Biology subjects

Gearing, L. J.

Publications and source records attributed to Gearing, L. J..

10 recordsLinked to original sources

bioRxiv2025

Annexin A2 mediates RIG-I-like receptor responses to viral infection

RIG-I and MDA5 are critical sensors of virus infection and detect many important human pathogens including SARS-CoV-2, influenza A virus (IAV), Zika virus and West Nile virus (WNV). MDA5 is activated by binding to double-stranded RNA generated during infection and induces strong pro-inflammatory and antiviral responses mediated largely via type I interferons. Activation of MDA5 is also implicated in monogenic (e.g. Aicardi-Goutieres syndrome) and complex polygenic (e.g. systemic lupus erythematosus) autoinflammatory diseases, demonstrating the importance of appropriate regulation of this pathway. Yet, how MDA5 is regulated is poorly defined. We employed SILAC-mass spectrometry to discover MDA5 binding partners in virus-infected cells. Our screen revealed Annexin A2 (ANXA2) as an interactor of MDA5 specifically during infection. Direct binding of ANXA2 and MDA5 was recapitulated in vitro and required Ca2+, and ANXA2 promoted MDA5 oligomerisation in cells. Loss of ANXA2 in human cells significantly blunted interferon responses to EMCV, WNV and IAV, demonstrating a role for ANXA2 in activation of both MDA5 and RIG-I. Using human induced pluripotent stem cells, we found that ANXA2 was required for potent neuronal cell responses to WNV infection and macrophage responses to multiple viral pathogens. Thus, we find that ANXA2 is a critical mediator of RIG-I-like receptor pathways.

immunology↗

bioRxiv2024

Mdx mice dosed with antisense to CD49d and dystrophin exon skip morpholino; reduced force loss and affected gene expression pathways support ATL1102 combination therapy in DMD patients

BackgroundVLA-4 is a disease progression biomarker in patients with Duchenne Muscular Dystrophy (DMD) including those treated with corticosteroids. ATL1102 an antisense oligonucleotide (ASO) inhibitor of human CD49d chain of adhesion molecule VLA-4 shows promising phase-2 results in non-ambulant DMD stabilizing upper limb function (PUL2.0), grip strength, and MRI muscle fat fraction, compared to worsening with corticosteroids. MethodsASO to mouse CD49d (ISIS348574) was used in combination with a known mdx dystrophin morpholino exon-23 skipping restoration drug (PMO), dose-time chosen for low dystrophin restoration. Mdx mice were treated once weekly for 8 weeks with ASO, control mismatch oligonucleotide, saline, or PMO alone for 4 weeks, and PMO in combination with ASO or mismatch. ResultsASO+PMO demonstrated increased specific maximum force and eccentric muscle force retention in the exterior digitorum longus (EDL) muscle after 1-7 muscle eccentric contractions relative to saline. Area-under-curve force remaining after 8-10 contractions was higher for ASO+PMO versus PMO monotherapy and ASO monotherapy, PMO monotherapy versus saline, and the ASO monotherapy versus saline and mismatch. RNA-sequencing of quadriceps muscle evaluated gene expression changes, with false discovery rate (FDR) adjusted p-values up to <0.1. ASO monotherapy at FDR<0.05 showed 2 unique genes, Gm2a in immune neutrophil function and Trdn with Ryr2 muscle calcium channel function, versus mdx saline and none with MM. The lowest FDR PMO gene was another calcium channel Cacna1s, with PMO+MM FDR<0.05. ASO+PMO treatment at FDR<0.05 modulated 55 genes, 53 unique to the combination and 2* also in ASO FDR<0.06. Affected genes were involved in immune response (Btla*, Ppml1, Tnfsm13), lipolysis (Fabp4*, G0s2), fibrosis (Igfbp-7, Calu), muscle cell (Asb15) and muscle stem cell function (Adam10, Mt-Tp, Myom1). ConclusionASO+PMO EDL muscle function protection in mdx mice, and gene expression pathways affected, support the development of ATL1102 in combination therapy with conditionally approved morpholino dystrophin restoration drugs in DMD patients.

molecular biology↗

bioRxiv2023

Mammalian cells internalize bacteriophages and utilize them as a food source to enhance cellular growth and survival

There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate diverse and unexplored symbioses. Yet the impact these bacteriophages may have on mammalian cellular and immunological processes is poorly understood. Here we applied highly purified phage T4, free from bacterial by-products and endotoxins to mammalian cells and analyzed the cellular responses using luciferase reporter and antibody microarray assays. Phage preparations were applied in vitro to either A549 lung epithelial cells, MDCK-I kidney cells, or primary mouse bone marrow derived macrophages with the phage-free supernatant serving as a comparative control. Highly purified T4 phages were rapidly internalized by mammalian cells and accumulated within macropinosomes but did not activate the inflammatory DNA response TLR9 or cGAS-STING pathways. Following eight hours of incubation with T4 phage, whole cell lysates were analyzed via antibody microarray that detected expression and phosphorylation levels of human signaling proteins. T4 phage internalization led to the activation of AKT-dependent pathways, resulting in an increase in cell metabolism, survival, and actin reorganization, the last being critical for macropinocytosis and potentially regulating a positive feedback loop to drive further phage internalization. T4 phages additionally down-regulated CDK1 and its downstream effectors, leading to an inhibition of cell cycle progression and an increase in cellular growth through a prolonged G1 phase. These interactions demonstrate that highly purified T4 phages do not activate DNA-mediated inflammatory pathways but do trigger protein phosphorylation cascades that promote cellular growth and survival. We conclude that mammalian cells are internalizing bacteriophages as a food source to promote cellular growth and metabolism.

