Biology subjects

Dupont, A.

Publications and source records attributed to Dupont, A..

14 recordsLinked to original sources

bioRxiv2026

Rev-erbα inhibits vascular calcification by repressing osteogenic reprogramming in atherosclerosis

Background: Atherosclerotic plaque rupture is the most deleterious atherogenic event, responsible for the majority of fatal acute atherothrombotic and myocardial infarctions. Intimal microcalcification is a major cause of atherosclerotic plaque instability. Yet, a thorough characterization of the mechanisms controlling intimal calcification is needed to develop innovative therapeutic strategies to treat high risk patients. The nuclear receptor Rev-erb regulates lipoprotein metabolism and exerts anti-inflammatory activities. Here, we hypothesized that Rev-erb modulates atherogenesis by regulating arterial calcification processes. Methods: We used a multi-omics approach in the ANGIOSAFE and the ATHEROPORTAL human cohort to identify pathways and factors associated with vascular calcification in diabetic patients. We then compared REV-ERB expression between calcified and non-calcified areas of human endarterectomies using laser capture microdissection assays (n=11-22/group). We assessed the role of Rev-erb on calcium deposition and expression of osteoblast markers in aortic roots of 18-month-old Ldlr-/-Rev-erb-/- and Ldlr-/-Rev-erb+/+ mice (n=10/group). Rev-erb-dependent molecular pathways that drive calcification were identified using gene expression profiling in aortic plaques from Ldlr-/-Rev-erb-/- and Ldlr-/-Rev-erb+/+ mice (n=8-10/group). We then confirmed omics data using primary aortic smooth muscle cells (SMCs) (n=3-6) in vitro assessing inflammation-driven calcification process as well as Rev-erb-dependent transcriptional mechanisms. Results: REV-ERB expression is significantly lower in circulating anti-inflammatory classical CD14+CD16- monocytes from diabetic patients with low coronary artery calcium (CAC) compared to those exhibiting high CAC scores while its expression is lower in highly calcified plaques from patients with diabetes mellitus compared to those with no diabetes or no calcification. Consistently, REV-ERB is markedly downregulated in calcified areas of human endarterectomy samples, while remaining higher in non-calcified regions. Rev-erb deficient Ldlr-/- mice exhibit accelerated atherogenesis and vascular calcification, and aortic smooth muscle cells (SMCs) exhibit a reprogramming toward an osteochondroblastic phenotype. Functional in vitro studies show that Rev-erb maintains SMC identity by preventing their IL-1{beta}-driven transdifferentiation into osteochondroblast-like cells, notably through the repression of key osteogenic regulators. Finally, while hyaluronic acid degradation is known to promote intimal calcification, we demonstrate that Rev-erb represses the hyaluronidase Cemip expression during SMC transdifferentiation. Conclusions: Rev-erb is identified as an important brake on SMC-driven vascular calcification, suppressing both osteogenic reprogramming and matrix-remodeling pathways. Thus, this study opens new avenues for developing novel therapeutic tools targeting Rev-erb to reduce vascular calcification and associated cardiovascular risk in high-risk patients.

pathology↗

bioRxiv2026

Swimming motility in the gut microbiota is diverse and increased in inflammation.

Swimming motility has long been studied as a virulence mechanism of enteric pathogens, while the resident microbiota's motility has only been inferred from proxies or explored through a few model species. This study presents a direct, functional analysis of gut bacterial motility in health and inflammation. Using phase-contrast microscopy and high-throughput 3D tracking, we quantified motile bacteria and characterized their swimming behaviours directly in diluted fresh gut content. In healthy mice, fewer than 3% of bacteria were motile along the digestive tract, and their swimming patterns were dominated not by the run-tumble behavior of model gut species but by diverse behaviours rich in reverses. In five mouse models with intestinal inflammation (spanning chemical, genetic, dietary and infectious etiologies) the motile fraction rose by at least 4-fold, correlating with elevated Lipocalin-2 where measured. Reverse-rich patterns remained prevalent in these inflamed conditions, with the notable exception of Salmonella infection. Paired metagenomics and metatranscriptomics showed enrichment of flagellar genes, while communities transferred into cecal water from inflamed mice raised their motile fraction within an hour, indicating that the rise reflects both enrichment of motile taxa and rapid modulation within existing populations. In vitro assays with human-derived isolates confirmed motility across several phyla, with variability down to strain level, and identified oxygen and viscosity as key modulators. These findings support increased motility as a hallmark of the inflamed gut and challenge established assumptions about gut bacterial motility.

microbiology↗

bioRxiv2026

Identification of Seed Metabolites and Microbiota members associated with Germination and Emergence in Common Bean

Seed quality is a complex trait shaped by morphological, biochemical and microbiological properties that are rarely characterised simultaneously, limiting our ability to identify robust predictive indicators of germination speed and seedling emergence across varieties. Here, we performed a multi-factor characterisation of eight common bean (Phaseolus vulgaris L.) varieties, combining seed morphometrics, untargeted GC-MS metabolomics on three seed organs, and amplicon sequencing of bacterial and fungal communities, to identify indicators of germination speed and emergence percentage. The eight varieties showed substantial variation in both traits, used as physiological seed quality proxies. Seed weight and size variation between varieties were correlated with germination speed. The intravariety variance of seed weight was independently correlated with emergence performance. Metabolome composition differed strongly across seed organs, with variety as the dominant driver. Individual-seed metabolomic profiles in the plumule and cotyledon were associated with germination speed but not emergence, yielding 16 plumule and three cotyledon candidate metabolite markers. Fungal community composition was associated with both germination speed and emergence, while bacterial communities were associated with emergence only. Nine fungal and four bacterial taxa were identified as candidate indicators. Inter-kingdom co-occurrence network analysis revealed that fungi with similar germination speed associations tend to cluster in the same modules, suggesting that community-level modules rather than individual taxa may constitute more robust microbial indicators. These results demonstrate that germination speed and emergence capacity are governed by distinct seed properties, and provide morphological, metabolic and microbial candidate indicators for integration into targeted seed quality assessment frameworks for common bean.

