Biology subjects

Jordan, S.

Publications and source records attributed to Jordan, S..

10 recordsLinked to original sources

bioRxiv2026

Single-cell profiling of innate and adaptive immune dysregulation in Long COVID

The COVID-19 pandemic has infected more than 778 million people worldwide. Roughly 7% of these patients progress to Long COVID (LC), suffering from persistent symptoms and cognitive impairment well past the acute stage. As the mechanisms of LC remain elusive, we utilized single-cell profiling (SCP) on 156,478 peripheral blood mononuclear cells (PBMCs) from 20 LC patients and 18 recovered controls (RC) to characterize the disease-associated immune dysregulation. Comparative analysis of LC and RC profiles revealed cellular heterogeneity along with differential abundances across B, T, and myeloid cell compartments. The focused analysis on the B-cell compartment showed that naive B cells in the LC exhibit elevated IL4R expression and BCR signaling, indicative of sustained antigen exposure and aberrant chronic activation. Concurrently, monocytes adopted heightened interferon signaling and enhanced migratory states, culminating into impaired myeloid differentiation. Furthermore, the T-cell compartment exhibited a functional dichotomy, maintaining sustained quiescence in the central memory compartment while displaying chronic exhaustion within effector memory populations. This dysregulation of effector immunity extended to the NK compartment, where terminally differentiated cells exhibited increased cytotoxicity yet compromised regulatory function, potentially contributing to poor viral clearance. Cellular communication analysis further supports this NK cell dysfunction that is likely driven by galectin and prostaglandin signaling involving monocytes and B cells. We stratified LC patients into mild and severe groups based on symptom and cognitive severity, identifying a distinct immune signature where severe disease is linked to chronic AP-1-mediated inflammation in NK cells and CD14+ monocytes. In contrast, patients with mild symptoms retain functionally competent NK cells with significantly lower exhaustion and apoptosis scores. Collectively, these insights into persistent immune remodeling provide a crucial framework for future biomarker discovery and the development of targeted therapeutic strategies. Abstract (Short)COVID-19 has affected >778 million worldwide, with [~]7% developing Long COVID (LC), characterized by persistent symptoms and cognitive impairment. The mechanisms of LC remain elusive; we utilized single-cell profiling on 156,478 peripheral blood mononuclear cells from LC and recovered controls. Comparative analysis revealed cellular heterogeneity and differential abundance across multiple immune compartments. B-cells exhibited hallmarks of sustained antigen exposure and aberrant activation. Concurrently, monocytes adopted heightened interferon signaling, enhanced migratory states, and impaired differentiation. T-cells exhibited chronic exhaustion within the effector memory populations. Dysregulated effector immunity extended to NK, with increased expression of cytotoxic genes yet compromised regulatory function, potentially contributing to viral clearance. LC patients with severe symptoms showed enhanced AP-1-mediated inflammation in NK cells and CD14+ monocytes, whereas mild cases had fitter NK cells with significantly lower exhaustion and apoptosis. Collectively, these insights provide a framework for biomarker discovery and the development of targeted LC therapeutic strategies.

genomics↗

bioRxiv2026

A Stepwise Thiol Dioxygenation Mechanism in Mercaptosuccinate Dioxygenase Revealed by A Combined Experimental and Computational Study

Thiol dioxygenases (TDOs) catalyze the incorporation of molecular oxygen into thiol metabolites and N-terminal cysteine residues of regulatory proteins, thereby playing critical roles in sulfur metabolism and oxygen sensing. Despite extensive study over the past two decades, the molecular basis for substrate recognition and the catalytic mechanism of TDOs remains controversial, owing to the scarcity of substrate-bound structures and direct evidence for catalytic intermediates. Herein, we present a comprehensive study of mercaptosuccinate dioxygenase (MSDO), a TDO originally identified in Variovorax paradoxus B4, using a combination of structural, biochemical, spectroscopic, and computational approaches. MSDO oxidizes both (S)- and (R)-mercaptosuccinate (MS) with similar Km values but exhibits approximately 2.5-fold higher turnover for the (S)-enantiomer. Crystal structures of MSDO reveal that both (S)- and (R)-MS coordinate the iron in a bidentate mode via their thiolate and proximal carboxylate groups, with the distal carboxylate adopting distinct orientations. Two active-site Arg residues recognize the substrate carboxylate groups and thereby stabilize a flexible C-terminal loop, underpinning a catalytic site gating mechanism in MSDO. EPR spectroscopy corroborates bidentate coordination, showing conversion of a high-spin {FeNO}7 complex to a low-spin species upon substrate binding. Time-resolved in crystallo reactions capture two key iron-bound intermediates, namely an unprecedented monooxygenated sulfenate and a dioxygenated sulfinate product. These structural snapshots are supported by DFT calculations that point to a stepwise oxygen atom transfer pathway. Computational analysis further accounts for the kinetic differences between the substrate enantiomers, as rationalized by structural comparisons, active-site geometry, and second coordination sphere interactions. Together, these results elucidate fundamental principles of TDO catalysis and advance our understanding of nonheme iron-dependent oxygen activation.

