Biology subjects

Weber, C.

Publications and source records attributed to Weber, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Pathogenicity of autoreactive TH17 cells is modulated by the TRPM7 kinase

The melastatin-like transient receptor potential channel, TRPM7, is crucial for signaling in leukocytes. It harbors a channel domain, permeable to divalent cations as well as a serine/threonine -kinase, phosphorylating inter alia SMAD2. TRPM7 kinase activity is essential for the differentiation of non-pathogenic T helper 17 (TH17) cells as well as for T cell colonization and alloreactivity in the gut. As pathogenic TH17 (pTH17) cells drive autoimmune diseases, we studied TRPM7 kinase involvement in pTH17 polarization and function as well as in the development of multiple sclerosis (MS), using human T cells and established murine experimental autoimmune encephalomyelitis (EAE) models. Our results reveal an elevated TRPM7 activity in T effector cells derived from the cerebrospinal fluid (CSF) of MS patients, in line with higher functional TRPM7 expression on human TH17 cells. Utilizing a mouse line with disrupted kinase activity (Trpm7R/R), we uncovered both impaired differentiation of pathogenic TH17 cells as well as a significantly milder course of TH17-mediated transfer EAE in Trpm7R/R mice compared to Trpm7+/+ controls. In the CNS of Trpm7R/R mice, the number of FOXP3+ T cells (Tregs) was increased, while fewer TH17 cells infiltrated the CNS due to a migration defect of transferred pTH17 cells in the Trpm7R/R hosts and a failure to reactivate in the intestine, due to reduced MHCII signaling. Thus, inactivation of TRPM7 kinase may represent a promising therapeutic strategy targeting both differentiation and reactivation of pTH17 cells while preserving Tregs function and thereby dampening CNS inflammation in MS.

immunology↗

bioRxiv2026

Mapping excitatory synaptic plasticity evoked by single-dose psilocybin in mice

A single dose of psilocybin can induce long-lasting antidepressant effects. The neurobiological mechanisms underlying such sustained antidepressant effect remain insufficiently understood, particularly at the level of synaptic function and drug-target specificity. Here, we aimed to delineate single-dose psilocybin-induced excitatory synaptic plasticity. Synaptic plasticity was assessed by whole-cell patch-clamp recording of excitatory synaptic transmission 24 h after treating mice with single-dose psilocybin. We correlated the recordings with transcriptomics data and used a conditional single-vector CRISPR/SaCas9-dependent knock-out strategy to validate the role of the 5-HT2A receptor. Psilocybin selectively increased the frequency of miniature excitatory postsynaptic currents in specific cortical sub-regions and in the amygdala. Frequency correlated with the expression levels of psilocin-targeted serotonin receptors, when expression heterogeneity between cortical subregions and along the anterior-posterior axis was accounted for. Post-synaptic Htr2a knock-out in the insular/orbitofrontal cortex precluded psilocybin-induced 24-h plasticity. These findings demonstrate that lasting psilocybin-induced effects on excitatory synaptic transmission manifest with brain-region specificity, likely reflecting a functional consequence of synapse formation. This work establishes a foundation for a circuit-specific, mechanistic understanding of functional aspects of psilocybin-induced neuroplasticity.

neuroscience↗

bioRxiv2026

Direct interaction between miR-210-5p and HIF-1α regulates HIF-dependent transcription

Hypoxia-inducible factors (HIFs) coordinate cellular adaptation to oxygen deprivation, yet whether hypoxia-induced microRNAs directly regulate HIF-dependent transcription remains unknown. Here, we identify miR-210-5p as a nuclear hypoxamiR that directly binds HIF-1 and enhances HIF-dependent transcription. Hypoxia induced rapid, HIF-dependent nuclear accumulation of mature miR-210-5p across multiple cell types. Biophysical analyses demonstrated direct interaction between miR-210-5p and the HIF-1 bHLH-PAS domain, while mutational studies identified a conserved 5'motif required for HIF-1 binding but dispensable for repression of the canonical cytoplasmic target ISCU. Functionally, transcriptional activity closely correlated with HIF-1-binding affinity, as binding-deficient variants failed to activate HIF reporters or endogenous target genes. Although AGO2 contributed to hypoxic transcriptional responses, miR-210-5p interacted directly with HIF-1 independently of AGO2. In ischemic myocardium, nuclear enrichment of miR-210-5p and its proximity to HIF-1 support the physiological relevance of this mechanism, revealing a previously unrecognized RNA-mediated layer of HIF transcriptional regulation.

