Biology subjects

Johnston, S.

Publications and source records attributed to Johnston, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Macrophages use sub-micron actin ridges in phagocytosis of encapsulated fungal pathogens

Ingestion and killing of pathogens by phagocytic cells is a key aspect of animal immunity. Cryptococcus neoformans is a major pathogen of AIDS patients that has a polysaccharide capsule that is critical for virulence. Phagocytic function is necessary for normal immunity to cryptococcal infection, and we sought to determine how Cryptococcus capsule prevents phagocytosis. In doing so, we discovered a new sub-micron actin structure, the ridge, that is present on macrophages, neutrophils and amoebae. Macrophages preferentially bind cryptococci via ridges and suppression of ridges is sufficient to prevent phagocytosis. Ridges are present on macrophages in vivo and are lost in interleukin 10 stimulated macrophages. The discovery and functional description of macrophage surface ridges fills a critical gap in our understanding of how phagocytes ingest encapsulated fungal pathogens, a crucial step in treating infection.

cell biology↗

bioRxiv2026

Genomic history and selection in Roman and early medieval Britain

Leading biomedical resources rely on genome variation in Britain1-3, but the historical processes that shaped present-day fine-scale diversity remain debated4-13. Here we sequenced 1039 ancient shotgun genomes from Britain (median 1.4-fold coverage), primarily dating to the first millennium CE. We imputed [~]660 million variants in the UK Biobank14-16 and employed genealogy-based ancestry reconstruction. We found an association between Iron Age consanguinity and matrilineal burial practices17, later disrupted following the Roman Conquest. Despite this societal impact, only 20% of Roman-period individuals carried detectable ancestry from outside Britain. In contrast, from the 6th century CE we detect widespread influx of ancestry in over 70% of individuals in southernAnglo-Saxon Britain, with limited local admixture. We find previously underappreciated heterogeneity, with ancestries associated with Central and Southern Europe rising in prevalence from the 7th century CE. We demonstrate distinct Scandinavian-related ancestry in many Viking-associated contexts, but show that the population-level impact of the Viking Age in Britain was limited. Finally, we detect pre-medieval selection on variants linked with key immunity genes TLR10-TLR1 and IRF8. These results identify population-level and selective processes that shape variation and disease risk in Britain today.

genomics↗

bioRxiv2025

Human airway epithelia clear rhinovirus-infected cells using two waves of cell extrusion

Epithelial barriers represent the first line of defence against pathogens, yet their role in innate immunity is typ-ically relegated to pathogen detection and immune cell recruitment. This perspective ignores a fundamental evolutionary principle: epithelia defended against pathogens long before complex immune systems evolved. Here, we demonstrate that human bronchial epithelial monolayers retain this ancestral capacity, autono-mously clearing rhinovirus (RV) within 24 hours by selectively extruding infected cells--a process we term virus-induced cell extrusion (VICE). VICE occurs in two waves: a rapid response occurring independently of virus entry, followed by a replication-dependent wave. Barrier-defective epithelia that cannot extrude fail to clear RV. While extrusion maintains barrier integrity and eliminates local infection, it also expels virus-laden cells, promoting transmission. Thus, VICE enables leukocyte-independent epithelial defence while inadver-tently promoting viral transmission, reflecting an evolutionary strategy that prioritizes barrier integrity over containment. These findings redefine epithelia as central players in viral pathogenesis and host protection.

cell biology↗

bioRxiv2025

Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma

Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Given that neutrophils are known to display a prominent discordance between mRNA and protein abundance, we developed ultra-sensitive mini-bulk and single cell proteomic (SCP) workflows to study the heterogeneity of peripheral blood and tumour associated neutrophils (TAN) from patients with glioblastoma. Mini-bulk analysis enabled a deeper protein coverage of circulating immature, mature and TAN populations, defining signatures of maturity and demonstrating that TANs resemble mature circulating neutrophils. Analysis of the SCP data resulted in the detection of >1,100 proteins from a single TAN providing a detailed characterization of neutrophil subsets in glioblastoma. Our approach shows evidence of pathogenic and anti-tumorigenic clusters and discovers cell states invisible to scRNAseq, opening new opportunities to selectively target pro-tumoural neutrophil states.