biochemistry↗

bioRxiv2025

Tankyrase inhibition demonstrates anti-fibrotic effects in preclinical pulmonary fibrosis models

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with limited treatment options. Although transforming growth factor beta 1 (TGFB1, TGF{beta}) is a key driver of fibrosis, additional signaling pathways, including wingless-type mammary tumor virus integration site (WNT)/{beta}-catenin and yes-associated protein 1 (YAP), contribute to IPF pathogenesis. Clinical data indicate that inhibition of TGF{beta} alone provides limited efficacy or is associated with toxicity, underscoring the need for alternative therapeutic approaches. Tankyrase (TNKS) 1 and 2 are post-translational regulators of WNT/{beta}-catenin and YAP signaling and therefore represent promising antifibrotic targets. OM-153, a potent and selective TNKS inhibitor, exhibits pharmacological properties suitable for preclinical development in IPF. MethodsPrimary normal human lung fibroblasts (NHLF), Scar-in-a-Jar assays, lung-on-a-chip models, and precision-cut lung slices (PCLS) from non-pulmonary fibrosis (non-PF) tissue were stimulated with an IPF-relevant cytokine cocktail (IPF-RC) designed to accurately recapitulate the pro-fibrotic environment and compared to TGF{beta}. These models, with bleomycin-challenged mice and PCLS from end-stage pulmonary fibrosis (PF) patients, were treated with OM-153. Fibrosis markers, extracellular matrix (ECM) components, and signaling pathway-specific gene expression or protein markers were assessed by real-time qRT-PCR, RNA sequencing, immunoblotting, ELISA, and immunofluorescence. ResultsOM-153 stabilized the direct TNKS targets axin 1 (AXIN1) and angiomotin-like 1 (AMOTL1), suppressed WNT/{beta}-catenin and YAP signaling. In parallel, it reduced profibrotic ECM expression across in vitro, in vivo, and ex vivo IPF models. ConclusionsSelective TNKS inhibition by OM-153 demonstrates broad antifibrotic activity in multiple preclinical models, supporting further development as a potential disease-modifying strategy for IPF. Shareable abstractOur findings show that the potent and selective TNKS inhibitor OM-153 suppresses WNT/{beta}-catenin and YAP signaling, reducing pro-fibrotic ECM expression in preclinical IPF models, supporting TNKS inhibition as a novel antifibrotic strategy.

cell biology↗

bioRxiv2025

The accessory type III secretion system effectors shape intestinal inflammatory infection outcomes

Injection of effectors via a type III secretion system (T3SS) is an infection strategy shared by various Gram-negative bacterial pathogens, many infecting mucosal surfaces. While individual T3SS effectors are well characterized, their network-level organization and the distinction between core and accessory effectors remain incompletely understood. Here, by systematically dissecting the T3SS effector network of the enteric mouse pathogen Citrobacter rodentium (CR) we identified a subset of 12 accessory effectors that, while dispensable for colonization, significantly alter infection outcomes. A strain lacking the accessory effectors (CRM12) remained virulent in susceptible mouse hosts yet resulted in reduced epithelial barrier damage, inflammation, and immune cell infiltration in resistant mice. Deep proteomic analysis specifically targeting CR-attached colonic epithelial cells revealed that, despite lacking 39% of its effector repertoire, infection with CRM12 results in similar changes to global protein expression as seen in mice infected with the wild-type strain, though key regulators of barrier integrity were differentially expressed. Using a host model with impaired barrier repair, we confirmed that accessory effectors shape infection outcomes without significantly impacting virulence. This study refines the concept of core and accessory effectors, providing a basis for further studies into effector-driven host adaptation.