molecular biology↗

bioRxiv2026

Exosome-mediated LNA anti-miR delivery achieves potent miR-21 inhibition and PTEN restoration in podocytes.

BackgroundPodocyte injury and loss are central drivers of chronic kidney disease (CKD) progression and are involved in the majority of glomerular diseases. Among the molecular pathways implicated in podocyte dysfunction, microRNA-21 (miR-21) is consistently upregulated during glomerular injury and suppresses protective target genes including PTEN. Although anti-miR-21 approaches have shown high efficacy in preclinical models for Alport Syndrome and diabetic nephropathy, clinical translation of free anti-miR-21 oligonucleotides remains challenging, potentially reflecting limited glomerular and podocyte target engagement. Here, we show that an exosome-mediated delivery of an LNA-miR-21 inhibitor results in a higher intracellular uptake, leading to functional miR-21 inhibition and PTEN restoration in podocytes. MethodsExosomes were isolated from immortalized murine podocytes SVI and were directly loaded with fluorescently-labeled LNA anti-miR-21 (LNA-21) and anti-miR-Ctrl. Exosome integrity was assessed by transmission electron microscopy, dynamic light scattering and Western blot analysis of CD9 and TSG101. Uptake efficiency and intracellular delivery were analyzed by confocal laser-scanning microscopy, time-series imaging (2-48 h) and (imaging) flow cytometry. Functional efficacy was evaluated by TaqMan RT-qPCR and PTEN protein expression in differentiated SVI podocytes, primary murine podocytes and puromycin aminonucleoside (PAN)-injured primary glomeruli. ResultsExosome number, morphology and marker expression remained unchanged after direct LNA-miR-21 loading. Time-series imaging demonstrated progressive intracellular accumulation of exosome-delivered LNA-21 cargo from 2 to 48 h, whereas free LNA-21 showed no detectable uptake. Flow cytometry and imaging flow cytometry confirmed an efficient (76.6%) intracellular delivery exclusively via exosomes. Exosome-mediated LNA-21 delivery induced a robust miR-21 suppression, resulting in an 99% reduction in immortalized podocytes, a 97% reduction in primary podocytes and a 97% reduction in PAN-injured glomeruli (all p < 0.05). In contrast, free LNA-21 did not achieve significant suppression in all investigated models. To evaluate the functional consequences of miR-21 inhibition, we examined PTEN expression, as PTEN is a known direct target of miR-21. Notably, restoration of PTEN protein expression was observed only following exosome-mediated LNA delivery which was confirmed by Western blot and immunofluorescence, suggesting efficient functional inhibition of miR-21 in podocytes. Transfection of scrambled controls confirmed sequence specificity throughout. ConclusionThese findings demonstrate that exosome-mediated LNA delivery overcomes the limited uptake of free inhibitor oligonucleotides in podocytes and enables functional inhibition of miR-21 across multiple experimental systems. These data provide mechanistic proof-of-principle for exosome-based miR inhibitor delivery as a potential strategy to improve podocyte-targeted therapies in CKD.

cell biology↗

bioRxiv2026

Exploring lipid nanoparticle design spaces using self-regulating microfluidic machines and multiplexed in vivo biodistribution

