Search bioRxiv⌕ Search

Biology subjects

Dockrell, D. H.

Publications and source records attributed to Dockrell, D. H..

10 recordsLinked to original sources

Intestinal bacteria hijack an evolutionarily conserved epithelial repair signal

Apoptosis in the gut triggers an expansion in the Enterobacteriaceae family of bacteria, causing both prolonged tissue injury and delayed repair. However, the mechanisms linking the Enterobacteriaceae bloom and subsequent deleterious tissue response are relatively unknown. Here, we establish purines as a major component of the apoptotic secretome that are consumed by bacteria. Explicitly, we identify hypoxanthine as a critical metabolite that is taken up and metabolised by both pathogenic and commensal species within the Enterobacteriaceae family. Epithelial cells release hypoxanthine into the extracellular space during early stages of apoptosis via the upregulation of equilibrative nucleoside transporters 1/2 (ENT1/2). Critically, beyond simply linking host and microbe, we delineate a connection between the release of hypoxanthine from the dying cell and the ability of the host to repair damaged epithelial tissue. Hypoxanthine is a potent promoter of epithelial cell repair in both gut and skin across the phylogenetic tree including humans, mice, zebrafish, and fruit flies and promotes similar ATP production and cellular proliferation in eukaryotic and microbial recipients. Thus, the preferential utilisation of hypoxanthine by the Enterobacteriaceae directly competes with the host for a core reparative signal.

microbiology↗

DYNAMIC CHANGES TO THE INTESTINAL ENVIRONMENT OCCUR THROUGHOUT RECOVERY FROM EXPERIMENTAL ISCHAEMIC STROKE

Stroke survivors experience a plethora of complications during recovery, including gastrointestinal symptoms. Intestinal dysfunction is reported to occur rapidly following stroke in both humans and animal models and alterations such as reduced barrier integrity, lymphocyte loss, and an altered microbiota have been suggested to contribute to poor neurological outcomes. Despite the persistence of gastrointestinal symptoms in many stroke survivors, how the intestinal environment changes over the course of stroke recovery remains poorly understood. Here, we use an experimental model of ischemic stroke to profile the gastrointestinal tract over a three month period of recovery.We have shown that experimental stroke leads to structural alterations to the colon, impaired transit times and an altered bacterial community composition. No impairments to barrier function were detected at any time point and transit times recover within 2 weeks post stroke. In contrast, structural and bacterial community alterations remain up to 3 months post stroke and are accompanied by abnormalities that develop only during chronic recovery, such as altered antibody coating of bacteria. These results suggest that the gastrointestinal system is dynamically altered over the course of experimental stroke recovery and that certain defects persist chronically after stroke.

immunology↗

Chromium/cadmium plays a pivotal role to emerge amoxicillin resistant Staphylococcus aureus

RationaleThe rapid emergence of resistant bacteria is occurring worldwide, endangering the efficacy of antimicrobials. Apart from horizontal gene transfer and plasmid mediated antimicrobial resistance (AMR) acquisition, co-exposure of heavy metals and antibiotics cause to emerge AMR Enterobacteriaceae. Heavy metals and antimicrobials co-exist in many environmental settings. We hypothesized that heavy metals and lower dose of antibiotic co-exposure may alter levels of antimicrobial susceptibility and facilitate to emerge AMR bacteria. MethodsThe growth kinetics of antimicrobial susceptible Staphylococcus aureus ST80 was carried out in the presence of chromium/cadmium salt and a lower dose of antibiotics. Subsequently, the antimicrobials susceptibility patterns of heavy metals pre-exposed for 48 hours Staphylococcus aureus ST 80 was determined by Kirby-Bauer disc diffusion method. ResultsThe antimicrobial susceptibility profile revealed that the zone of inhibition (ZOI) for ampicillin, amoxicillin, ciprofloxacin and doxycycline significantly decreased in chromium pre-exposed Staphylococcus compared to unexposed bacteria. However, cadmium pre-exposed bacteria only showed significant decreased ZOI for amoxicillin. Moreover, the MIC of amoxicillin was increased by 8-fold in chromium and 32-fold in cadmium with a low-dose of amoxicillin co-exposed bacteria. Besides, the RT-qPCR data demonstrated that chromium and a low-dose of amoxicillin pre-exposed significantly increased the mRNA expression of femX (25-fold), mepA (19-fold) and norA (17-fold) in S. aureus. In essence, minimum levels of chromium/cadmium and a MIC of amoxicillin exposure induced efflux pumps, which might responsible to emerge amoxicillin resistant S. aureus.

microbiology↗

Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages.