microbiology↗

bioRxiv2024

Decellularized biohybrid nerve promotes motor axon projections

Developing nerve grafts with intact mesostructures, superior conductivity, minimal immunogenicity, and improved tissue integration is essential for the treatment and restoration of neurological dysfunctions. A key factor is promoting directed axon growth into the grafts. To achieve this, we developed biohybrid nerves using decellularized rat sciatic nerve modified by in situ polymerization of poly(3,4-ethylenedioxythiophene) (PEDOT). We compared nine biohybrid nerves with varying polymerization conditions and cycles, selecting the best candidate through material characterization. Our results showed that a 1:1 ratio of FeCl3 oxidant to ethylenedioxythiophene (EDOT) monomer, cycled twice, provided superior conductivity (>0.2 mS/cm), mechanical alignment, intact mesostructures, and high compatibility with cells and blood. To test the biohybrid nerves effectiveness in promoting motor axon growth, we used human Spinal Cord Spheroids (hSCSs) from HUES 3 Hb9:GFP cells, with motor axons labeled with green fluorescent protein (GFP). Seeding hSCS onto one end of the conduit allowed motor axon outgrowth into the biohybrid nerve. Our construct effectively promoted directed motor axon growth, which improved significantly after seeding the grafts with Schwann cells. This study presents a promising approach for reconstructing axonal tracts in humans.

bioengineering↗

bioRxiv2021

4D live-cell imaging of microgametogenesis in the human malaria parasite Plasmodium falciparum

Formation of gametes in the malaria parasite occurs in the midgut of the mosquito and is critical to onward parasite transmission. Transformation of the male gametocyte into microgametes, called microgametogenesis, is an explosive cellular event and one of the fastest eukaryotic DNA replication events known. The transformation of one microgametocyte into eight flagellated microgametes requires reorganisation of the parasite cytoskeleton, replication of the 22.9 Mb genome, axoneme formation and host erythrocyte egress, all of which occur simultaneously in <20 minutes. Whilst high-resolution imaging has been a powerful tool for defining stages of microgametogenesis, it has largely been limited to fixed parasite samples, given the speed of the process and parasite photosensitivity. Here, we have developed a live-cell fluorescence imaging workflow that captures the explosive dynamics of microgametogenesis in full. Using the most virulent human malaria parasite, Plasmodium falciparum, our live-cell approach combines three-dimensional imaging through time (4D imaging) and covers early microgametocyte development through to microgamete release. Combining live-cell stains for DNA, tubulin and the host erythrocyte membrane, 4D imaging enables definition of the positioning of newly replicated and segregated DNA. It also shows the microtubular cytoskeleton, location of newly formed basal bodies and elongation of axonemes, as well as behaviour of the erythrocyte membrane, including its specific perforation prior to microgamete egress. 4D imaging was additionally undertaken in the presence of known transmission-blocking inhibitors and the untested proteasomal inhibitor bortezomib. Here, for the first time we find that bortezomib inhibition results in a clear block of DNA replication, full axoneme nucleation and elongation. These data not only define a framework for understanding microgametogenesis in general but also suggest that the process is critically dependent on proteasomal activity, helping to identify potentially novel targets for transmission-blocking antimalarial drug development.

microbiology↗

bioRxiv2021

Sand dropseed (Sporobolus cryptandrus) - A new pest in Eurasian sand areas?

For the effective control of an invasive species, gathering as much information as possible on its ecology, establishment and persistence in the subjected communities is of utmost importance. We aimed to review the current distribution and characteristics of Sporobolus cryptandrus (sand dropseed), an invasive C4 grass species of North American origin recently discovered in Hungary. We aimed to provide information on (i) its current distribution paying special attention to its invasion in Eurasia; (ii) the characteristics of the invaded habitats in Central Europe; (iii) seed bank formation and germination characteristics, crucial factors in early establishment; and (iv) the effects of its increasing cover on vegetation composition. Finally, we aimed to (v) point out further research directions that could enable us to understand the invasion success of this potential invasive species. Field surveys uncovered large stands of the species in Central and Eastern Hungary with most of the locations in the former, especially the Kiskunsag region. The species invaded disturbed stands of dry and open sand grasslands, closed dune slack grasslands and it also penetrates into natural open sand grasslands from neighbouring disturbed habitats. Increasing cover of Sporobolus cryptandrus caused a decline in species richness and abundance of subordinate species both in the vegetation and seed banks, but a low density of Sporobolus cryptandrus can even have a weak positive effect on these characteristics. Viable seeds of Sporobolus were detected from all soil layers (2.5 cm layers measured from the surface to 10 cm in depth), which indicates that the species is able to form a persistent seed bank (1,114 to 3,077 seeds/m2 with increasing scores towards higher abundance of the species in vegetation). Germination of Sporobolus cryptandrus was negatively affected by both litter cover and 1 cm deep soil burial. To sum up, Sporobolus cryptandrus can be considered as a transformer invasive species, whose spread forms a high risk for dry sand and steppe grasslands in Eurasia. We can conclude that for the effective suppression of the species it is necessary: (i) to clarify the origin of the detected populations; (ii) to assess its competitive ability including its potential allelopathic effects; (iii) to assess its seed bank formation potential in habitats with different abiotic conditions; and (iv) to assess the possibility of its suppression by natural enemies and management techniques such as mowing or livestock grazing.

