Biology subjects

Walker, S. A.

Publications and source records attributed to Walker, S. A..

7 recordsLinked to original sources

bioRxiv2026

Domain-swapped LuxR-type quorum sensing receptors reveal divergent ligand-response mechanisms among homologs

Many common bacteria use quorum sensing to regulate cell density-dependent phenotypes, including luminescence, biofilm formation, virulence, and symbiosis. The LuxI/R system is the best-characterized quorum sensing pathway in Gram-negative bacteria and consists of a LuxI-type synthase that produces an N-acyl L-homoserine lactone (AHL) autoinducer and a LuxR-type transcription factor that is regulated by AHL binding. Binding of native AHL signal promotes DNA binding and transcriptional regulation in some LuxR homologs (associative-type), while other homologs regulate transcription in the absence of ligand and are inactivated by native signal binding (dissociative-type). To better characterize what features determine ligand-response type, we generated structural mutants of two associative receptors (LasR of Pseudomonas aeruginosa and MrtR of Mesorhizobium tianshanense) and two dissociative receptors (EsaR of Pantoea stewartii and ExpR2 of Pectobacterium versatile). Swapping domains between these receptors revealed that the ligand-binding domain primarily determines associative vs. dissociative activity in response to native AHL agonists. Further, non-native AHL-derived antagonists maintained their activity profiles in receptors with interchanged DNA-binding domains. We also found that the extended linker between domains observed in the dissociative receptors does not determine mechanism of ligand response, and that inter-domain interactions may play an important role in activation for some receptors but not others. Notably, deletion of just one residue from the dissociative receptor EsaR produced a mutant with associative activity, the first time such mechanism switching has been reported for a LuxR-type receptor. These findings illuminate features essential for ligand response and highlight the mechanistic diversity of the LuxR family. IMPORTANCELuxI/R quorum sensing regulates various cell density-dependent phenotypes in Gram-negative bacteria. Prior research has developed small molecule modulators of LuxR-type receptors, with potential applications in anti-virulence, anti-biofouling, and bioengineering. Competitive antagonists have been reported for receptors active in the presence of native ligand but not for receptors active in its absence. A lack of knowledge about the molecular mechanisms of receptor response to ligand limits both our fundamental understanding of the LuxI/R quorum sensing process and the rational design of chemical modulators with superior activity profiles. We used a structural mutagenesis strategy with four LuxR-type receptors that operate via two distinct mechanisms to begin to dissect the structural features that drive differences in ligand response between receptors. These insights could aid in efforts to characterize novel LuxR homologs, understand potential interspecies communication via quorum sensing, and develop improved chemical probes to alter LuxR-type receptor activity.

microbiology↗

bioRxiv2026

Do drugs with biliary toxicity cause cholangiocarcinoma?

AO_SCPLOWBSTRACTC_SCPLOWMany commonly used therapeutic drugs cause biliary toxicity, but it is unclear if they are directly responsible for the increasing incidence of cholangiocarcinoma (CCA). We tested experimentally and analyzed through a cohort approach whether drugs, such as the commonly used antibiotic Augmentin, which is a poster-child of biliary toxicity, are causally linked to CCA development. Using sophisticated analytical tools in cholangiocytes, including single extracellular vesicle (EV) analysis, we found no evidence that Augmentin increases the cholangiocyte malignancy marker YAP1 or phospho-YAP1. Furthermore, we analyzed the CCA incidence in our healthcare system and determined it to be 0.0932% (Augmentin group) and 0.0799% (amoxicillin control group). Although the Augmentin group showed a numerically higher CCA incidence, the association did not reach statistical significance (RR = 1.1669, 95% CI 0.6200-2.1961; Fishers exact test, P = 0.7493). Similarly, we found no evidence for cholangiocarcinoma development with other commonly used drugs, including chlorpromazine, floxuridine, 5-fluorouracil, flucloxacillin and terbinafine. We conclude that there is no direct causal relationship between clinical Augmentin doses and CCA development.

cancer biology↗

bioRxiv2023

Adventitial mast cell activation disrupts endothelial cell/pericyte interactions during early life allergic asthma