immunology↗

bioRxiv2024

SIRT6 loss causes intervertebral disc degeneration in mice by promoting senescence and SASP status

Intervertebral disc degeneration is a major risk factor contributing to chronic low back and neck pain. While the etiological factors for disc degeneration vary, age is still one of the most important risk factors. Recent studies have shown the promising role of SIRT6 in mammalian aging and skeletal tissue health, however its role in the intervertebral disc health remains unexplored. We investigated the contribution of SIRT6 to disc health by studying the age-dependent spinal phenotype of mice with conditional deletion of Sirt6 in the disc (AcanCreERT2; Sirt6fl/fl). Histological studies showed a degenerative phenotype in knockout mice compared to Sirt6fl/fl control mice at 12 months which became pronounced at 24 months. RNA-Seq analysis of NP and AF tissues, quantitative histone analysis, and in vitro multiomics employing RNA-seq with ATAC-seq revealed that SIRT6-loss resulted in changes in acetylation and methylation status of specific Histone 3 lysine residues, thereby affecting DNA accessibility and transcriptomic landscape. A decrease in autophagy and an increase in DNA damage were also noted in Sirt6-deficient cells. Further mechanistic insights revealed that loss of SIRT6 increased senescence and SASP burden in the disc characterized by increased p21, {gamma}H2AX, IL-6, and TGF-{beta} abundance. Taken together our study highlights the contribution of SIRT6 in modulating DNA damage, autophagy and cell senescence, and its importance in maintaining disc health during aging thereby underscoring it as a potential therapeutic target to treat intervertebral disc degeneration.

molecular biology↗

bioRxiv2024

Exploring the role of E. faecalis Enterococcal Polysaccharide Antigen (EPA) and lipoproteins in evasion of phagocytosis

Enterococcus faecalis is an opportunistic pathogen frequently causing nosocomial infections. The virulence of this organism is underpinned by its capacity to evade phagocytosis, allowing dissemination in the host. Immune evasion requires a surface polysaccharide produced by all enterococci, known as the Enterococcal Polysaccharide Antigen (EPA). EPA consists of a cell wall-anchored rhamnose backbone substituted by strain-specific polysaccharides called "decorations", essential for the biological activity of this polymer. However, the structural determinants required for innate immune evasion remain unknown, partly due to a lack of suitable validated assays. Here, we describe a quantitative, in vitro assay to investigate how EPA decorations alter phagocytosis. Using the E. faecalis model strain OG1RF, we demonstrate that a mutant with a deletion of the locus encoding EPA decorations can be used as a platform strain to express heterologous decorations, thereby providing an experimental system to investigate the inhibition of phagocytosis by strain-specific decorations. We show that the aggregation of cells lacking decorations is increasing phagocytosis and that this process does not involve the recognition of lipoproteins by macrophages. Collectively, our work provides novel insights into innate immune evasion by enterococci and paves the way for further studies to explore the structure/function relationship of EPA decorations.

microbiology↗

bioRxiv2024

AMHY and sex determination in egg-laying mammals

The sex chromosomes of egg-laying mammals (monotremes), which lack the sex determining gene SRY1, evolved independently to those of all therian mammals2,3. Here we characterise the candidate monotreme sex determining gene, the Y-localised anti-Mullerian hormone gene (AMHY)4,3 and trace its expression during the period of sexual differentiation. Monotreme AMHX and AMHY gametologues have significant sequence divergence at the promoter, gene and protein level, likely following an original allele inversion in the common monotreme ancestor but retain conserved features of TGF-{beta} molecules. Expression of sexual differentiation genes in the echidna fetal gonad were significantly different from that of therian mammals. AMHY expression was seen exclusively in the male gonad during sexual differentiation, whereas AMHX was expressed in both sexes. Experimental ectopic expression of platypus AMHX or AMHY in the chicken embryo did not masculinise the female urogenital system, a possible result of mammalian specific changes to AMH proteins preventing function in the chicken. Our results provide fundamental insight into the first steps of monotreme sex chromosome evolution and sex determination with developmental expression data strongly supporting AMHY as the primary male sex determination gene.