Individual responses to SARS-CoV-2 infection vary significantly, ranging from mild courses of infection that do not require hospitalisation to the development of disease which not only requires hospitalisation but can be fatal. Whilst many immunological studies have revealed fundamental insights into SARS-CoV-2 infection and COVID-19, mathematical and computational modelling can offer an additional perspective and enhance understanding. The majority of mathematical models for the within-host spread of SARS-CoV-2 infection are ordinary differential equations, which neglect spatial variation. In this article, we present a hybrid, multiscale, individual-based model to study the within-host spread of SARS-CoV-2 infection. The model incorporates epithelial cells (each containing a dynamical model for viral entry and replication), macrophages and a subset of cytokines. We investigate the role of increasing initial viral deposition, increasing delay in type I interferon secretion from epithelial cells (as well as the magnitude of secretion), increasing macrophage virus internalisation rate and macrophage activation, on the spread of infection.

systems biology↗

Systematic comparison of ranking aggregation methods for gene lists in experimental results

A common experimental output in biomedical science is a list of genes implicated in a given biological process or disease. The results of a group of studies answering the same, or similar, questions can be combined by meta-analysis to find a consensus or a more reliable answer. Ranking aggregation methods can be used to combine gene lists from various sources in meta-analyses. Evaluating a ranking aggregation method on a specific type of dataset before using it is required to support the reliability of the result since the property of a dataset can influence the performance of an algorithm. Evaluation of aggregation methods is usually based on a simulated database especially for the algorithms designed for gene lists because of the lack of a known truth for real data. However, simulated datasets tend to be too small compared to experimental data and neglect key features, including heterogeneity of quality, relevance and the inclusion of unranked lists. In this study, a group of existing methods and their variations which are suitable for meta-analysis of gene lists are compared using simulated and real data. Simulated data was used to explore the performance of the aggregation methods as a function of emulating the common scenarios of real genomics data, with various heterogeneity of quality, noise level, and a mix of unranked and ranked data using 20000 possible entities. In addition to the evaluation with simulated data, a comparison using real genomic data on the SARS-CoV-2 virus, cancer (NSCLC), and bacteria (macrophage apoptosis) was performed. We summarise our evaluation results in terms of a simple flowchart to select a ranking aggregation method for genomics data.

bioinformatics↗

The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair

Alveolar macrophages are the most abundant macrophages in the healthy lung where they play key roles in homeostasis and immune surveillance against air-borne pathogens. Tissue-specific differentiation and survival of alveolar macrophages relies on niche-derived factors, such as colony stimulating factor 2 (CSF-2) and transforming growth factor beta (TGF-{beta}). However, the nature of the downstream molecular pathways that regulate the identity and function of alveolar macrophages and their response to injury remains poorly understood. Here, we identify that the transcriptional factor EGR2 is an evolutionarily conserved feature of lung alveolar macrophages and show that cell-intrinsic EGR2 is indispensable for the tissue-specific identity of alveolar macrophages. Mechanistically, we show that EGR2 is driven by TGF-{beta} and CSF-2 in a PPAR-{gamma}-dependent manner to control alveolar macrophage differentiation. Functionally, EGR2 was dispensable for lipid handling, but crucial for the effective elimination of the respiratory pathogen Streptococcus pneumoniae. Finally, we show that EGR2 is required for repopulation of the alveolar niche following sterile, bleomycin-induced lung injury and demonstrate that EGR2-dependent, monocyte-derived alveolar macrophages are vital for effective tissue repair following injury. Collectively, we demonstrate that EGR2 is an indispensable component of the transcriptional network controlling the identity and function of alveolar macrophages in health and disease. One Sentence SummaryEGR2 controls alveolar macrophage function in health and disease

immunology↗

Classical macrophage polarisation is limited by human β-defensin 3 via an autocrine IL-4 dependent process.