Allergic asthma generally starts during early life and is linked to substantial tissue remodelling and lung dysfunction. Although angiogenesis is a feature of the disrupted airway, the impact of allergic asthma on the pulmonary microcirculation during early life is unknown. Here, using quantitative imaging in precision-cut lung slices (PCLS), we report that exposure of neonatal mice to house dust mite (HDM) extract disrupts endothelial cell/pericyte interactions in adventitial areas. Central to the blood vessel structure, the loss of pericyte coverage was driven by mast cell (MCs) proteases, such as tryptase, that can induce pericyte retraction and loss of the critical adhesion molecule N-Cadherin. Furthermore, spatial transcriptomics of paediatric asthmatic endobronchial biopsies suggests intense vascular stress and remodelling linked with increased expression of MC activation pathways in regions enriched in blood vessels. These data provide previously unappreciated insights into the pathophysiology of allergic asthma with potential long-term vascular defects.

immunology↗

bioRxiv2022

Lung extracellular matrix modulates KRT5+ basal cell activity in pulmonary fibrosis

Aberrant expansion of KRT5+ basal cells in the distal lung accompanies progressive alveolar epithelial cell loss and tissue remodelling during fibrogenesis in idiopathic pulmonary fibrosis (IPF). The mechanisms determining activity of KRT5+ cells in IPF have not been delineated. Here, we reveal a potential mechanism by which KRT5+ cells migrate within the fibrotic lung, navigating regional differences in collagen topography. In vitro, KRT5+ cell migratory characteristics and expression of remodelling genes are modulated by extracellular matrix (ECM) composition and organisation. Mass spectrometry-based proteomics revealed compositional differences in ECM components secreted by primary human lung fibroblasts (HLF) from IPF patients compared to controls. Over-expression of ECM glycoprotein, Secreted Protein Acidic and Cysteine Rich (SPARC) in the IPF HLF matrix restricts KRT5+ cell migration in vitro. Together, our findings demonstrate how changes to the ECM in IPF directly influence KRT5+ cell behaviour and function contributing to remodelling events in the fibrotic niche.

cell biology↗

bioRxiv2020

Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

Antimicrobial resistance (AMR) is a global health threat, especially in low-/middle-income countries (LMICs), where there is limited surveillance to inform empiric antibiotic treatment guidelines. Enterobacterales are amongst the most important causes of drug-resistant bacterial infections. We developed a novel AMR surveillance approach for Enterobacterales by profiling pooled human faecal metagenomes from three sites (n=563 individuals; Cambodia, Kenya, UK) to derive a taxonomy-adjusted AMR metric ("resistance potential") which could be used to predict the aggregate percentage of resistant invasive Enterobacterales infections within each setting. Samples were sequenced (Illumina); taxonomic and resistance gene profiling was performed using ResPipe. Data on organisms causing bacteraemia and meningitis and antibiotic susceptibility test results from 2010-2017 were collated for each site. Bayesian generalised linear models with a binomial likelihood were fitted to determine the capacity of the resistance potential to predict AMR in Enterobacterales infections in each setting. The most informative model accurately predicted the numbers of resistant infections in the target populations for 14/14 of antibiotics in the UK, 12/12 in Kenya, and 9/12 in Cambodia. Intermittent metagenomics of pooled human samples could represent a powerful pragmatic and economical approach for determining and monitoring AMR in clinical infections, especially in resource-limited settings.

genomics↗

bioRxiv2018

Therapeutic ICOS blockade reduces T follicular helper cells and improves allergic airway disease

Allergic asthma is a disease of chronic airway inflammation and remodelling, characterised by a dysregulated type 2 response and allergen-specific IgE. T follicular helper cells (TFH) are critical to antibody production and have recently been implicated in allergic airway disease (AAD) pathogenesis. The role of TFH in established disease and the therapeutic potential of targeting them are however not fully understood. Using two aeroallergen driven murine models of chronic AAD, TFH were first identified in the lung draining lymph nodes but with prolonged exposure were present in the lung itself. Sustained allergen exposure led to the accumulation of TFH, and concomitant development of germinal centre B cells. Blockade of Inducible T cell co-stimulator (ICOS) signalling during established AAD depleted TFH without adversely affecting the differentiation of other CD4+ T cell subsets. This resulted in impaired germinal centre responses, reduced allergen specific IgE and ameliorated inflammation and airway hyper-responsiveness, including reduced pulmonary IL-13. TFH did not however appear to produce IL-13 directly, suggesting they indirectly promote type-2 inflammation in the lungs. These data show that TFH play a pivotal role in the regulation of AAD and that targeting the ICOS-L pathway could represent a novel therapeutic approach in this disease.

