broader role for the microbiota as a major modulator of systemic immunity has been proposed; however, evidence and a mechanism for this role have remained elusive. We show that the microbiota are a source of peptidoglycan that systemically primes the innate immune system, enhancing killing by bone marrow-derived neutrophils of two major pathogens: Streptococcus pneumoniae and Staphylococcus aureus. This requires signaling via the pattern recognition receptor nucleotide-binding, oligomerization domain-containing protein-1 (Nod1, which recognizes meso-diaminopimelic acid (mesoDAP)-containing peptidoglycan found predominantly in Gram-negative bacteria), but not Nod2 (which detects peptidoglycan found in Gram-positive and Gram-negative bacteria) or Toll-like receptor 4 (Tlr4, which recognizes lipopolysaccharide). We show translocation of peptidoglycan from the gut to neutrophils in the bone marrow and show that peptidoglycan concentrations in sera correlate with neutrophil function. In vivo administration of Nod1 ligands is sufficient to restore neutrophil function after microbiota depletion. Nod1(-/-) mice are more susceptible than wild-type mice to early pneumococcal sepsis, demonstrating a role for Nod1 in priming innate defenses facilitating a rapid response to infection. These data establish a mechanism for systemic immunomodulation by the microbiota and highlight potential adverse consequences of microbiota disruption by broad-spectrum antibiotics on innate immune defense to infection.

JOURNAL ARTICLE

Kawai F, Clarke TB, Roper DI, Han G-J, Hwang KY, Unzai S, Obayashi E, Park S-Y, Tame JRHet al., 2010, Crystal Structures of Penicillin-Binding Proteins 4 and 5 from Haemophilus influenzae, Journal of Molecular Biology, Vol: 396, Pages: 634-645, ISSN: 0022-2836

JOURNAL ARTICLE

Clarke TB, Kawai F, Park S-Y, Tame JRH, Dowson CG, Roper DIet al., 2009, Mutational analysis of the substrate specificity of Escherichia coli penicillin binding protein 4., Biochemistry, Vol: 48, Pages: 2675-2683

Escherichia coli PBP4 is the archetypal class C, low molecular mass penicillin binding protein (LMM-PBP) and possesses both dd-carboxypeptidase and dd-endopeptidase activity. In contrast to other classes of PBP, class C LMM-PBPs show high dd-carboxypeptidase activity and rapidly hydrolyze synthetic fragments of peptidoglycan. The recently solved X-ray crystal structures of three class C LMM-PBPs (E. coli PBP4, Bacillus subtilis PBP4a, and Actinomadura R39 dd-peptidase) have identified several residues that form a pocket in the active site unique to this class of PBP. The X-ray cocrystal structure of the Actinomadura R39 DD-peptidase with a cephalosporin bearing a peptidoglycan-mimetic side chain showed that residues of this pocket interact with the third position meso-2,6-diaminopimelic acid residue of the peptidoglycan stem peptide. Equivalent residues of E. coli PBP4 (Asp155, Phe160, Arg361, and Gln422) were mutated, and the effect on both DD-carboxypeptidase and DD-endopeptidase activities was determined. Using N-acetylmuramyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine as substrate, mutation of Asp155, Phe160, Arg361, and Gln422 to alanine reduced k(cat)/K(m) by 12.7-, 1.9-, 24.5-, and 13.8-fold, respectively. None of the k(cat) values deviated significantly from wild-type PBP4. PBP4 DD-endopeptidase activity was also affected, with substitution of Asp155, Arg361, and Gln422 reducing specific activity by 22%, 56%, and 40%, respectively. This provides the first direct demonstration of the importance of residues forming a subsite to accommodate meso-2,6-diaminopimelic acid in both the DD-carboxypeptidase and DD-endopeptidase activities of a class C LMM-PBP.

JOURNAL ARTICLE

Paradis-Bleau C, Lloyd A, Sanschagrin F, Maaroufi H, Clarke T, Blewett A, Dowson C, Roper DI, Bugg TDH, Levesque RCet al., 2009, Pseudomonas aeruginosa MurE amide ligase: enzyme kinetics and peptide inhibitor, Biochemical Journal, Vol: 421, Pages: 263-272, ISSN: 0264-6021

JOURNAL ARTICLE

Zhang Z, Clarke TB, Weiser JN, 2009, Cellular effectors mediating Th17-dependent clearance of pneumococcal colonization in mice., J Clin Invest, Vol: 119, Pages: 1899-1909

Microbial colonization of mucosal surfaces may be an initial event in the progression to disease, and it is often a transient process. For the extracellular pathogen Streptococcus pneumoniae studied in a mouse model, nasopharyngeal carriage is eliminated over a period of weeks and requires cellular rather than humoral immunity. Here, we demonstrate that primary infection led to TLR2-dependent recruitment of monocyte/macrophages into the upper airway lumen, where they engulfed pneumococci. Pharmacologic depletion of luminal monocyte/macrophages by intranasal instillation of liposomal clodronate diminished pneumococcal clearance. Efficient clearance of colonization required TLR2 signaling to generate a population of pneumococcal-specific IL-17-expressing CD4+ T cells. Depletion of either IL-17A or CD4+ T cells was sufficient to block the recruitment of monocyte/macrophages that allowed for effective late pneumococcal clearance. In contrast with naive mice, previously colonized mice showed enhanced early clearance that correlated with a more robust influx of luminal neutrophils. As for primary colonization, these cellular responses required Th17 immunity. Our findings demonstrate that monocyte/macrophages and neutrophils recruited to the mucosal surface are key effectors in clearing primary and secondary bacterial colonization, respectively.

JOURNAL ARTICLE

Paradis-Bleau C, Lloyd A, Sanschagrin F, Clarke T, Blewett A, Bugg TDH, Levesque RCet al., 2008, Phage display-derived inhibitor of the essential cell wall biosynthesis enzyme MurF, BMC Biochemistry, Vol: 9, Pages: 33-33, ISSN: 1471-2091

JOURNAL ARTICLE

Lysenko ES, Clarke TB, Shchepetov M, Ratner AJ, Roper DI, Dowson CG, Weiser JNet al., 2007, Nod1 signaling overcomes resistance of S. pneumoniae to opsonophagocytic killing., PLoS Pathog, Vol: 3

Airway infection by the Gram-positive pathogen Streptococcus pneumoniae (Sp) leads to recruitment of neutrophils but limited bacterial killing by these cells. Co-colonization by Sp and a Gram-negative species, Haemophilus influenzae (Hi), provides sufficient stimulus to induce neutrophil and complement-mediated clearance of Sp from the mucosal surface in a murine model. Products from Hi, but not Sp, also promote killing of Sp by ex vivo neutrophil-enriched peritoneal exudate cells. Here we identify the stimulus from Hi as its peptidoglycan. Enhancement of opsonophagocytic killing was facilitated by signaling through nucleotide-binding oligomerization domain-1 (Nod1), which is involved in recognition of gamma-D-glutamyl-meso-diaminopimelic acid (meso-DAP) contained in cell walls of Hi but not Sp. Neutrophils from mice treated with Hi or compounds containing meso-DAP, including synthetic peptidoglycan fragments, showed increased Sp killing in a Nod1-dependent manner. Moreover, Nod1(-/-) mice showed reduced Hi-induced clearance of Sp during co-colonization. These observations offer insight into mechanisms of microbial competition and demonstrate the importance of Nod1 in neutrophil-mediated clearance of bacteria in vivo.

JOURNAL ARTICLE

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