evolutionary biology↗

bioRxiv2023

Increased HIF-2α Activity in the Nucleus Pulposus Causes Intervertebral Disc Degeneration in the Aging Mouse Spine

Hypoxia-inducible factors (HIFs) are essential to the homeostasis of hypoxic tissues. Although HIF-2, is expressed in nucleus pulposus (NP) cells, consequences of elevated HIF-2 activity on disc health remains unknown. We expressed HIF-2 with proline to alanine substitutions (P405A;P531A) in the Oxygen-dependent degradation domain (HIF-2dPA) in the NP tissue using an inducible, nucleus pulposus-specific K19CreERT allele to study HIF-2 function in the adult intervertebral disc. Expression of HIF-2 in NP impacted disc morphology, as evident from small but significantly higher scores of degeneration in NP of 24-month-old K19CreERT; HIF-2dPA (K19-dPA) mice. Noteworthy, comparisons of grades within each genotype between 14 months and 24 months indicated that HIF-2 overexpression contributed to more pronounced changes than aging alone. The annulus fibrosus (AF) compartment in the 14-month-old K19-dPA mice exhibited lower collagen turnover and Fourier transform-infrared (FTIR) spectroscopic imaging analyses showed changes in the biochemical composition of the 14-and 24-month-old K19-dPA mice. Moreover, there were changes in aggrecan, chondroitin sulfate, and COMP abundance without alterations in NP phenotypic marker CA3, suggesting the overexpression of HIF-2 had some impact on matrix composition but not the cell phenotype. Mechanistically, the global transcriptomic analysis showed enrichment of differentially expressed genes in themes closely related to NP cell function such as cilia, SLIT/ROBO pathway, and HIF/Hypoxia signaling at both 14- and 24-months. Together, these findings underscore the role of HIF-2 in the pathogenesis of disc degeneration in the aged spine.

cell biology↗

bioRxiv2023

Ageing-related defects in macrophage function are driven by MYC and USF1 transcriptional programmes

Macrophages are central innate immune cells whose function declines with age. The molecular mechanisms underlying age-related immunity changes remain poorly understood, particularly in human macrophages. We report a substantial reduction in phagocytosis, migration and chemotaxis in human monocyte-derived macrophages (MDMs) from older (>50 years) compared with younger (18-30 years) donors, alongside downregulation of transcription factors MYC and USF1 with age. In MDMs from young donors, knockdown of MYC or USF1 decreased phagocytosis and chemotaxis and altered expression of genes associated with these functions, as well as adhesion and extracellular matrix remodelling. A concordant dysregulation of MYC and USF1 target genes was also seen in MDMs from older donors. Furthermore, older age and loss of either MYC or USF1 in MDMs led to an increased cell size, altered morphology and reduced actin content. Together, these results define MYC and USF1 as key drivers of MDM age-related functional decline and identify downstream targets to improve macrophage function in ageing.

immunology↗

bioRxiv2023

Candida albicans cells lacking AP-2 have defective hyphae and are avirulent despite increased host uptake and intracellular proliferation in macrophages