Delivering therapeutic mRNA relies on lipid nanoparticles (LNPs). Finding optimal process parameters for new lipid combinations in LNP formulations remains a challenge. In our work, we used an automated, self-regulating microfluidic platform that actively changes process parameters to tune LNP formulations for preset, desired quality standards. We tested new LNPs by swapping poly(ethylene glycol) (PEG) lipopolymers for alternatives based on poly(2-methyl-2-oxazoline) (PMeOx) and poly(2-ethyl-2-oxazoline) (PEtOx). For each lipopolymer variant, the platform independently identified optimal production conditions in four or fewer iterative cycles, yielding particles of the preset size and high mRNA encapsulation. Small-angle X-ray scattering revealed that smaller LNPs modified with PEtOx had more structural surface variety and higher mRNA loading efficiency. When multiplexing these formulations in mice, the PEtOx-containing LNPs accumulated more in bone marrow compared to those with PEG, indicating trends that the chemistry of the lipopolymer affects the biodistribution of the resulting LNPs. By combining automated formulation and in vivo multiplexed testing, our approach provides a practical way to rapidly plan, formulate, and evaluate large pharmaceutical design spaces, to select excipients and process parameters yielding optimal biological performance of LNPs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/729611v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1a08b68org.highwire.dtl.DTLVardef@120724corg.highwire.dtl.DTLVardef@12fed98org.highwire.dtl.DTLVardef@197aa41_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Expanding the genetic code with diverse backbone structures across diverse sequence contexts

Expanding the genetic code to enable the selective and specific incorporation of non-canonical monomers (ncMs), beyond -L amino acids with variant sidechains, is a key outstanding challenge. Here we discover orthogonal aminoacyl-tRNA synthetases that selectively and specifically acylate their cognate orthogonal tRNA in vivo with eleven new ncMs spanning five different chemical classes: ,-disubstituted-amino acids, malonic acids, carboxylic acids, {beta}2-amino acids and N-cyclic amino acids. We demonstrate that co-translational incorporation of ,-disubstituted-amino acids, {beta}2-amino acids, {beta}3-amino acids and N-cyclic amino acids is strongly dependent on the codons either side of the codon used to direct ncM incorporation, with several ncMs incorporated at less than 1% of sequence contexts. We evolve orthogonal tRNAs that enable the incorporation of previously unincorporated ncMs, enable the incorporation of ncMs at >95% of sequence contexts and, increase the incorporation efficiency at challenging sequence contexts up to 40-fold. We demonstrate the encoded cellular synthesis of proteins and macrocycles containing ncMs and, explicitly demonstrate that our evolved tRNAs provide direct access to a wider range of genetically encoded macrocyclic sequences containing ncMs. Our results provide a foundation for composing, discovering and manufacturing proteins and peptides with functions augmented by ncMs.

synthetic biology↗

bioRxiv2026

Minimal-invasive myocardial infarction model reproduces patient immune responses and reveals a pathogenic role for immature neutrophils

Myocardial infarction (MI) triggers a systemic neutrophil response, yet the roles of distinct neutrophil subsets in cardiac remodeling remain unclear. Studying this requires murine models that accurately mirror human neutrophil dynamics. Here, we show that a minimally invasive intact-chest MI model is more pathophysiologically relevant than the standard open-chest approach for investigating post-MI immune responses. In the open-chest model, surgical trauma disrupts bone marrow homeostasis, releases large numbers of immature neutrophils, and masks MI-specific immune mechanisms. In contrast, the intact-chest model preserves bone marrow integrity and induces only a modest rise in circulating immature neutrophils, closely reflecting MI patient profiles. We further demonstrate that accumulation of immature neutrophils in the infarcted heart exacerbates cardiac dysfunction. Beyond neutrophils, the overall cardiac immune landscape differs markedly between both models. Collectively, our findings establish the intact-chest model as superior for studying post-MI inflammation and reveal immature neutrophils as mediators of adverse cardiac remodeling.

immunology↗

bioRxiv2026

IMAGENE: Single-cell association of live cell imaging and gene expression profiles of non-adherent cells through photoactivatable adhesives

