Biology subjects

Clark, A. R.

Publications and source records attributed to Clark, A. R..

10 recordsLinked to original sources

bioRxiv2026

ER shaping proteins guide spindle elongation and division during rapid cleavage mitoses

The ER is a complex network of membranes that inhabits much of the cytoplasm of cells - however, this network undergoes a massive condensation and rapid remodeling during cell division. In Drosophila cleavage divisions, this results in a tight association of the ER with centrosomes and mitotic spindle poles. Previous work has shown that this relationship between the ER and centrosomes must be finely tuned to enable successful spindle elongation, and that overaccumulation of the ER in these stages can result in failed centrosome maturation. During interphase, the ER exists in tubular and sheet-like arrangements, with a variety of "shaping" proteins enforcing these topologies. Here, we examine the contributions of these ER shaping proteins to the rapid changes that occur during cleavage mitoses in the Drosophila embryo. A screen of ER shaping proteins revealed that disruption of Reep-family proteins leads to mitotic failures at characteristic cleavage stages. Compromising ReepA, the Drosophila ortholog of the Reep1-4 subfamily, had a lesser impact on early embryonic mitoses. However, ReepB (the ortholog of the Reep5-6 subfamily) disruption, significantly affects ER mitotic coat morphologies, resulting in a frilled ER phenotype and a reduction of ER adherence to the spindle space accompanied by division failures. Overexpressing ReepA does not rescue ReepB mitotic or ER morphology defects and instead introduces local condensates of abnormal ER structures. These data suggest that dedicated Reep proteins guide ER mitotic properties at specific early developmental stages. Using a cell-based in vitro analysis of Drosophila Reeps, we identify differential "tubulating" properties of ReepA and ReepB. Together these data suggest that the minutes-scale ER remodeling required for early mitoses is governed by shaping proteins, and that ReepB family members are especially important in some of the most rapid cleavage divisions that occur in early embryo.

cell biology↗

bioRxiv2026

A Computational Functional Tissue Unit of the Human Myometrium for In Silico Study of Gestational Excitability and Pathophysiology

The human myometrium undergoes a dramatic transformation during pregnancy, shifting from quiescence to highly synchronised contractility. Understanding this transition is crucial for addressing pathologies such as preterm labour and dystocia (ineffective labour). We present a multi-scale Functional Tissue Unit (FTU) model allowing us to investigate how tissue-level excitability emerges from single-cell electrophysiology. We propose a heterogeneity-driven selection mechanism, wherein a sub-population of cells with high intrinsic excitability dynamically emerges as pace-makers. This active process complements passive depolarisation by interstitial cells, allowing spontaneous excitation to arise without a fixed anatomical pacemaker. Stochastic simulations produced an average burst frequency of 0.047 Hz ({approx}2.8 bursts per minute), closely consistent with clinical measurements of 2-3 contractions per minute during active labour, and demonstrated that this function is robust to spatial topological changes. Furthermore, implementation of inflammation-induced remodelling simulations successfully linked molecular-level changes to a preterm labour phenotype. This model provides a platform for investigating uterine contractility and serves as a component for future whole-organ Physiome models.

bioengineering↗

bioRxiv2025

Dexamethasone inhibits the LPS-induced activation of hypoxia-inducible factor 1 alpha (HIF-1α) in macrophages independently of the DUSP1-p38-TTP-HIF-1α regulatory axis.

The oxygen-sensitive transcription factor HIF-1 (hypoxia-inducible factor 1) is a master regulator of cellular and organism-level adaptations to decreasing oxygen availability. Under conditions of oxygen sufficiency HIF-1 is constitutively produced and degraded. In response to hypoxia, the degradation pathway is inhibited and HIF-1 protein accumulates via mechanisms that are now well understood. Additional signals combine with the oxygen-sensitive protein degradation pathway to modulate the expression and/or activity of HIF-1. In the context of the immune system, HIF-1 can be activated under normoxic conditions by a variety of stimuli, including the pro-inflammatory agonist lipopolysaccharide. Here we use a variety of genetic and pharmacological approaches to reveal that lipopolysaccharide-induced HIF-1 accumulation in primary macrophages is dependent on mitogen-activated protein kinase p38. This response is not dependent on modulation of HIF-1 protein stability: instead, it involves the phosphorylation and inactivation of tristetraprolin, an mRNA destabilizing protein that targets Hif1a mRNA for degradation. We previously reported that the glucocorticoid dexamethasone inhibits lipopolysaccharide-induced HIF-1 accumulation and metabolic reprograming in primary macrophages. Here we tested and disproved the hypothesis that dexamethasone prevents HIF-1 accumulation by inducing expression of dual specificity phosphatase 1 and thereby inhibiting p38 function. Hence two novel mechanisms critically regulate HIF-1 activation in lipopolysaccharide-treated macrophages: a p38-dependent mechanism that operates at the post-transcriptional level to control Hif1a mRNA expression, and a glucocorticoid-sensitive mechanism that operates at the post-translational level to control HIF-1 protein stability. Combined targeting of these two mechanisms may exert therapeutic effects in contexts where HIF-1 contributes to immune-mediated inflammatory pathology.