Candida albicans is a commensal microbe and opportunistic human pathogen. The yeast can be recognised and taken up by macrophages via interactions with its cell wall, a complex polysaccharide structure containing several components that are specifically recognised by immune cell receptors. Following uptake Candida can respond in the host environment by switching from a yeast to hyphal morphology which facilitates escape from macrophages and allows subsequent invasion of host tissues. Disruption of Candidas ability to form hyphae results in reduced virulence and fitness for survival in the host environment. Candida albicans cells lacking AP-2, an endocytic adaptor complex, have increased cell wall chitin and morphologically defective hyphae in vitro. Previous studies have correlated increased chitin with decreased recognition by macrophages, possibly due to masking of cell wall beta-glucan which is recognised by dectin receptors. Despite the cell wall changes in the mutant strain there was an unexpected increased uptake of the mutant. Increased chitin did not reduce phagocytosis and additional uptake was not due to compensatory elevated exposure of beta-glucan, highlighting the importance of cell wall components beyond chitin and glucan for macrophage engagement and uptake. Furthermore, the apm4 mutant exhibited parasitism of macrophages, surviving and proliferating within the phagosome, a phenotype that was then replicated with a well-characterised yeast locked mutant. Finally, the combined phenotype of reduced hyphal formation but continued proliferation resulted in reduced virulence despite an equivalent burden of infection to a wild-type Candida infection, as determined using a zebrafish larval model of candidiasis.

microbiology↗

bioRxiv2022

IL-33-induced neutrophilic inflammation and NETosis underlie rhinovirus-triggered exacerbations of asthma

Rhinovirus-induced neutrophil extracellular traps (NETs) contribute to acute asthma exacerbations, however the molecular factors that trigger NETosis in this context remain ill-defined. Here, we sought to implicate a role for IL-33, an epithelial cell-derived alarmin rapidly released in response to infection. In mice with chronic experimental asthma (CEA), but not naive controls, rhinovirus inoculation induced an early (1 day post infection; dpi) inflammatory response dominated by neutrophils, neutrophil-associated cytokines (IL-1, IL-1{beta}, CXCL1) and NETosis, followed by a later, type-2 inflammatory phase (3-7 dpi), characterized by eosinophils, elevated IL-4 levels, and goblet cell hyperplasia. Notably, both phases were ablated by HpARI (Heligmosomoides polygyrus Alarmin Release Inhibitor), which blocks IL-33 release and signalling. Instillation of exogenous IL-33 recapitulated the rhinovirus-induced early phase, including the increased presence of NETs in the airway mucosa, in a PAD4-dependent manner. Ex vivo IL-33-stimulated neutrophils from mice with CEA, but not naive mice, underwent NETosis, and produced greater amounts of IL-1/{beta}, IL-4, and IL-5. In nasal samples from rhinovirus-infected people with asthma, but not healthy controls, IL-33 levels correlated with neutrophil elastase and dsDNA. Our findings suggest that IL-33 blockade ameliorates the severity of an asthma exacerbation by attenuating neutrophil recruitment and the downstream generation of NETs.

immunology↗

bioRxiv2022

Resting-state aperiodic neural activity as a novel objective marker of daytime somnolence

Study ObjectivesCurrent assessment of excessive daytime somnolence (EDS) requires subjective measurements such as the Epworth Sleepiness Scale (ESS), and/or resource intensive sleep laboratory investigations. Recent work 1,2 has called for more non-performance-based measures of EDS. One promising non-performance-based measure of EDS is the aperiodic component of electroencephalography (EEG). Aperiodic (non-oscillatory) activity reflects excitation/inhibition ratios of neural populations and is altered in various states of consciousness, and thus may be a potential biomarker of hypersomnolence. MethodsWe retrospectively analysed EEG data from patients who underwent a Multiple Sleep Latency Test (MSLT) and determined whether aperiodic neural activity is predictive of EDS. Participants having undergone laboratory polysomnogram and next day MSLT were grouped into MSLT+ (n = 26) and MSLT- (n = 33) groups (mean sleep latency of < 8min and > 10min, respectively) and compared against a non-clinical (Control) group of participants (n = 26). ResultsWhile the MSLT+ and MSLT- groups did not differ in their aperiodic activity, the Control group had a significantly flatter slope and larger offset compared to both MSLT+ and MSLT- groups. Logistic regression machine learning predicted group status (i.e., symptomatic, non-symptomatic) with 90% accuracy based on the aperiodic slope while controlling for age. Slow oscillation-spindle coupling was also significantly stronger in the Control group relative to MSLT+ and MSLT- groups. ConclusionsOur results provide first evidence that aperiodic neural dynamics and sleep-based cross-frequency coupling is predictive of EDS, thereby providing a novel avenue for basic and applied research in the study of sleepiness.