Live cell imaging is uniquely placed to study cell behavior as it preserves spatial context and enables non-destructive observations over time. Integrating live cell imaging and molecular phenotypes with single-cell resolution is key to uncovering the relationship between the behavioral and morphological signatures of cells, and their molecular states. Non-adherent cells - as are most immune cells - however, present unique challenges in linking live cell imaging and fixed cell assays with single-cell resolution due to the difficulty of identifying individual cells across experimental modalities. To overcome this issue, we developed IMAGENE, an experimental and computational pipeline that leverages previously reported photoactivatable biocompatible adhesive material (PA-BAM) coatings for on-the-fly cell immobilization. We demonstrate the IMAGENE experimental and computational pipeline by generating a dataset of label-free time-lapse videos of primary human naive CD8+ T cells following 24 hours of polyclonal stimulation. Individual cells, including highly motile cells, can be matched to expression profiles of genes of interest obtained through KrakenFISH, a modified version of the previously reported autoFISH setup for automated, single-molecule fluorescence in situ hybridization (smFISH) experiments that supports sample parallelization. We use this data to train explainable machine learning models that predict expression levels of individual genes, with variable performance, from hand-crafted dynamic and spatial features obtained from live cell imaging.

bioengineering↗

bioRxiv2026

Cardiorenal and hepatic dysfunctions underlie metabolic alterations in the spinocerebellar ataxia type 7 mice

Spinocerebellar ataxia type 7 (SCA7) is a polyglutamine expansion disorder characterized by progressive cerebellar and retinal degeneration leading to ataxia and blindness. While mutant ATXN7 is ubiquitously expressed, most studies have focused on neurological symptoms, and peripheral contributions to pathology remain poorly understood. Here, we investigated systemic abnormalities in SCA7140Q/5Q knock-in mice, a model of early-onset disease. Using longitudinal metabolic profiling, ultrasound imaging, and histopathology, we identified early and progressive dysfunction of the kidney, liver, and heart. Renal impairment was marked by uremia, polyuria with abnormal calcium and glucose excretion, tubular epithelial cell loss, and podocyte dedifferentiation, including the reappearance of primary cilia and pedicel effacement. Hepatic alterations included dysregulated lipid metabolism, elevated bilirubin, and reduced iron levels, contributing to anemia. Cardiac dysfunction manifested as reduced stroke volume as early as 11 weeks, suggesting a cardiorenal syndrome. Together, these organ-specific changes resulted in systemic metabolic disturbances such as dyslipidemia, iron deficiency anemia, thrombocytosis, and chronic inflammation, detectable before the onset of motor incoordination. Our findings demonstrate that peripheral organ dysfunction is an early and integral feature of SCA7 pathogenesis, with renal and cardiac impairments emerging prior to neurological decline. These results highlight the value of systemic biomarkers for disease monitoring and suggest that targeting peripheral pathology may provide therapeutic benefit. More broadly, they underscore the need to view SCA7 not solely as a neurodegenerative disorder but as a multi-organ disease.

pathology↗

bioRxiv2025

Neural CXCR4 contributes to neuroimmune modulation of atherosclerosis in a cardio-metabolic Ldlr-/- mouse model