Human {beta}-defensin 3 (HBD3), is an anti-microbial host-defence peptide, that can rapidly enter macrophages to modulate TLR4 responses to lipopolysaccharide. However, the molecular mechanisms by which HBD3 exerts this anti-inflammatory influence remain unclear. Here, we show mice deleted for the orthologue of HBD3 have an increased acute lipopolysaccharide response in vivo. Furthermore, we found that HBD3 limited the response of macrophages to classical activation, and contemporaneously drove expression of IL-4. An increase in markers of alternative activation, and a change in metabolic flux was also observed. Consistent with these results, HBD3 enhanced the IL-4 mediated polarisation of naive macrophages. Finally, we demonstrate that the ability of HBD3 to limit macrophage classical activation requires IL-4R. These data reveal a previously unrecognised role for HBD3 in influencing the polarisation state of macrophages to enable a state conducive for repair and resolution. SYNOPSIS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/442606v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@f81c9aorg.highwire.dtl.DTLVardef@11dca23org.highwire.dtl.DTLVardef@c1e241org.highwire.dtl.DTLVardef@ed46ed_HPS_FORMAT_FIGEXP M_FIG C_FIG The anti-microbial host-defence peptide, Human {beta}-defensin 3 (HBD3), is shown here to modulate the inflammatory response to classical activation by promoting alternative activation through IL-4R, to enable a state conducive for repair and resolution. O_LIKnockout mice for the orthologous gene for HBD3, demonstrate increased acute lipopolysaccharide inflammatory response. C_LIO_LIHBD3 limited the classical activation of macrophages polarised with LPS/IFN{gamma} and drove expression of IL-4. Cells also displayed increase in alternative activation markers and promotion of oxidative phosphorylation. C_LIO_LIHBD3 enhanced the IL-4-mediated activation of naive macrophages. C_LIO_LIThe ability of HBD3 to limit macrophage classical activation and contemporaneously promote alternative activation required IL-4R. C_LI

immunology↗

Ezh2 restrains macrophage inflammatory responses, and is critical for neutrophil migration in response to pulmonary infection.

Mucosal immunity is critical to survival, with huge attention at present due to the Coronovirus pandemic. Epigenetic factors are increasingly recognized as important determinants of immune responses, and EZH2 closest to application due to the availability of highly-specific and efficacious antagonists. However, very little is known about the role of EZH2 in the myeloid lineage, with some conflicting reports. Here we show EZH2 acts in macrophages to limit inflammatory responses to activation, and selective genetic deletion results in a remarkable gain in protection from infection with the prevalent lung pathogen, pneumococcus. In contrast, EZH2 is required for neutrophil chemotaxis, and animals lacking neutrophil EZH2 show increased susceptibility to pneumococcus. In summary, EZH2 shows complex, and divergent roles in different myeloid cells, likely contributing to the earlier conflicting reports. Compounds targeting EZH2 are likely to impair mucosal immunity, however, may prove useful for conditions driven by pulmonary neutrophil influx, such as adult respiratory distress syndrome (ARDS). DigestEpigenetic control of mucosal immunity is important, and has translational relevance with the advent of inhibitor drugs now in the clinic for cancer indications. Here we show divergent role for EZH2 in macrophages and neutrophils. Loss of EZH2 in macrophages results in a gain of inflammatory and immune function, and protection from pneumonia. However, EZH2 is required for neutrophil chemotaxis, resulting in impaired anti-bacterial defence. We show that inhibition, or loss of EZH2 in macrophages results in a gain of immune function, with increased responses to infectious mimics such as LPS. However, the impact was far more dramatic in-vivo, with striking protection from the consequences of infection with pneumococcal bacteria. Loss of EZH2 resulted in a gain in activity of a number of inflammatory signaling cascades, including NFkB, PPARg, and IRFs1, and 7. This widespread macrophage re-programming varied between macrophages sites of origin, with the greatest impact seen in peritoneal macrophages which resulted in emergence of a new population of MerTK low cells. In contrast, in the neutrophils loss of EZH2 greatly impairs motility, and chemotaxis. This results in dramatic impairment of immune responses to the same pneumococcal infection. Extension of these studies to the mucosal epithelium revealed that EZH2 in bronchoalveolar epithelial cells had no impact on responses to infection with influenza. Taken together EZH2 plays diverse roles in the myeloid lineage, with profound impacts on inflammatory responses. The most striking observation was the difference seen between macrophages and neutrophils. EZH2 inhibition is likely to greatly impair mucosal immunity. Impact StatementHere we show a striking, but highly cell-type specific impact of the EZH2 methyltransferase on inflammatory, and anti-infective circuits; inhibition of EZH2 in macrophages augments macrophage cytokine production, but by impairing neutrophil migration impairs anti-bacterial responses.

cell biology↗

Pneumolysin is responsible for differential gene expression and modifications in the epigenetic landscape of primary monocyte derived macrophages.

