Biology subjects

Johnston, S. A.

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

10 recordsLinked to original sources

bioRxiv2025

Microscaled Cell Surface Proteomics for Cryo-preserved and Tissue Samples

Cell surface proteins (CSPs) regulate key cellular functions and represent valuable targets for diagnostics and therapeutics. Despite advances in proteomic workflows, CSP analysis from cryopreserved or low-input clinical samples remains limited by technical constraints, including reduced membrane integrity, inefficient labeling, and high background. To address these challenges, we optimized and benchmarked two complementary surface enrichment strategies compatible with low-input applications (fewer than 1 million cells) and real-world sample types, including fresh, viably cryopreserved, and dissociated solid tissues. We systematically compared oxidation-based N-glycoprotein capture and WGA-HRP-mediated proximity labeling across a range of input amounts using both solid tumor (A549) and hematologic cancer (KMS-12-BM) cell lines. The N-glycopeptide method yielded superior specificity in low-input contexts, while WGA-HRP captured complementary CSP subsets. Together, the methods identified more than 700 CSPs, with approximately 175 unique identifications per protocol. Both workflows detected dynamic EGFR internalization following EGF stimulation and maintained high reproducibility (Pearson correlation greater than 0.9) between fresh and cryopreserved preparations. To extend these findings to tissue-derived samples, we optimized dissociation protocols for healthy endometrium and applied the N-glycopeptide method to cryopreserved dissociated endometrium from three healthy donors. Enzymatic dissociation enabled accurate CSP profiling from fewer than 1 to 2 million cells. This study provides a systematic comparison of two leading surface proteomics approaches, validates their performance on cryopreserved and low-input specimens, and demonstrates applicability to clinically relevant tissues. Our optimized workflows enable robust surfaceome characterization in translational settings where sample quantity and preservation methods are often limiting, opening new avenues for biomarker discovery and patient stratification.

cell biology↗

bioRxiv2023

Candida albicans suppression of neutrophil reactive nitrogen species is rescued by host Hif-1alpha in vivo

Candida albicans is a human commensal that can cause life-threatening invasive infection in immunocompromised individuals. Human immunity to C. albicans infection is thought to be largely dependent on neutrophil reactive oxygen and nitrogen species (ROS/RNS) generation by neutrophils. Despite this, our understanding of innate immune killing and escape by C. albicans is primarily studied in macrophages and the precise mechanisms of evasion are unclear in neutrophils. Here we sought to determine the importance of neutrophil reactive nitrogen species (RNS) production during C. albicans infection in vivo. Using a zebrafish model, we found that C. albicans rapidly downregulated neutrophil RNS below basal levels during the first day post infection, a time at which neutrophil RNS is upregulated in bacterial infections as an important host-defense mechanism, indicating fungal evasion of host neutrophils. We confirmed downregulation of RNS in human primary neutrophils and with clinical Candida spp. isolates, including emerging human pathogens C. auris and C. glabrata. Using a zebrafish arginase 2 transgenic line and a C. albicans car1{Delta} mutant, we show that both host and fungal arginase contribute the reduction in neutrophil RNS. Despite pathogen downregulation, upregulation of neutrophil RNS via Hypoxia inducible factor (Hif)-1 stabilisation, was sufficient to improve C. albicans infection survival, dependent on the presence of neutrophils and Nitric oxide synthase 2 (Nos2). Finally, restoration of neutrophil RNS, via Hif-1 stabilisation, was synergistic with clinically relevant antifungal treatment, increasing survival and clearance of C. albicans infections. Together, these data demonstrate that restoration of the neutrophil RNS response in C. albicans infection improves infection outcomes, highlighting the potential of targeting Hif-1 and RNS in host directed therapies against fungal infections.

immunology↗

bioRxiv2019

The mouse lung early cellular innate immune response is not sufficient to control fungal infection with Cryptococcus neoformans