BackgroundAtherosclerosis is a chronic inflammatory disease characterized by metabolic and immune dysregulation. Emerging evidence suggests that specific central nervous system (CNS) regions modulate its progression via neuroimmune cardiovascular interfaces (NICIs). While the C-X-C motif chemokine receptor 4 (CXCR4) is known to participate in atherogenesis by regulating immune cell dynamics and vascular wall responses, the role of neural CXCR4 in atherosclerotic plaque formation remains unclear. MethodsWe generated a Nestin-Cre-mediated conditional Cxcr4 knockout mouse model on a low-density lipoprotein receptor-deficient (Ldlr-/-) background and fed these mice a western diet (WD) for up to 12 weeks to induce atherosclerosis. To evaluate the impact of neural CXCR4 function, we quantified atherosclerotic plaque burden, systemic metabolic parameters and circulating immune cell profiles, comparing neural Cxcr4-deficient mice with corresponding genetic controls. Spatial transcriptomics and RNAscope were employed to map Cxcr4 mRNA and its non-canonical ligand macrophage migration inhibitory factor (Mif) mRNA in neuroimmune-regulatory brain regions, and to assess diet-induced expression changes in relation to neuroinflammatory responses. ResultsNeural conditional deletion of Cxcr4 in Ldlr-/- mice significantly reduced atherosclerotic plaque formation in the aortic arch and aorta, without affecting body weight, lipid levels, glucose tolerance, or circulating immune cells. Cxcr4 gene expression was found to be uniformly low across hypothalamic subregions implicated in neuroimmune regulation of systemic inflammation and atherogenesis. Importantly, WD feeding did not modify this consistently low expression in male Ldlr-/- mice. In contrast, Mif mRNA expression was significantly upregulated in the PVN after 5-day WD feeding, but not after 8 weeks. Exploratory spatial transcriptomic analysis of PVN-containing coronal brain sections from male Ldlr-/- mice suggested that 5-day WD exposure is associated with MIF-CXCR4 signaling and downstream neuroinflammatory pathways in the PVN. ConclusionsThis study identifies neural CXCR4 as a component of neuroimmune modulation in atherosclerosis, exerting its effect independently of systemic metabolic or inflammatory changes. Short-term WD exposure activated gene expression of the CXCR4 ligand Mif in the PVN, pointing to a neuroimmune axis that may promote vascular inflammation and atherosclerotic plaque development. These findings establish a link between CNS CXCR4 and vascular disease and suggest that MIF-CXCR4-dependent neuroimmune pathways may play a role in cardiometabolic risk. Trial registrationNot applicable.

immunology↗

bioRxiv2025

Towards a multi-metric assessment of river restoration ecological outcomes across projects and contexts

The assessment of the ecological outcomes of river restoration projects remains a complex undertaking due to the high variability of responses observed. This variability is dependent on a number of factors, including the location of the site under study, the indicators and taxa utilised in the analysis. In this study, a multi-metric and multi-contextual approach was applied to analyse 62 river restoration projects located in France, Germany and the Netherlands. This methodological approach facilitated the characterisation of the responses exhibited by macroinvertebrate communities in response to restoration initiatives, and the subsequent identification of the environmental contexts and the categories of restoration measures that exerted influence on these responses. Utilising log-response ratios based on both taxonomic and functional ecological metrics, a k-means clustering analysis was performed. This analysis yielded two distinct groups of sites: the first exhibiting predominantly positive responses to restoration, and the second demonstrating neutral or marginally negative responses. Positive responses have been shown to be associated with ambitious restoration projects, which are characterised by measures targeting regional-scale processes. These measures include the implementation of projects designed to improve river longitudinal continuity in degraded catchment areas, where the density of obstacles and the intensity of agricultural use are particularly high. Conversely, restoration initiatives targeting local-scale issues within more natural contexts or at high altitude exhibited minimal to no ecological response. This study emphasises the significance of an integrated approach that incorporates various facets (taxonomic and functional) of biodiversity, along with a meticulous examination of the environmental context and project construction, to enhance the evaluation of the ecological benefits of river restoration. The findings of this study may also be applicable in the context of fieldwork, providing practitioners with a framework to inform the design of restoration projects.

ecology↗

bioRxiv2025

Galectin-1 induces macrophage immunometabolic reprogramming, modulates T cell immunity and attenuates atherosclerotic plaque formation