immunology↗

bioRxiv2024

Internal unwinding mechanism of a replicative helicase

Ring-shaped hexameric helicases are nucleotide hydrolases that unwind double-stranded DNA into single strands, a necessary step in DNA replication. Two main questions are critical to understanding their function: the location of DNA strand separation within the helicase, and the precise dynamic linkage between nucleotide hydrolysis and DNA translocation. We explore these questions by employing cryo-EM to visualize the translocation mechanics of a AAA+ helicase, the SV40 Large Tumor Antigen (LTag), on forked DNA. We find the DNA fork nexus is positioned deep within the core helicase domain, with each DNA-binding loop from the six subunits securing the tracking strand by forming a paired staircase spiral that substitutes the passive strand. This structure forges an internal separation wedge, channeling the passive strand through a gap in the subunit C-tiers at the back of the helicase. Via cryo-EM continuous heterogeneity analysis we capture, and exhaustively model, a seamless spectrum of conformations of translocating LTag at high resolution. ATP hydrolysis at the tightest inter-subunit interface operates like an entropy switch, triggering coordinated rigid-body rotations of the subunit C-tiers and DNA-binding loops, resulting in directional escorting of the tracking strand through the central channel, concomitantly setting preparatory steps for cycle restart. Overall, we demonstrate a dynamic model for hydrolysis-coupled translocation and DNA unwinding by a model helicase active in replication, with implications for origin unwinding. High structural conservation of core helicase regions suggests this mechanism is applicable to hexameric helicases across domains.

biophysics↗

bioRxiv2024

Discrete and conserved inflammatory signatures drive thrombosis in different organs after Salmonella infection

Inflammation-induced thrombosis is a common consequence of bacterial and viral infections, such as those caused by Salmonella Typhimurium (STm) and SARS-CoV-2. The identification of multi-organ thrombosis and the chronological differences in its induction and resolution raises significant challenges for successfully targeting multi-organ infection-associated thrombosis. Here, we identified specific pathways and effector cells driving thrombosis in the spleen and liver following STm infection. Thrombosis in the spleen is independent of IFN-{gamma} or the platelet C-type lectin-like receptor CLEC-2, while both molecules were previously identified as key drivers of thrombosis in the liver. Furthermore, we identified platelets, monocytes, and neutrophils as core constituents of thrombi in both organs. Depleting neutrophils or monocytic cells independently abrogated thrombus formation. Nevertheless, blocking TNF, which is expressed by both myeloid cell types, diminished both thrombosis and inflammation which correlates with reduced endothelial expression of E-selectin and leukocyte infiltration. Moreover, tissue factor and P-selectin glycoprotein ligand 1 inhibition impair thrombosis in both spleen and liver, identifying multiple common checkpoints to target multi-organ thrombosis. Therefore, organ-specific, and broad mechanisms driving thrombosis potentially allow tailored treatments based on the clinical need and to define the most adequate strategy to target both thrombosis and inflammation associated with systemic infections.

immunology↗

bioRxiv2023

The glucocorticoid dexamethasone inhibits HIF-1alpha stabilisation and metabolic reprogramming in lipopolysaccharide-stimulated primary macrophages.

Synthetic glucocorticoids are used to treat many chronic and acute inflammatory conditions. Frequent adverse effects of prolonged exposure to glucocorticoids include disturbances of glucose homeostasis, caused by changes of glucose traffic and metabolism in muscle, liver and adipose tissues. Macrophages are important targets for the anti-inflammatory actions of glucocorticoids. These cells rely on aerobic glycolysis to support various pro-inflammatory and antimicrobial functions. Employing a potent pro-inflammatory stimulus in two commonly-used model systems (mouse bone marrow-derived and human monocyte-derived macrophages), we showed that the synthetic glucocorticoid dexamethasone inhibited lipopolysaccharide-mediated activation of the hypoxia- inducible transcription factor HIF-1, a critical driver of glycolysis. In both cell types, dexamethasone-mediated inhibition of HIF-1 reduced the expression of the glucose transporter GLUT1, which imports glucose to fuel aerobic glycolysis. Aside from this conserved response, other metabolic effects of lipopolysaccharide and dexamethasone differed between human and mouse macrophages. These findings suggest that glucocorticoids exert anti-inflammatory effects by impairing HIF-1-dependent glucose uptake in activated macrophages. Furthermore, harmful and beneficial (anti-inflammatory) effects of glucocorticoids may have a shared mechanistic basis, depending on alteration of glucose utilisation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/558626v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@4edbb5org.highwire.dtl.DTLVardef@13a5ab2org.highwire.dtl.DTLVardef@18776borg.highwire.dtl.DTLVardef@4816fa_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

The glucocorticoid dexamethasone impairs the expression of anti-viral mediators in activated macrophages by inhibiting both expression and function of interferon beta.

