Biology subjects

Clough, B.

Publications and source records attributed to Clough, B..

8 recordsLinked to original sources

bioRxiv2026

Golgi-localised Guanylate-binding protein 5 enhances glycolysis in macrophages

Guanylate-binding proteins (GBPs) are part of a family of large interferon gamma (IFN{psi})-inducible GTPases, with ascribed roles in infection control and induction of programmed cell death. While pathogen-specific functions of GBPs have been studied in detail, their broader regulation of frontline immune defences remain unexplored. Here, we analysed the global contribution of human GBP1-5 to cellular metabolism in IFN{psi}-stimulated macrophages. We found a robust role of GBP2 and GBP5 in macrophage glycolysis. Only GBP5, and not GBP2 deficiency impaired surface expression and cytokine production of classically IFN{psi}/LPS-activated macrophages. The GTPase activity of GBP5 was required for the regulation of glycolysis and cytokine production. We found that GBP5 deficiency impaired cellular glucose uptake and lactate production specifically. Isotopic tracing with [U-13C6]-Glucose confirmed a decrease in several glycolytic intermediates, including glucose 6-phosphate, pyruvate, and lactate, but stable levels of traced tricarboxylic acid cycle (TCA) intermediates. Elevated ribose-5-phosphate and glycerol levels suggest an altered cytosolic redox balance and enhanced breakdown of fatty acids. GBP5 localised predominantly to the cis-Golgi and in the absence of GBP5 we observed increased Golgi fragmentation, however the total Golgi size remained unchanged. Our results underscore the fundamental role of GBP5 in glycolytic fluxes and Golgi integrity in IFN{psi}-stimulated macrophages, highlighting its significance in immune function in general and immunometabolism specifically.

immunology↗

bioRxiv2025

Strain-dependent contribution of the AcrAB-TolC efflux pump to Klebsiella pneumoniae physiology

Klebsiella pneumoniae is a prominent opportunistic pathogen increasingly associated with multidrug resistance and virulence. One of the main mechanisms of antimicrobial resistance in K. pneumoniae is active efflux, primarily mediated by the Resistance-Nodulation-Division (RND) family of pumps. AcrAB-TolC is the key RND efflux pump in K. pneumoniae, regulated by the transcriptional activator RamA and its repressor RamR. Although overexpression of AcrAB-TolC has been linked to drug resistance in various clinical strains, its physiological roles in K. pneumoniae remain insufficiently studied. In this study, we generated isogenic deletions of acrB and ramR in both the genetically tractable K. pneumoniae Ecl8 and the virulent ATCC 43816 strains. We examined the phenotype of the {Delta}acrB and {Delta}ramR mutants by assessing antimicrobial susceptibility, biofilm formation, growth under infection-related conditions, and both in vitro and in vivo infection models. Loss of acrB increased susceptibility to drugs, decreased biofilm formation, and reduced in vitro virulence in both Ecl8 and ATCC 43816. However, only in Ecl8 was the loss of AcrB found to diminish growth under infection-like conditions and decrease in vivo virulence in the Galleria mellonella infection model. In contrast, in ATCC 43816, it had no effect. Our findings suggest that AcrAB-TolC exhibits strain-specific physiological functions, highlighting its dual role in antimicrobial resistance and pathogenicity, and thereby broadening our understanding of efflux-mediated adaptations in K. pneumoniae. Exploring the broader functions of RND efflux pumps in K. pneumoniae can provide insights into the potential effects of targeting them with inhibitor molecules. ImportanceInfections caused by multidrug-resistant bacterial pathogens are among the most urgent global public health challenges. Specifically, Klebsiella pneumoniae is classified by the World Health Organisation as a critical priority pathogen for the development of new treatments. Resistance-Nodulation-Division (RND) efflux pumps significantly contribute to multidrug resistance and virulence, making them promising targets for drug development. In this study, we demonstrated that the RND efflux pump AcrAB-TolC in K. pneumoniae is essential for drug efflux, biofilm formation, and in vitro virulence. Notably, we identified strain-specific roles for AcrAB-TolC in supporting growth under infection-related conditions and virulence in the Galleria mellonella infection model. Our findings highlight that the function of RND efflux pumps can vary between strains within a species. This implies that targeting RND efflux pumps with inhibitors may yield different effects depending on the strain background.