Background and aimsAtherosclerosis is a chronic immunometabolic disease driven by lipid accumulation and immune cell infiltration. Macrophages and T cells play key roles throughout plaque development. Galectin-1 (Gal-1), a glycan-binding protein, modulates immune functions in these cells and has been reported to attenuate atherosclerosis, though its mechanisms remain incompletely understood. Here, we investigated the effects of Gal-1 on macrophages and T cells during plaque formation. MethodsEffects of Gal-1 on atherosclerosis, macrophages and T cells during lesion formation were studied in Apoe-/- mice treated with recombinant Gal-1. Complementary mouse peritoneal foam cell and in vitro macrophage and T cell cultures experiments were performed to study T cell differentiation, macrophage function, polarization end energy metabolism. The impact of Gal-1 on human macrophages was further evaluated in endarterectomy specimens. ResultsGal-1 treatment reduced lesion size and increased circulating IL-10 levels, inversely correlating with plaque burden. Unexpectedly, IL-10 neutralization also mitigated atherosclerosis, indicating that its action is at least partially IL-10-independent. In plaques, Gal-1 promoted anti-inflammatory macrophage phenotypes, mirrored by a quiescent metabolic and anti-inflammatory profile in foamy macrophages ex vivo. The use of the Gal-1E71Q variant revealed that these effects were only partly dependent on glycan binding. Beyond IL-10, Gal-1 reshaped cytokine profiles by increasing IL-17, IL-22, and IL-23, consistent with a macrophage-driven regulatory Th17 response, alongside higher frequencies of IL-10-producing and regulatory T cells. ConclusionGal-1 protects against atherosclerosis associated with reprogramming macrophages and tuning T cell immunity through glycan-dependent and -independent pathways.

immunology↗

bioRxiv2025

Self-Reactive B Cells in Artery Tertiary Lymphoid Organs Encode Pathogenic High Affinity Autoantibody in Atherosclerosis

Artery tertiary lymphoid organs (ATLOs) emerge in atherosclerosis which is a chronic inflammatory artery disease with an autoimmune component. However, whether disease-relevant autoimmune B cells emerge in ATLOs and their impacts remains unknown. To map atherosclerosis-specific humoral autoimmunity and define its roles, we isolated germinal-center (GC) B cells from ATLOs and lymph-nodes, expression-cloned 60 autoantibodies and screened them for arterial wall reactivity. ATLO-derived autoantibodies markedly skewed to atherosclerosis-relevant autoantigens versus those of lymph-nodes. One ATLO GC-derived autoantibody bound to histone 2B (H2B) with high-affinity ([~]25 nM). Moreover, vaccination with H2B or adoptive transfer of its cognate autoantibody markedly accelerated atherosclerosis suggesting that ATLOs fail to delete pathogenic high-affinity self-reactive B cells. In a human cohort, total circulating anti H2B antibody titers positively correlated with aortic and coronary artery calcification. We conclude that ATLOs harbor a dysregulated immune tolerance environment permissive for autoreactive B cells that express pathogenic autoantibodies driving atherosclerosis.

immunology↗

bioRxiv2025

Quantitative ethology of schistosome miracidia characterizes a conserved snail peptide that inhibits penetration

Over 700 million people are at risk of contracting schistosomiasis due to regular exposure to freshwater sources where infected snails, the obligate intermediate hosts of schistosomes, are endemic. Although mass drug administration of praziquantel effectively controls the disease in most regions, achieving elimination will require reducing populations of infected snails that shed the human-infective larval stage. Considerable effort has focused on parasite development and immunological responses after snail penetration, but comparatively little is known about the molecular and behavioral host seeking events that precede it, primarily due to technical and physical constraints. To address this gap, we developed a custom imaging and computational system for tracking and screening schistosome miracidia, the snail-infective larval form that hatches from eggs. Our system employs an array of cameras without magnification and acrylic devices that maintain miracidia within the focal plane, create a field of view over 200,000 times the area of a single miracidium, and support the formation of stable chemical gradients. Using this platform, we perform quantitative ethology of miracidia at an unprecedented scale and extract features that drive the emergent chemoklinokinetic behavior in response to snail cues. We demonstrate that miracidia accumulate at the edge of a gradient of snail cues by increasing key chemoklinokinetic features upon leaving the region of a cue, corroborating previous reports. In contrast, miracidia do not exhibit these behaviors when the cue is uniform, demonstrating that they represent a specific sensory response rather than generic neuromuscular activity. We further find that a previously identified stimulatory snail peptide only partially recapitulates the full chemoklinokinetic profile, and homologues from closely related species elicit divergent behavioral outcomes. Notably, some of these snail peptides can mask a natural gradient and inhibit miracidia penetration of snails. This work establishes a scalable behavioral platform for probing parasite- snail interactions and identifies a peptide scaffold that potently blocks snail penetration.