Cryptococcus neoformans causes life-threatening infection in the immunocompromised. This and other opportunistic pathogens are an increasing threat as immunosuppression increases globally. To counter antibiotic resistance, there is precedent for developing immune enhancing therapy. However, our understanding of how immunocompetent patients resolve these infections is poor as opportunistic infections typically resolve subclinically. Because this has led to a lack of clinical data, we rely on animal models. Current in vivo infection models either lack mammalian immunity or are not compatible with long term high content imaging required to model the complexities of human host-pathogen interactions. Therefore, we have developed an ex vivo murine precision cut lung slice (PCLS) model to understand innate immunity in cryptococcosis. C57BL/6 mice were sacrificed 0 or 24 hours post infection with KN99 cryptococci. Lungs were inflated with 37{degrees}C agarose, 300m thick PCLS were prepared on a vibratome and imaged by confocal or wide-field fluorescence microscopy. Using PCLS and immunofluorescence, we demonstrate cryptococcal replication and clearance rates are balanced over the first 24 hours of infection. Cell-mediated immunity is alveolar macrophage centric, although alveolar macrophages demonstrate limited phagocytosis of cryptococci and enable intracellular cryptococcal replication. Cryptococcus neoformans responded to the lung environment by forming enlarged cells, although these were not large enough to be titan cells. To further understand cryptococcal proliferation in vivo, we also infected animals with plb1 mutant Cryptococcus neoformans that has been shown to exhibit proliferation defects in vivo. We found no difference in fungal burden with plb1 infected animals 24 hours post infection, but observed significantly larger fungal cells and no incidences of phagocytosis. Thus, the PCLS model can be used to assess the lung immune response early in cryptococcal infection, demonstrating that resident lung macrophages cannot control cryptococcal infection and offer an intracellular niche for Cryptococcus neoformans growth.

immunology↗

bioRxiv2019

Neutrophils use selective autophagy receptor p62 to target Staphylococcus aureus for degradation in the zebrafish model

Autophagy leads to degradation of cellular components and has an important role in restricting intracellular pathogens. Autophagy receptors, including p62, target invading intracellular pathogens to the autophagy pathway for degradation. Staphylococcus aureus is a significant pathogen of humans and often life-threatening in the immunocompromised. Increasing evidence demonstrates that S. aureus is an intracellular pathogen of immune cells and may use neutrophils as proliferative niche but the intracellular fate of S. aureus following phagocytosis by neutrophils has not previously been analysed in vivo. In vitro, p62 is able to co-localise with intracellular Staphylococcus aureus, but whether p62 is beneficial or detrimental in host defence against S. aureus in vivo had not been determined. Here we use zebrafish to determine the fate and location of S. aureus within neutrophils throughout infection. We show that Lc3 and p62 recruitment to phagocytosed S. aureus is altered depending on the bacterial location within the neutrophil. We also show rapid Lc3 marking of bacterial phagosomes within neutrophils which may be associated with subsequent bacterial degradation. Finally, we find that p62 is important for controlling cytosolic bacteria demonstrating for the first time a key role of p62 in autophagic control of S. aureus in neutrophils.

immunology↗

bioRxiv2019

The autophagic response to Staphylococcus aureus provides an intracellular niche in neutrophils

Staphylococcus aureus is a major human pathogen causing multiple pathologies, from cutaneous lesions to life-threatening sepsis. Although neutrophils contribute to immunity against S. aureus, multiple lines of evidence suggest that these phagocytes can provide an intracellular niche for staphylococcal dissemination. However, the mechanism of neutrophil subversion by intracellular S. aureus remains unknown. Targeting of intracellular pathogens by autophagy is recognised as an important component of host innate immunity, but whether autophagy is beneficial or detrimental to S. aureus-infected hosts remains controversial. Here, using larval zebrafish we show that S. aureus is rapidly decorated by the autophagy marker Lc3 following engulfment by macrophages and neutrophils. Upon phagocytosis by neutrophils, Lc3-positive, non-acidified spacious phagosomes are formed. This response is dependent on phagocyte NADPH oxidase as both cyba knockdown and diphenyleneiodonium (DPI) treatment inhibited Lc3 decoration of phagosomes. Importantly, NADPH oxidase inhibition diverted neutrophil S. aureus processing into tight acidified vesicles, which resulted in increased host resistance to the infection. Some intracellular bacteria within neutrophils were also tagged by p62-GFP fusion protein and loss of p62 impaired host defence. Taken together, we have shown that intracellular handling of S. aureus by neutrophils is best explained by Lc3-associated phagocytosis (LAP), which appears to provide an intracellular niche for bacterial pathogenesis, while the selective autophagy receptor p62 is host-protective. The antagonistic roles of LAP and p62-mediated pathways in S. aureus-infected neutrophils may explain the conflicting reports relating to anti-staphylococcal autophagy and provide new insights for therapeutic strategies against antimicrobial resistant staphylococci.