microbiology↗

bioRxiv2023

The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes an acute respiratory distress syndrome (ARDS) that resembles surfactant deficient RDS. Using a novel multi-cell type, human induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system, validated against primary lung cells, we found that inflammatory cytokine/chemokine production and interferon (IFN) responses are dynamically regulated autonomously within the lung following SARS-CoV-2 infection, an intrinsic defense mechanism mediated by surfactant proteins (SP). Single cell RNA sequencing revealed broad infectability of most lung cell types through canonical (ACE2) and non-canonical (endocytotic) viral entry routes. SARS-CoV-2 triggers rapid apoptosis, impairing viral dissemination. In the absence of surfactant protein B (SP-B), resistance to infection was impaired and cytokine/chemokine production and IFN responses were modulated. Exogenous surfactant, recombinant SP-B, or genomic correction of the SP-B deletion restored resistance to SARS-CoV-2 and improved viability.

immunology↗

bioRxiv2022

Constitutive expression and distinct properties of IFN-epsilon protect the female reproductive tract from Zika virus infection

The immunological surveillance factors controlling vulnerability of the female reproductive tract (FRT) to sexually transmitted viral infections are not well understood. Interferon-epsilon (IFN{varepsilon}) is a distinct, immunoregulatory type-I IFN that is constitutively expressed by FRT epithelium and is not induced by pathogens like other antiviral IFNs , {beta} and {lambda}. We show the necessity of IFN{varepsilon} for Zika Virus (ZIKV) protection by: increased susceptibility of IFN{varepsilon}-/- mice; their "rescue" by intravaginal recombinant IFN{varepsilon} treatment and blockade of protective endogenous IFN{varepsilon} by neutralising antibody. Complementary studies in human FRT cell lines showed IFN{varepsilon} had potent anti-ZIKV activity, associated with transcriptome responses similar to IFN{lambda} but lacking the proinflammatory gene signature of IFN. IFN{varepsilon} activated STAT1/2 pathways similar to IFN and {lambda} that were inhibited by ZIKV-encoded non-structural (NS) proteins, but not if IFN{varepsilon} exposure preceded infection. This scenario is provided by the constitutive expression of endogenous IFN{varepsilon}. However, the IFN{varepsilon} expression was not inhibited by ZIKV NS proteins despite their ability to antagonise the expression of IFN{beta} or {lambda}. Thus, the constitutive expression of IFN{varepsilon} provides cellular resistance to viral strategies of antagonism and maximises the antiviral activity of the FRT. These results show that the unique spatiotemporal properties of IFN{varepsilon} provides an innate immune surveillance network in the FRT that is a significant barrier to viral infection with important implications for prevention and therapy. Author SummaryThe female reproductive tract (FRT) is vulnerable to sexually transmitted infections and therefore a well-tuned immune surveillance system is crucial for maintaining a healthy FRT. However, our understanding of the factors that impact viral infection of the FRT and the host response are not well understood. In this work we investigate the role of a hormonally regulated type I interferon, IFN epsilon (IFN{varepsilon}) in control of Zika virus (ZIKV) infection of the FRT. IFN{varepsilon} is unique compared to other canonical type-I IFNs in that it is constitutively expressed by epithelial cells of the FRT with expression levels controlled by progesterone and not in response to viral infection. We demonstrate that IFN{varepsilon} has anti-ZIKV properties using a combination of IFN{varepsilon} KO mice, blockade of endogenous IFN{varepsilon} by neutralising Abs and rescue of IFN{varepsilon} KO mice by recombinant IFN{varepsilon} administered directly to the FRT. Furthermore, we complemented our in vivo studies using human FRT derived cell lines. Importantly, ZIKV NS proteins did not block IFN{varepsilon} expression despite their ability to antagonise the expression of IFN{beta} or {lambda}. Collectively this work implicates IFN{varepsilon} as a key type-I IFN that provides a distinct homeostatic antiviral environment in the FRT.

immunology↗

bioRxiv2022

Proliferation is a driver of quorum sensing in an in vitro model of tissue resident macrophages