animal behavior and cognition↗

bioRxiv2025

Epithelia mediate inflammation with myeloid cells in Crohn's disease patients under treatment

Many Crohn's disease patients fail to respond to biologic therapies targeting canonical immune pathways, and the mechanisms underlying treatment non-response remain poorly understood. Integrating single-cell and spatial transcriptomics, we generated a comprehensive mucosal atlas of 380,000 cells spanning the terminal ileum and ascending colon of healthy donors and Crohn's disease patients receiving biologics. We revealed site-specific programs centered on TNF-expressing macrophages embedded within epithelial-stromal networks: follicle-associated enterocytes dictated immune activation in the ileum, while FAP-expressing stromal cells served this role in the colon. Co-expression network analysis further identified lineage-specific programs associating non-response, including a novel epithelial marker BPIFB1 independent of known genetic risk loci. Co-expression marker Z-scores significantly differed between responders and non-responders in published datasets. Together, these findings define a non-responder-specific epithelial-stromal-immune ecosystem that sustains chronic inflammation, providing a framework for stratifying treatment resistance and informing therapeutic strategies in Crohn's disease and other barrier organ disorders.

immunology↗

bioRxiv2025

A graphical user interface for wrmXpress 2.0 streamlines helminth phenotypic screening

Image-based phenotypic screening is a fundamental technique used to better understand the basic biology of helminths and advance discovery of new anthelmintics. Miniaturization of screening platforms and automated microscopy have led to a surge in imaging data and necessitated software to organize and analyze these data. Traditionally, these analyses are performed remotely on high-performance computers, often requiring an understanding of a command-line interface (CLI) and the ability to write scripts to control the software or job scheduler. Requiring access to specialized computing equipment and advanced computational skills raises the barrier to entry for these sorts of studies. The development of efficient, performant computer and graphical processing units for personal computers and cheaper imaging solutions has made the requirement of remote servers superfluous for many small to medium-scale screens, but most analytical software still require interaction with a CLI. To democratize the analysis of image-based phenotypic screens, we have developed a graphical user interface (GUI) for wrmXpress, a tool that integrates many popular computational pipelines for analyzing imaging data of parasitic and free-living worms. The GUI operates on any personal computer using the operating systems native web browser, allowing users to configure and run analyses using a point-and-click approach. Containerization of the application eliminates the need to install specialized programming libraries and dependencies, further increasing the ease of use. GUI development required a substantial reorganization of the wrmXpress backend codebase, which allowed for the addition a new pipeline for high-resolution tracking of worm behavior, and we demonstrate its functionality by showing that praziquantel modulates the behavior of Schistosoma mansoni miracidia. These advances make cutting-edge analyses of image-based phenotyping of worms more equitable and accessible.

bioinformatics↗

bioRxiv2025

Olfactory receptor 2 drives abdominal aortic aneurysm by promoting CX3CR1-mediated monocyte recruitment