immunology↗

bioRxiv2018

Redistribution of a glucuronoxylomannan epitope towards the capsule surface coincides with Titanisation in the human fungal pathogen Cryptococcus neoformans

Disseminated infections with the fungal species Cryptococcus neoformans or, less frequently, C. gattii, are a leading cause of mortality in immunocompromised individuals. Central to the virulence of both species is an elaborate polysaccharide capsule that consists predominantly of glucuronoxylomannan (GXM). Due to its abundance, GXM is an ideal target for host antibodies, and several monoclonal antibodies (mAbs) have previously been derived using purified GXM or whole capsular preparations as antigen. In addition to their application in the diagnosis of cryptococcosis, anti-GXM mAbs are invaluable tools for studying capsule structure. In this study, we report the production and characterisation of a novel anti-GXM mAb, Crp127, that unexpectedly reveals a role for GXM remodelling during the process of fungal Titanisation. We show that Crp127 recognises a GXM epitope in an O-acetylation dependent, but xylosylation-independent, manner. The epitope is differentially expressed by the four main serotypes of Cryptococcus neoformans and gattii, is heterogeneously expressed within clonal populations of C. gattii serotype B strains and is typically confined to the central region of the enlarged capsule. Uniquely, however, this epitope redistributes to the capsular surface in Titan cells, a recently recognised subset of giant fungal cells that are produced in the host lung and are critical for successful infection. Crp127 therefore highlights hitherto unexpected features of cryptococcal morphological change and may hold significant therapeutic potential in differentially identifying cryptococcal strains and subtypes.\n\nImportanceCryptococcus neoformans and Cryptococcus gattii are the etiological agents of cryptococcosis, an invasive fungal infection responsible for approximately 200,000 deaths each year and 15% of AIDS-related deaths annually. Whilst the main virulence factor for both species is a highly variable polysaccharide capsule, formation of Titan cells also underlies the pathogenesis of C. neoformans. Previous studies have shown that capsule composition differs between yeast and Titan cells, however no clear distinctions in the expression or localisation of specific capsular epitopes have been made. In this study, we characterise a novel monoclonal antibody (mAb) specific to a capsular epitope that is differentially distributed throughout the capsules produced by yeast and Titan cells. Whilst this epitope is found within the midzone of yeast capsules, the presentation of this epitope on the surface of Titan cell capsules may represent a way in which these cell types are perceived differently by the immune system.

microbiology↗

bioRxiv2018

Alternative oxidase induction protects Candida albicans from respiratory stress and promotes hyphal growth

The human fungal pathogen Candida albicans possesses two genes expressing a cyanide-insensitive Alternative Oxidase (Aox) enzymes in addition to classical and parallel electron transfer chains (ETC). In this study, we examine the role of Aox in C. albicans under conditions of respiratory stress, which may be inflicted during its interaction with the human host or co-colonising bacteria. We find that the level of Aox expression is sufficient to modulate resistance to classical ETC inhibition under respiratory stress and are linked to gene expression changes that can promote both survival and pathogenicity. For example we demonstrate that Aox function is important for the regulation of filamentation in C. albicans and observe that cells lacking Aox function lose virulence in a zebrafish infection model. Our investigations also identify that pyocyanin, a phenazine produced by the co-colonising bacterium Pseudomonas aeruginosa, inhibits Aox-based respiration in C. albicans. These results suggest that Aox plays important roles within respiratory stress response pathways which C. albicans may utilise both as a commensal organism and as a pathogen.

microbiology↗

bioRxiv2018

Inhibition of classical and alternative modes of respiration in C. albicans leads to cell wall remodelling and increased macrophage recognition