microbiology↗

bioRxiv2023

Differential development of antibiotic resistance and virulence between Acinetobacter species

The two species that account for most cases of Acinetobacter-associated bacteraemia in the UK are Acinetobacter lwoffii, often a commensal but also an emerging pathogen, and A. baumannii, a well-known antibiotic-resistant species. While these species both cause similar types of human infection and occupy the same niche, A. lwoffii (unlike A. baumannii) has thus far remained susceptible to antibiotics. Comparatively little is known about the biology of A. lwoffii and this is the largest study on it conducted to date, providing valuable insights into its behaviour and potential threat to human health. This study aimed to explain the antibiotic susceptibility, virulence, and fundamental biological differences between these two species. The relative susceptibility of A. lwoffii, was explained as it encoded fewer antibiotic resistance and efflux pump genes than A. baumannii (9 and 30 respectively). While both species had markers of horizontal gene transfer, A. lwoffii encoded more DNA defence systems and harboured a far more restricted range of plasmids. Furthermore, A. lwoffii displayed a reduced ability to select for antibiotic resistance mutations, form biofilm and infect both in vivo and in vitro models of infection. This study suggests that the emerging pathogen A. lwoffii has remained susceptible to antibiotics because mechanisms exist to make it highly selective about the DNA it acquires, and we hypothesise that the fact that it only harbours a single RND system restricts the ability to select for resistance mutations. This provides valuable insights into how development of resistance can be constrained in Gram negative bacteria. ImportanceAcinetobacter lwoffii is often a harmless commensal but is also an emerging pathogen and is the most common cause of Acinetobacter-derived blood stream infections in England and Wales. In contrast to the well-studied, and often highly drug resistant A. baumannii, A. lwoffii has remained susceptible to antibiotics. This study explains why this organism has not evolved resistance to antibiotics. These new insights are important to understand why and how some species develop antibiotic resistance, while others do not and could inform future novel treatment strategies.

microbiology↗

bioRxiv2023

p97/VCP targets Toxoplasma gondii vacuoles for parasite restriction in interferon-stimulated human cells

Infection with the parasite Toxoplasma gondii leads to production of interferon gamma (IFN{gamma}) that stimulates cells to upregulate defence proteins targeting the parasite for cell intrinsic elimination or growth restriction. Various host defence mechanisms operate at the parasitophorous vacuole (PV) in different human cell types leading to PV disruption, acidification, or membrane envelopment. Ubiquitin and p62 are players in all human host control mechanisms of Toxoplasma, but other unifying proteins have not been identified. Here, we show that p97/valosin-containing protein (VCP), as well as its associated proteins ANKRD13A and UBXD1 control Toxoplasma infection while recruited to the PV in IFN{gamma}-stimulated endothelial cells. Convergent deposition of ANKRD13A, p97/VCP and UBXD1 onto the same vacuole is dependent on vacuolar ubiquitination and observed within 2h post-infection. ANKRD13A, p97/VCP and UBXD1 all drive the acidification mechanism of the vacuole, which is the IFN{gamma}-dependent control pathway of Toxoplasma in endothelial cells. We assessed p97/VCP in Toxoplasma control in various human cells and demonstrate that p97/VCP is a universal IFN{gamma}-dependent host restriction factor targeting the Toxoplasma PV in epithelial (HeLa) and endothelial cells (HUVEC), fibroblasts (HFF) and macrophages (THP1).

immunology↗

bioRxiv2021

Toxoplasma-proximal and distal control by GBPs in human macrophages

Human guanylate-binding proteins (GBPs) are key players of interferon-gamma (IFN{gamma})-induced cell intrinsic defense mechanisms targeting intracellular pathogens. In this study we combine the well-established Toxoplasma gondii infection model with three in vitro macrophage culture systems to delineate the contribution of individual GBP family members to control this apicomplexan parasite. Use of high-throughput imaging assays and genome engineering allowed us to define a role for GBP1, 2 and 5 in parasite infection control. While GBP1 performs a pathogen-proximal, parasiticidal and growth-restricting function through accumulation at the parasitophorous vacuole of intracellular Toxoplasma, GBP2 and 5 perform a pathogen-distal, growth-restricting role. We further find that mutants of the GTPase or isoprenylation site of GBP1/2/5 affect their normal function in Toxoplasma control by leading to mis-localization of the proteins.