Epigenetic modifications regulate gene expression in the host response to a diverse range of pathogens. The extent and consequences of epigenetic modification during macrophage responses to Streptococcus pneumoniae, and the role of pneumolysin, a key Streptococcus pneumoniae virulence factor, in influencing these responses, are currently unknown. To investigate this, we infected human monocyte derived macrophages (MDMs) with Streptococcus pneumoniae and addressed whether pneumolysin altered the epigenetic landscape and the associated acute macrophage transcriptional response using a combined transcriptomic and proteomic approach. Transcriptomic analysis identified 503 genes that were differentially expressed in a pneumolysin-dependent manner in these samples. Pathway analysis highlighted the involvement of transcriptional responses to core innate responses to pneumococci including modules associated with metabolic pathways activated in response to infection, oxidative stress responses and NF{kappa}B, NOD-like receptor and TNF signalling pathways. Quantitative proteomic analysis confirmed pneumolysin-regulated protein expression, early after bacterial challenge, in representative transcriptional modules associated with innate immune responses. In parallel, quantitative mass spectrometry identified global changes in the relative abundance of histone post translational modifications (PTMs) upon pneumococcal challenge. We identified an increase in the relative abundance of H3K4me1, H4K16ac and a decrease in H3K9me2 and H3K79me2 in a PLY-dependent fashion. We confirmed that pneumolysin blunted early transcriptional responses involving TNF- and IL-6 expression. Vorinostat, a histone deacetylase inhibitor, similarly downregulated TNF production, reprising the pattern observed with pneumolysin. In conclusion, widespread changes in the macrophage transcriptional response are regulated by pneumolysin and are associated with global changes in histone PTMs. Modulating histone PTMs can reverse pneumolysin-associated transcriptional changes influencing innate immune responses, suggesting that epigenetic modification by pneumolysin plays a role in dampening the innate responses to pneumococci. Author summaryPneumolysin is a toxin that contributes to how Streptococcus pneumoniae, the leading cause of pneumonia, causes disease. In this study, the toxin alters gene expression in immune cells called macrophages, one of the first lines of defence against bacteria at sites of infection. Modulation involved multiple immune responses, including generation of chemical signals coordinating responses in immune cells termed cytokines. In addition, changes were observed in histone proteins that are involved in controlling gene expression in the cell. Pneumolysin reduced early production of the cytokine TNF- and a medicine vorinostat that modifies these epigenetic histone modifications had a similar affect, suggesting epigenetic mechanisms contribute to the ability of pneumolysin to reduce immune responses.

molecular biology↗

Polymersomes Targeting Mononuclear Phagocytes

Mononuclear phagocytes such as monocytes, tissue-specific macrophages and dendritic cells are primary actors in both innate and adaptive immunity, as well as tissue homoeostasis. They have key roles in a range of physiological and pathological processes, so any strategy targeting these cells will have wide-ranging impact. These phagocytes can be parasitized by intracellular bacteria, turning them from housekeepers to hiding places and favouring chronic and/or disseminated infection. One of the most infamous is the bacteria that cause tuberculosis, which is the most pandemic and one of the deadliest disease with one third of the worlds population infected, and 1.8 million deaths worldwide in 2015. Here we demonstrate the effective targeting and intracellular delivery of antibiotics to both circulating monocytes and resident macrophages, using pH sensitive nanoscopic polymersomes made of poly(2-(methacryloyloxy)ethyl phosphorylcholine)-co-poly(2-(di-isopropylamino)ethyl methacrylate) (PMPC-PDPA). Polymersome selectivity to mononuclear phagocytes is demonstrated and ascribed to the polymerised phosphorylcholine motifs affinity toward scavenger receptors. Finally, we demonstrate the successful exploitation of this targeting for the effective eradication of intracellular bacteria that cause tuberculosis Mycobacterium tuberculosis as well as other intracellular parasites including the Mycobacterium bovis, Mycobacterium marinum and the most common bacteria associated with antibiotic resistance, the Staphylococcus aureus.

immunology↗