Macrophages coordinate the initial host inflammatory response to tissue infection, as well as mediating the reparative phase, by producing growth factors that promote tissue repair. One model of this functional dichotomy is that peripherally recruited monocyte-derived macrophages drive acute inflammatory responses to infection, whereas tissue-resident macrophages are responsible for tissue repair. Alternatively, inflammation and repair may be inter-dependent molecular programs, such that both recruited and resident cells have equivalent capacity to contribute. Repeated exposure to pathogenic challenge results in innate tolerance, which may also alter the contributions of discrete macrophage populations to inflammation or repair. In this study a village model of tissue resident and recruited macrophages was created using induced pluripotent stem cell-derived macrophages and peripheral blood monocyte-derived macrophages, respectively. Population responses to repeated exposure to lipopolysaccharide were assessed with single-cell RNA sequencing and donors demultiplexed with Vireo. A subset of genes escaped classical tolerance programs in the iPSC, but not monocyte-derived macrophages, and this was associated with differences in their proliferative capacity. This suggests that targeting the proliferative resident macrophages would be most effective to limit inflammatory signaling.

systems biology↗

bioRxiv2020

KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+ T cell differentiation.

Naive CD8+ T cell activation results in an autonomous program of cellular proliferation and differentiation. However, the mechanisms that underpin this process are unclear. Here we profiled genome-wide changes in chromatin accessibility, gene transcription and the deposition of a key chromatin modification (H3K27me3) early after naive CD8+ T cell activation. Rapid upregulation of the histone demethylase, KDM6B, prior to first cell division was required for initiating H3K27me3 removal at genes essential for subsequent T cell differentiation and proliferation. Inhibition of KDM6B-dependent H3K27me3 demethylation limited the magnitude of an effective primary virus-specific CD8+ T cell response and the formation of memory CD8+ T cell populations. Accordingly, we define the early spatio-temporal events underpinning early lineage-specific epigenetic reprogramming that is necessary for autonomous CD8+ T cell proliferation and differentiation.

immunology↗

bioRxiv2019

Xmas ESC: A new female embryonic stem cell system that reveals the BAF complex as a key regulator of the establishment of X chromosome inactivation

Although female pluripotency significantly differs to male, complications with in vitro culture of female embryonic stem cells (ESC) have severely limited the use and study of these cells. We report a replenishable female ESC system, Xmas, that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. We utilised our Xmas ESC system to screen for regulators of the female-specific process of X chromosome inactivation, revealing chromatin remodellers Smarcc1 and Smarca4 as key regulators of establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation.

cell biology↗

bioRxiv2019

CiiiDER: a new tool for predicting and analysing transcription factor binding sites

The availability of large amounts of high-throughput genomic, transcriptomic and epigenomic data has provided opportunity to understand regulation of the cellular transcriptome with an unprecedented level of detail. As a result, research has advanced from identifying gene expression patterns associated with particular conditions to elucidating signalling pathways that regulate expression. There are over 1,000 transcription factors (TFs) in vertebrates that play a role in this regulation. Determining which of these are likely to be controlling a set of genes can be assisted by computational prediction, utilising experimentally verified binding site motifs.\n\nHere we present CiiiDER, an integrated computational toolkit for transcription factor binding analysis, written in the Java programming language, to make it independent of computer operating system. It is operated through an intuitive graphical user interface with interactive, high-quality visual outputs, making it accessible to all researchers. CiiiDER predicts transcription factor binding sites (TFBSs) across regulatory regions of interest, such as promoters and enhancers derived from any species. It can perform an enrichment analysis to identify TFs that are significantly over- or under-represented in comparison to a bespoke background set and thereby elucidate pathways regulating sets of genes of pathophysiological importance.\n\nCiiiDER is available from www.ciiider.org.

bioinformatics↗

bioRxiv2018

Human IFNε: Spaciotemporal expression, hormone regulation and innate immunity in the female reproductive tract

Interferon epsilon (IFN{varepsilon}) plays an important role in regulating protective immunity in the female reproductive tract in mouse models; but the expression and regulation of this IFN{varepsilon} in the human FRT had not yet been characterised. Here we show that IFN{varepsilon} is selectively and highly expressed in the human FRT, a unique characteristic among the many types of IFN. IFN{varepsilon} has distinct expression patterns in upper compared with lower FRT where it is predominantly expressed in the basal layers of the stratified squamous epithelia. We demonstrate direct regulation of IFN{varepsilon} expression is suppressed by progesterone consistent with its inverse correlation with progesterone receptor expression, but only in the endometrium where its expression therefore fluctuates throughout the menstrual cycle. We show that IFN{varepsilon} regulates immunoregulatory IFN regulated genes (IRGs) in FRT epithelial cells. The characterisation of huIFN{varepsilon} expression in both the upper and the lower FRT epithelia and its protective properties make this IFN well placed to be an important player in mediating hormonal control of FRT immune response and susceptibility to FRT infection.\n\nSummaryBourke et al. characterise the novel type I interferon epsilon (IFN{varepsilon}), as the only IFN constitutively expressed throughout the human female reproductive tract (FRT), where it is hormonally regulated and modules IFN dependent FRT immunity.

immunology↗