BackgroundAbdominal aortic aneurysms (AAA) are characterized by an intricate interplay of extracellular matrix degradation and inflammation. Macrophages are centrally involved in these processes. The mechanisms underlying macrophage activation in AAA remain incompletely understood. Vascular macrophages have been shown to express olfactory receptor 2 (Olfr2), a G-protein coupled receptor involved in mediating the sense of smelling and regulating inflammatory activity in macrophages. Whether Olfr2 plays a role in modulating macrophage responses in AAA formation remains unknown. Methods & ResultsIn silico micro-array analysis showed increased expression of the human Olfr2 orthologue OR6A2 in AAA tissue compared to healthy aorta. Flow cytometric analysis revealed increased expression of OR6A2 on classical, non-classical, and intermediate monocytes of patients with a large AAA (> 5cm) in comparison to patients with smaller AAA (< 5cm). Up to 30% of vascular macrophages expressed OR6A2 in human AAA and Olfr2 in mouse AAA tissue. Olfr2 expression peaked on major histocompatibility complex II-high (MHCIIhigh) and C-C chemokine receptor type 2-low (CCR2low) aortic monocytes and macrophages on day 7 following experimental AAA initiation and decreased to baseline expression on day 28. Olfr2 gene (Olfr2-/-) deficiency protected mice from AAA formation, which was accompanied by lowered ECM degradation, reduced macrophage infiltration and increased smooth muscle cell content. Conversely, treatment with the Olfr2 agonist octanal exacerbated AAA formation and inflammation, while the antagonist citral reduced AAA formation in comparison to vehicle treated mice. Bulk transcriptome analysis of aortic tissue revealed reduced inflammatory gene expression in Olfr2-/- mice at day 7 following AAA initiation. Spectral flow cytometry resolved 20 aortic immune cell populations, which were largely reduced in quantity by Olfr2-deficiency at day 7 and day 28 post experimental AAA formation, while circulating leukocyte counts and monocyte subset distribution were not altered between Olfr2+/+ and Olfr2-/- mice. Circulating Ly6Chigh-monocytes exhibited reduced expression of the CX3C motif chemokine receptor 1 (CX3CR1) and CCR2 during AAA formation. Transcriptional analysis of monocytes confirmed downregulation of pathways associated with cell adhesion, motility and migration. In vitro, Olfr2-/- monocytes showed impaired migration towards the CX3CR1 ligand CX3CL1. Competitive transfer of Olfr2+/+ and Olfr2-/- monocytes confirmed reduced migratory capacity of Olfr2-/- monocytes into the developing AAA. ConclusionWe demonstrate a critical relevance for Olfr2 in the modulation of the inflammatory response underlying AAA, which is mediated by enhanced monocyte recruitment.

immunology↗

bioRxiv2025

Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant

Distal 1q21.1 deletions and duplications are associated with variable phenotypes including autism, head circumference and height defects. To elucidate which gene(s) are responsible for the 1q21.1 duplication/deletion-associated phenotypes, we performed gene manipulation in zebrafish and mice. We modeled 1q21.1 duplication by overexpressing the eight human protein-coding genes in zebrafish. We found that overexpression of CHD1L only led to macrocephaly and increased larval body length, whereas chd1l deletion caused opposite phenotypes. These mirrored phenotypes were also observed in mouse embryos. Transcriptomic, cistromic, and chromatin accessibility analyses of CHD1L knock-out hiPSC-derived neuronal progenitor cells revealed that CHD1L regulates the expression levels and chromatin accessibility of genes involved in neuronal differentiation and synaptogenesis, including autism genes. Moreover, we found that CHD1L favors telencephalon development during forebrain regionalization by facilitating chromatin accessibility to pioneer transcription factors including SOX2 and OTX2 while simultaneously compacting chromatin through its interaction with the repressor NuRD complex. Last, atypical 1q21.1 CNV encompassing CHD1L and pathogenic missense and truncating CHD1L variants were found in individuals with autism. Overall, our data reveal a novel role for CHD1L as a master regulator of cell fate and its dosage imbalance contributes to the neuroanatomical and growth phenotypes associated with the 1q21.1 distal CNV. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/638841v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@7dd5borg.highwire.dtl.DTLVardef@55a12dorg.highwire.dtl.DTLVardef@1c8ce0corg.highwire.dtl.DTLVardef@4faf29_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