Glucocorticoids potently inhibit expression of many inflammatory mediators, and have been very widely used to treat both acute and chronic inflammatory diseases for more than seventy years. However, they can have several unwanted effects, amongst which immunosuppression is one of the most common. Here we investigated effects of the synthetic glucocorticoid dexamethasone on the responses of primary mouse bone marrow-derived macrophages to the pro-inflammatory agonist lipopolysaccharide (LPS). At the mRNA level, dexamethasone inhibited the LPS-induced expression of more than 100 genes that are involved in cell-intrinsic defence against viral pathogens. Expression of most of the corresponding proteins was also reduced by dexamethasone. This antiviral disarmament occurred at two distinct levels. First, dexamethasone strongly and dose-dependently inhibited the expression of the type I interferon IFN{beta} by LPS-activated macrophages. IFN{beta} mediates an autocrine positive feedback loop in LPS-treated macrophages, promoting the expression of antiviral genes and other interferon-stimulated genes. Hence reduction of IFN{beta} expression contributes to impaired expression of antiviral genes. Dexamethasone also acted downstream of IFN{beta} to inhibit expression of a subset of interferon-regulated genes. We tested a number of hypotheses based on previous publications, but found that no single mechanism could account for more than a small fraction of the broad suppressive impact of dexamethasone on macrophage type I interferon signaling, underlining the complexity of this pathway. Preliminary experiments indicated that dexamethasone exerted similar inhibitory effects on primary human monocyte-derived or alveolar macrophages.

immunology↗

bioRxiv2022

Multi-scale modelling of shear stress on the syncytiotrophoblast: Could maternal blood flow impact placental function across gestation?

The surface of the placenta is lined by a single multinucleated cell, the syncytiotrophoblast, which forms a functional barrier between maternal and fetal blood in pregnancy. The placenta plays a critical role in healthy fetal development and over the course of pregnancy forms a complex branching tree-like structure which bathes in maternal blood and serves a vital exchange function. It has been suggested that the structure of the placenta may evolve, in part, under the influence of the shear stress exerted by maternal blood flow over its surface, with the syncytiotrophoblast having a role in mechanosensing. However, data describing the mechano-sensitive nature of this cell, particularly in early gestation, is lacking. In this study we show that the syncytiotrophoblast expresses six proteins that have been related to shear sensing, and this expression is higher in the first trimester than at term. This suggests shear on the sycytiotrophoblast as an important factor influencing placental morphogenesis early in pregnancy. We then predict shear stress felt by the syncytiotrophoblast in first trimester and term placental tissue using a combination of porous medium modelling and explicit simulations of blood flow in realistic geometries derived from microCT imaging. Our models predict that typical shear stress on first-trimester tissue is higher than at term, supporting the feasibility of this mechanical stimulus as an important driver of healthy placental development.

bioengineering↗

bioRxiv2022

Accelerated cognitive decline in obese mouse model of Alzheimer's disease is linked to sialic acid-driven immune deregulation

Systemic immunity supports healthy brain homeostasis. Accordingly, conditions causing systemic immune deregulation may accelerate onset of neurodegeneration in predisposed individuals. Here we show that, in the 5xFAD mouse model of Alzheimers disease (AD), high-fat diet-induced obesity accelerated cognitive decline, which was associated with immune deviations comprising increased splenic frequencies of exhausted CD4+ T effector memory cells and CD4+FOXP3+ regulatory T cells (Tregs). Non-targeted plasma metabolomics identified N-acetylneuraminic acid (NANA), the predominant sialic acid, as the major obesity-induced metabolite in 5xFAD mice, the levels of which directly correlated with Tregs abundance and inversely correlated with cognitive performance. Visceral adipose tissue macrophages were identified by sNuc-Seq as one potential source of NANA. Exposure to NANA led to immune deregulation in middle-aged wild-type mice, and ex vivo in human T cells. Our study identified diet-induced immune deregulation, potentially via sialic acid, as a previously unrecognized link between obesity and AD.

neuroscience↗

bioRxiv2020

Single cell transcriptomics reveal disrupted kidney filter cell-cell interactions after early and selective podocyte injury

The health of the kidney filtration barrier requires communication between podocytes, endothelial cells and mesangial cells. Disruption of these cell-cell interactions is thought to contribute to disease progression in chronic kidney diseases (CKD). We recently demonstrated that podocyte ablation via doxycycline-inducible deletion of an essential endogenous molecule, CTCF (iCTCFpod-/-), is sufficient to drive progressive CKD. However, the earliest events connecting podocyte injury to disrupted intercellular communication within the kidney filter remain unclear. Here we performed single-cell RNA sequencing of kidney tissue from iCTCFpod-/- mice after one week of doxycycline induction to generate a map of the earliest transcriptional effects of podocyte injury on cell-cell interactions at single cell resolution. A subset of podocytes showed the earliest signs of injury due to disrupted gene programs for cytoskeletal regulation and mitochondrial function. Surviving podocytes upregulated Col4a5, causing reactive changes in integrin expression in endothelial populations and mesangial cells. Intercellular interaction analysis revealed several receptor-ligand-target gene programs as drivers of endothelial cell injury and abnormal matrix deposition. This analysis reveals the earliest disruptive changes within the kidney filter, pointing to new, actionable targets within a therapeutic window that may allow us to maximize the success of much needed therapeutic interventions for CKD.

cell biology↗