neuroscience↗

bioRxiv2021

Pupillometry and the vigilance decrement: Task-evoked but not baseline pupil measures reflect declining performance in visual vigilance tasks

Baseline and task-evoked pupil measures are known to reflect the activity of the nervous systems central arousal mechanisms. With the increasing availability, affordability and flexibility of video-based eye tracking hardware, these measures may one day find practical application in real-time biobehavioral monitoring systems to assess performance or fitness for duty in tasks requiring vigilant attention. But real-world vigilance tasks are predominantly visual in their nature and most research in this area has taken place in the auditory domain. Here we explore the relationship between pupil size--both baseline and task-evoked--and behavioral performance measures in two novel vigilance tasks requiring visual target detection: 1) a traditional vigilance task involving prolonged, continuous, and uninterrupted performance (n = 28), and 2) a psychomotor vigilance task (n = 25). In both tasks, behavioral performance and task- evoked pupil responses declined as time spent on task increased, corroborating previous reports in the literature of a vigilance decrement with a corresponding reduction in task-evoked pupil measures. Also in line with previous findings, baseline pupil size did not show a consistent relationship with performance measures. We discuss our findings considering the adaptive gain theory of locus coeruleus function and question the validity of the assumption that baseline (prestimulus) pupil size and task-evoked (poststimulus) pupil measures correspond to the tonic and phasic firing modes of the LC.

neuroscience↗

bioRxiv2021

TWIST1 interacts with adherens junction proteins during neural tube formation and regulates fate transition in cranial neural crest cells

Cell fate determination is a necessary and tightly regulated process for producing different cell types and structures during development. Cranial neural crest cells (CNCCs) are unique to vertebrate embryos and emerge from the neural fold borders into multiple cell lineages that differentiate into bone, cartilage, neurons, and glial cells. We previously reported that Irf6 genetically interacts with Twist1 during CNCC-derived tissue formation. Here, we investigated the mechanistic role of Twist1 and Irf6 at early stages of craniofacial development. Our data indicates that TWIST1 interacts with /{beta}/{gamma}-CATENINS during neural tube closure, and Irf6 is involved in the structural integrity of the neural tube. Twist1 suppresses Irf6 and other epithelial genes in CNCCs during epithelial-to-mesenchymal transition (EMT) process and cell migration. Conversely, a loss of Twist1 leads to a sustained expression of epithelial and cell adhesion markers in migratory CNCCs. Disruption of TWIST1 phosphorylation in vivo leads to epidermal blebbing, edema, neural tube defects, and CNCC-derived structural abnormalities. Altogether, this study describes an uncharacterized function of Twist1 and Irf6 in the neural tube and CNCCs and provides new target genes of Twist1 involved in cytoskeletal remodeling. Furthermore, the association between DNA variations within TWIST1 putative enhancers and human facial morphology is also investigated. SUMMARY STATEMENTThis study uncovers a new function of Twist1 in neural tube development and epithelial-to-mesenchymal transition in cranial neural crest cells. Data further shows that Twist1-interacting Irf6 is involved in regulating neural tube integrity.

developmental biology↗

bioRxiv2020

Rapid genomic expansion and purging associated with habitat transitions in a clade of beach crustaceans (Haustoriidae: Amphipoda)

Genome sizes vary by orders of magnitude across the Tree of Life and lack any correlation with organismal complexity. Some crustacean orders, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that natural selection may constrain genome sizes due to physiological pressures. In this study, we examine the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncover a 6-fold genome size variation within a clade that is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. Finally, we find evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays. Significance StatementThe evolution of genome size has been a long-standing puzzle in biology. In this work, we find that genome sizes may be driven by different selection regimes following shifts to a new habitat. Dramatic genome size changes can occur rapidly, in only a few million years. Data Availability StatementRaw data sheets have been deposited on Dryad: SUBMITTED. Raw sequence reads are available at from NCBI under Bioproject SUBMITTED.