ecology↗

bioRxiv2021

Plasmodium falciparum protein Pfs16 is a target for transmission-blocking antimalarial drug development

Phenotypic cell-based screens are critical to the discovery of new antimalarial lead compounds. However, identification and validation of cellular targets of lead compounds is required following discovery in a phenotypic screen. We recently discovered a Plasmodium transmission-blocking N-((4-hydroxychroman-4-yl)methyl)-sulfonamide (N-4HCS) compound, DDD01035881, in a phenotypic screen. DDD01035881 and its potent derivatives have been shown to block Plasmodium male gamete formation (microgametogenesis) with nanomolar activity. Here, we synthesised a photoactivatable N-4HCS derivative, probe 2, to identify the N-4HCS cellular target. Using probe 2 in photo-affinity labelling coupled with mass spectrometry, we identified the 16 kDa Plasmodium falciparum parasitophorous vacuole membrane protein Pfs16 as the likely cellular target of the N-4HCS series. Further validating Pfs16 as the cellular target of the N-4HCS series, the Cellular Thermal Shift Assay (CETSA) confirmed DDD01035881 stabilised Pfs16 in lysate from activated mature gametocytes. Additionally, photo-affinity labelling combined with in-gel fluorescence and immunoblot analysis confirmed the N-4HCS series interacted with Pfs16. High-resolution, widefield fluorescence and electron microscopy of N-4HCS-inhibited parasites was found to result in a cell morphology entirely consistent with targeted gene disruption of Pfs16. Taken together, these data strongly implicate Pfs16 as the target of DDD01035881 and establish the N-4HCS scaffold family as a powerful starting point from which future transmission-blocking antimalarials can be developed.

microbiology↗

bioRxiv2020

Identification and characterisation of a phospholipid scramblase in the malaria parasite Plasmodium falciparum

Recent studies highlight the emerging role of lipids as important messengers in malaria parasite biology. In an attempt to identify interacting proteins and regulators of these dynamic and versatile molecules, we hypothesised the involvement of phospholipid translocases and their substrates in the infection of the host erythrocyte by the malaria parasite Plasmodium spp. Here, using a data base mining approach, we have identified a putative phospholipid (PL) scramblase in P. falciparum (PfPLSCR) that is conserved across the genus and in closely related unicellular algae. By reconstituting recombinant PfPLSCR into liposomes, we demonstrate metal ion dependent PL translocase activity and substrate preference, confirming PfPLSCR as a bona fide scramblase. We confirm that PfPLSCR is expressed during asexual and sexual parasite development, localising to different membranous compartments of the parasite throughout the intra-erythrocytic life cycle. Two different gene knockout approaches, however, suggest that PfPLSCR is not essential for erythrocyte invasion and asexual parasite development, pointing towards a possible role in other stages of the parasite life cycle.

microbiology↗

bioRxiv2019

Dietary intake regulates the circulating inflammatory monocyte pool

Caloric restriction is known to improve inflammatory and autoimmune diseases. However, the mechanisms by which reduced caloric intake modulates inflammation are poorly understood. Here we show that short-term fasting reduced monocyte metabolic and inflammatory activity and drastically reduced the number of circulating monocytes. Regulation of peripheral monocyte numbers was dependent on dietary glucose and protein levels. Specifically, we found that activation of the low-energy sensor 5-AMP-activated protein kinase (AMPK) in hepatocytes and suppression of systemic CCL2 production by peroxisome proliferator-activator receptor alpha (PPAR) reduced monocyte mobilization from the bone marrow. Importantly, while caloric restriction improves chronic inflammatory diseases, fasting did not compromise monocyte emergency mobilization during acute infectious inflammation and tissue repair. These results reveal that caloric intake and liver energy sensors dictate the blood and tissue immune tone and link dietary habits to inflammatory disease outcome.\n\nHighlightsO_LIFasting reduces the numbers of peripheral pro-inflammatory monocytes in healthy humans and mice.\nC_LIO_LIA hepatic AMPK-PPAR energy-sensing axis controls homeostatic monocyte numbers via regulation of steady-state CCL2 production.\nC_LIO_LIFasting reduces monocyte metabolic and inflammatory activity.\nC_LIO_LIFasting improves chronic inflammatory diseases but does not compromise monocyte emergency mobilization during acute infectious inflammation and tissue repair.\nC_LI

immunology↗