The human fungal pathogen C. albicans requires respiratory function for normal growth, morphogenesis and virulence. As such the mitochondria represent an enticing target for the development of new antifungal strategies. This possibility is further bolstered by the presence of fungal specific characteristics. However, respiration in C. albicans, as is the case in many fungal organisms, is facilitated by redundant electron transport mechanisms that makes direct inhibition a challenge. In addition, many chemicals known to target the electron transport chain are highly toxic. Here we make use of chemicals with low toxicity in mammals to efficiently inhibit respiration in C. albicans. We find that use of the Nitric Oxide donor, Sodium Nitroprusside (SNP), and the alternative oxidase inhibitor, SHAM, prevent respiration, lead to a loss in viability and to cell wall rearrangements that increase the rate of uptake by macrophages in vitro and in vivo. We propose that SNP+SHAM treatment leads to transcriptional changes that drive cell wall re-arrangement but which also prime cells to activate transition to hyphal growth. In line with this we find that pre-treatment of C. albicans with SNP+SHAM leads to an increase in virulence. Our data reveals strong links between respiration, cell wall remodelling and activation of virulence factors. Our findings also demonstrate that respiration in C. albicans can be efficiently inhibited with chemicals which are not damaging to the mammalian host, but that we need to develop a deeper understanding of the roles of mitochondria in cellular signalling if they are to be developed successfully as a target for new antifungals.\n\nAuthor SummaryCurrent approaches to tackling fungal infections are limited and new targets must be identified to protect against the emergence of resistant strains. We investigate the potential of targeting mitochondria, organelles required for energy production, growth and virulence, in the yeast human fungal pathogen Candida albicans. Our findings suggest that mitochondria can be targeted using drugs that can be tolerated by humans and that this treatment enhances their recognition by immune cells. However release of C. albicans cells from mitochondrial inhibition appears to activate a stress response that increases traits associated with virulence. Our results make it clear that mitochondria are a valid target for the development of anti-fungal strategies but that we must determine the mechanisms by which they regulate stress signalling and virulence ahead of successful therapeutic advance.

microbiology↗

bioRxiv2018

Simu-dependent clearance of dying cells regulates macrophage function and inflammation resolution

Macrophages encounter and clear apoptotic cells during normal development and homeostasis, including at numerous sites of pathology. Clearance of apoptotic cells has been intensively studied, but the effects of macrophage-apoptotic cell interactions on macrophage behaviour are poorly understood. Using Drosophila embryos, we have exploited the ease of manipulating cell death and apoptotic cell clearance in this model to identify that the loss of the apoptotic cell clearance receptor Simu leads to perturbation of macrophage migration and inflammatory responses via pathological levels of apoptotic cells. Removal of apoptosis ameliorates these phenotypes, while acute induction of apoptosis phenocopies these defects and reveals that phagocytosis of apoptotic cells is not necessary for their anti-inflammatory action. Furthermore, Simu is necessary for clearance of necrotic debris and rentention of macrophages at wounds. Thus, Simu is a general detector of damaged self and represents a novel molecular player in controlling resolution of inflammation.

cell biology↗

bioRxiv2017

Mycophenolate mofetil increases susceptibility toopportunistic fungal infection independent of lymphocytes

Anti-proliferative agents that target lymphoid cells are common immunosuppressive agents used in the treatment of diverse autoimmune, graft versus host and inflammatory diseases. Mycophenolate mofetil (MMF) is an anti-proliferative agent that targets lymphoid dependence on inosine monophosphate dehydrogenase for the de novo purine synthesis of deoxyguanosine triphosphate (dGTP) for DNA replication. Here we show that MMF has a distinct and specific in vivo effect on macrophages, in the absence of lymphoid cells. This results in increased macrophage cell death that is dependent on the depletion of cellular GTP, independent of DNA synthesis. Furthermore, the macrophage specific effect of MMF treatment causes an increase in susceptibility to the opportunistic fungal infection Cryptococcus neoformans by reducing phagocytosis and increasing the release of intracellular pathogens via macrophage lysis. Our study demonstrates the need for a better mechanistic understanding of immunosuppressive treatments used in clinical practice and of the specific infection risks associated with certain treatment regimens.

immunology↗