evolutionary biology↗

bioRxiv2020

Cat fleas in flux: Rampant gene duplication, genome size plasticity, and paradoxical Wolbachia infection

BackgroundFleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e. the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea, Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe. ResultsBy combining Illumina and PacBio sequencing with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly for C. felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by [~]38% of protein-coding genes with two or more copies and over 4,000 tRNA genes. A broad range of genome size determinations (433-551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) in C. felis. Similarly broad genome sizes were also calculated for individuals of Xenopsylla cheopis (Oriental rat flea), indicating that this remarkable "genome-in-flux" phenomenon could be a siphonapteran-wide trait. Finally, from the C. felis sequence reads we also generated closed genomes for two novel strains of Wolbachia, one parasitic and one symbiotic, found to co-infect individual fleas. ConclusionRampant CNV in C. felis has dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novel Wolbachia endosymbionts - potential tools for blocking pathogen transmission - these oddities highlight a unique and underappreciated disease vector.

genomics↗

bioRxiv2020

An in vitro model to study the naive human peripheral blood mononuclear cell response to Cryptococcus neoformans infection

Cryptococcus neoformans is a facultative intracellular pathogenic yeast which causes cryptococcal meningitis. Infection most commonly occurs via the lungs in humans and is cleared without clinical signs in the immunocompetent, but may cause life-threatening infection in immunocompromised. C. neoformans can be phagocytosed by host phagocytes, but may manipulate the intracellular niche of phagocytes for replication and dissemination. The interaction of macrophages with cryptococcal cells has been studied in detail but little is known about the interaction between human peripheral blood mononuclear cells (PBMC) and C. neoformans. PBMCs are rapidly recruited to the site of initial infection in the lung, peripheral tissues, and also respond to cryptococci that disseminate via the bloodstream. Therefore, deciphering the interactions between PBMCs and cryptococci is an important but neglected aspect of our understanding of the immune response during cryptococcal infection. Here, using time lapse imaging of primary human PBMCs in vitro, we are able to measure the PBMC response to cryptococci. Using this approach we find that naive, undifferentiated human monocytes phagocytose cryptococcal cells, and that aggregates (swarms) of monocytes and T cells often form in response to engulfment of cryptococci. Interestingly, we find a correlation between the size of the PBMC aggregates and proliferative ability of the cryptococci within. While these aggregates slow intracellular cryptococcal growth, cryptococci are able to replicate within this niche and escape from PBMCs to replicate extracellularly. These results provide evidence for PBMC control of cryptococcal infection and provide a model for the in vitro study of cryptococcal granuloma biology.

immunology↗

bioRxiv2020

Blood vessel occlusion by Cryptococcus neoformans is a mechanism for hemorrhagic dissemination of infection

Meningitis caused by infectious pathogens are associated with vessel damage and infarct formation, however the physiological cause is unknown. Cryptococcus neoformans, is a human fungal pathogen and causative agent of cryptococcal meningitis, where vascular events are observed in up to 30% of cases, predominantly in severe infection. Therefore, we aimed to investigate how infection may lead to vessel damage and associated pathogen dissemination using a zebrafish model for in vivo live imaging. We find that cryptococcal cells become trapped within the vasculature (dependent on there size) and proliferate there resulting in vasodilation. Localised cryptococcal growth, originating from a single or small number of cryptococcal cells in the vasculature was associated with sites of dissemination and simultaneously with loss of blood vessel integrity. Using a cell-cell junction tension reporter we identified dissemination from intact blood vessels and where vessel rupture occurred. Finally, we manipulated blood vessel stifness via cell junctions and found increased stiffness resulted in increased dissemination. Therefore, global vascular vasodilation occurs following infection, resulting in increased vessel tension which subsequently increases dissemination events, representing a positive feedback loop. Thus, we identify a mechanism for blood vessel damage during cryptococcal infection that may represent a cause of vascular damage and cortical infarction more generally in infective meningitis.

pathology↗