immunology↗

bioRxiv2017

Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: an observational study

BackgroundThe incidence of Escherichia coli bloodstream infections (EC-BSIs), particularly those caused by antibiotic-resistant strains, is increasing in the UK and internationally. This is a major public health concern but the evidence base to guide interventions is limited.\n\nMethodsIncidence of EC-BSIs and E. coli urinary tract infections (EC-UTIs) in one UK region (Oxfordshire) were estimated from anonymised linked microbiological and hospital electronic health records, and modelled using negative binomial regression based on microbiological, clinical and healthcare exposure risk factors. Infection severity, 30-day allcause mortality, and community and hospital co-amoxiclav use were also investigated.\n\nFindingsFrom 1998-2016, 5706 EC-BSIs occurred in 5215 patients, and 228376 EC-UTIs in 137075 patients. 1365(24%) EC-BSIs were nosocomial (onset >48h post-admission), 1863(33%) were community (>365 days post-discharge), 1346(24%) were quasi-community (31-365 days post-discharge), and 1132(20%) were quasi-nosocomial ([≤]30 days postdischarge). 1413(20%) EC-BSIs and 36270(13%) EC-UTIs were co-amoxiclav-resistant (41% and 30%, respectively, in 2016). Increases in EC-BSIs were driven by increases in community (10%/year (95% CI:7%-13%)) and quasi-community (8%/year (95% CI:7%-10%)) cases. Changes in EC-BSI-associated 30-day mortality were at most modest (p>0{middle dot}03), and mortality was substantial (14-25% across groups). By contrast, co-amoxiclav-resistant EC-BSIs increased in all groups (by 11%-19%/year, significantly faster than susceptible EC-BSIs, pheterogeneity<0{middle dot}001), as did co-amoxiclav-resistant EC-UTIs (by 13%-29%/year, pheterogeneity*0{middle dot}001). Co-amoxiclav use in primary-care facilities was associated with subsequent co-amoxiclav-resistant EC-UTIs (p=0{middle dot}03) and all EC-UTIs (p=0{middle dot}002).\n\nInterpretationCurrent increases in EC-BSIs in Oxfordshire are primarily community-associated, with high rates of co-amoxiclav resistance, nevertheless not impacting mortality. Interventions should target primary-care facilities with high co-amoxiclav usage.\n\nFundingNational Institute for Health Research.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for publications from inception up until October 26, 2017, with the terms \"Escherichia coli\", \"E. coli\", \"bacteraemia\", \"bloodstream infection\", restricting the search to English language articles, and also reviewed references from retrieved articles. Escherichia coli (E. coli) is the most common cause of bloodstream infection, and the incidence of E. coli bloodstream infection, and particularly antibiotic-resistant infections, is increasing in the UK and internationally. Although the UK government aims to reduce healthcare-associated E. coli bloodstream infection, there is only limited evidence to inform appropriate interventions.\n\nAdded value of this studyWe investigated potential drivers for these increases in incidence by exploiting available linked electronic health records over 19 years for ~5200 patients with E. coli bloodstream infection and ~140000 with E. coli urinary tract infection, together with community antimicrobial prescribing data for the most recent six years. Our study identified several findings with significant implications for health policy and patient care: O_LIIncreases in the incidence of E. coli bloodstream infections were driven mainly by non-hospital-associated cases; however, neither patients with previous urinary tract infections nor having previously had urine specimens sent from catheters appeared to be driving the increases\nC_LIO_LICo-amoxiclav-resistant bloodstream infections rose significantly faster than co-amoxiclav-susceptible bloodstream infections, with the greatest number of co-amoxiclav-resistant bloodstream infections in 2016 being in patients discharged more than a month previously (i.e. community-associated)\nC_LIO_LIHigher co-amoxiclav use in primary care was associated with higher rates of both co-amoxiclav-resistant E. coli urinary tract infections and E. coli urinary tract infections overall, supporting drives to reduce broad-spectrum and inappropriate antibiotic use in primary care\nC_LIO_LIDespite substantial increases in co-amoxiclav-resistant bloodstream infections there was no evidence that mortality was increasing in these cases; this does not support moving to broader empiric antibiotic prescribing in hospitals (i.e. carbapenems, piperacillin-tazobactam)\nC_LI\n\nImplications of all available adviceThis suggests that government strategies to effectively reduce E. coli bloodstream infections should target community settings, as well as healthcare-associated settings. The absence of an increased mortality signal suggests that co-amoxiclav resistant E. coli infections are either being successfully treated by dual empiric therapy in severe cases (e.g. with concomitant gentamicin), can be \"rescued\" once isolate susceptibilities become available, or currently deployed phenotypic susceptibility testing breakpoints do not adequately correlate with clinical outcome.

epidemiology↗