microbiology↗

bioRxiv2019

Mimicry embedding for advanced neuralnetwork training of 3D biomedical micrographs

The use of deep neural networks (DNNs) for analysis of complex biomedical images shows great promise but is hampered by a lack of large verified datasets for rapid network evolution. Here we present a novel \"mimicry embedding\" strategy for rapid application of neural network architecture-based analysis of biomedical imaging datasets. Embedding of a novel biological dataset, such that it mimics a verified dataset, enables efficient deep learning and seamless architecture switching. We apply this strategy across various microbiological phenotypes; from super-resolved viruses to in vivo parasitic infections. We demonstrate that mimicry embedding enables efficient and accurate analysis of three-dimensional microscopy datasets. The results suggest that transfer learning from pre-trained network data may be a powerful general strategy for analysis of heterogeneous biomedical imaging datasets.

bioinformatics↗

bioRxiv2019

Differential spatiotemporal targeting of Toxoplasma and Salmonella by GBP1 assembles caspase signalling platforms

Guanylate binding proteins (GBPs), a family of interferon (IFN)-inducible GTPases, can promote cell-intrinsic defense by removal of intracellular microbial replicative niches through host cell death. GBPs target pathogen-containing vacuoles or the pathogen itself, and assist in membrane-disruption and release of microbial molecules that trigger cell death by activating the inflammasomes. We previously showed that GBP1 mediates atypical apoptosis or pyroptosis of human macrophages infected with Toxoplasma gondii (Tg) or Salmonella enterica Typhimurium (STm), respectively. In mice, the p47 Immunity-related GTPases (IRGs) control the recruitment of GBPs to microbe-containing vacuoles and subsequent cell death. However, humans are devoid of functional IRGs, and the pathogen-proximal immune detection mechanisms by GBP1 are poorly understood. Here, we describe two novel single-cell assays which show that GBP1 promotes the lysis of Tg-containing vacuoles and Tg plasma membrane, resulting in the cytosolic detection of Tg-DNA. In contrast, we show GBP1 only targets cytosolic STm and does not contribute to bacterial escape into the cytosol of human macrophages. GBP1 interacts with caspase-4 and recruits it directly to the bacterial surface, where caspase-4 can be activated by LPS. During STm infection, caspase-1 cleaves and inactivates GBP1 at Asp192, a site conserved in related mammalian GBP1 proteins but not in murine Gbps. STm-infected human macrophages expressing a cleavage-deficient GBP1 mutant exhibit higher pyroptosis due to the absence of caspase-1-mediated feedback inhibition of the GBP1-caspase-4 pathway. Our comparative studies elucidate microbe-specific spatiotemporal roles of GBP1 in detecting infection and the assembly and regulation of divergent caspase signaling platforms.

microbiology↗

bioRxiv2018

An Artificial Intelligence Workflow for Defining Host-Pathogen Interactions

For image-based infection biology, accurate unbiased quantification of host-pathogen interactions is essential, yet often performed manually or using limited enumeration employing simple image analysis algorithms based on image segmentation. Host protein recruitment to pathogens is often refractory to accurate automated assessment due to its heterogeneous nature. An intuitive intelligent image analysis program to assess host protein recruitment within general cellular pathogen defense is lacking. We present HRMAn (Host Response to Microbe Analysis), an open-source image analysis platform based on machine learning algorithms and deep learning. We show that HRMAn has the capability to learn phenotypes from the data, without relying on researcher-based assumptions. Using Toxoplasma gondii and Salmonella typhimurium we demonstrate HRMAns capacity to recognize, classify and quantify pathogen killing, replication and cellular defense responses.

microbiology↗