plant biology↗

bioRxiv2026

Neonatal liver niches program T cell tolerance

After birth, the immune system must learn to tolerate a rapidly changing milieu of commensals and self while remaining ready for pathogens. Here we characterize the neonatal liver as a central hub in this process: In postnatal week 1-2, the liver hosts a developmentally encoded, microbiota-independent expansion of regulatory T cells (Tregs) that coexists with microbiota-tuned conventional wave of activated CD4 T cells (Tconvs). Mechanistically, the Treg expansion is governed by MHCII-mediated antigen presentation by CCR7+ cDC1s, which establish tolerogenic DC:T cell clusters in the liver parenchyma, allowing for local expansion and control via PD-L1 checkpoints that selectively increase Tregs without unleashing Tconvs. Importantly, this transient, neonatal program predisposes hepatotropic viral infections to progress toward chronic disease but also protects the adult liver from steatotic disease. These data position the neonatal liver as a unique site of early life T-cell education with timing-sensitive implications for early-life interventions.

immunology↗

bioRxiv2025

Developmental factors drive the compartmentalised and discontinuous maturation of the small intestinal epithelium during the early postnatal period

The temporal, spatial and cellular diversity of the small intestinal epithelium during the postnatal period, a critical time window that accompanies the transition from placental energy supply to enteral feeding, the establishment of the enteric microbiota and postnatal immune maturation, has not been systematically investigated. Here, we used laser capture microdissection and bulk RNA-Seq, proteomics, and single cell RNA-Seq to analyse the total, organ site, crypt- and villus-specific intestinal epithelium of specific pathogen-free, germ-free and Salmonella-infected mice during the postnatal period. We identified key temporal and organ-site specific expression patterns that revealed a weak effect of the microbiota but strong influence of developmental regulators during early life. We also determined age-dependent signalling pathway and transcription factor activity and characterised age- and cell type-specific developmental trajectories revealing a distinct compartmentalised maturation process along the proximal-to-distal length and crypt-villus axis and a discontinuous appearance of goblet/Paneth cell and absorptive enterocyte transcriptional profiles. Finally, we described the cell type-specific response to neonatal enteric infection. Taken together, our findings identify the epithelium as an integral element in the maturation of postnatal mucosal tissues and in the establishment of host-microbe homeostasis.

immunology↗

bioRxiv2024

An unexplored diversity for adaptation of germination to high temperatures in Brassica species

Elevated temperatures inhibit the germination of a concerning number of crop species. One strategy to mitigate the impact of warming temperatures is to identify and introgress adaptive genes into elite germplasm. Diversity must be sought in wild populations, coupled with an understanding of the complex pattern of adaptation across a broad range of landscapes. By investigating the landraces, wild, and feral populations of Algeria, Italy, France, Slovenia, Spain, and Tunisia, we assessed the response of germination to temperature increase in an unexplored diversity of 117 accessions of B. rapa and 66 of B. oleracea. Our results show that both species exhibit heat tolerance to the temperature range tested, especially B. rapa with an increase in speed and uniformity of germination time, as well as an increase in germination rate as temperature increased. As for B. oleracea accessions, the ability to germinate under heat conditions depended on the geographical origin; in particular, southern populations showed a higher germination rate than northern populations, possibly in relation to their warmer climates of origin. These findings highlight the complex interplay between domestication, feralization, and current agronomic practices in shaping germination characteristics in Brassica species.

evolutionary biology↗

bioRxiv2024

Three-step scalable production of extracellular vesicles from pancreatic beta cells in stirred tank bioreactors promotes cell maturation and release of ectosomes with preserved immunomodulatory properties

Small extracellular vesicles (sEV) released by healthy beta cells are promising candidates for diabetes therapy thanks to their aptitude to modulate inflammation, to induce or maintain pancreatic function and to prevent pathogenic mechanisms. To advance the clinical development of therapeutics, there is a crucial need for scalable production methods. Stirred tank bioreactors (STR) are widely used in the industry due to their ability to provide homogeneous gas and nutrient supply, online monitoring, and efficient scale up. Anchorage- dependent cells can be cultured in STR on microcarriers or as spheroids, but may experience shear stress, which can affect sEV phenotype and function. Using pancreatic beta cells, this study identifies critical cell culturing parameters, including culture mode (monolayer vs. spheroids), medium formulation (with or without serum, glucose control), and process parameters (stirring, duration, cell density). The findings show that small spheroid culture promotes beta cell maturation without decreasing the yield of sEV per cell, despite a reduced cell surface exchange area. However, stirring increased expression of cellular stress markers and decreased cell viability. Set up of a three-step bioprocess allowed to maximize cell viability and sEV yields at high cell density over short production duration. sEV produced under these conditions maintained high purity, membrane integrity, and the aptitude to reduce T- lymphocyte proliferation and IFN-{gamma} cytokine secretion in a mixed lymphocyte reaction. Flow cytometry analysis revealed lower CD63/CD81 ratios in STR, indicating enhanced ectosome production. Switch from high glucose expansion to low glucose production medium further allowed to direct sorting of the antigen insulin into beta-sEV. This study demonstrates the feasibility of producing functional sEV from mature beta cells cultured as small spheroids, suitable for upscale. Production of sEV in STR may be particularly beneficial for ectosome- enriched compound loading for therapeutic applications. Graphical abstractRational development of a scalable bioprocess to control extracellular vesicles production & function. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/611247v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@6eaefeorg.highwire.dtl.DTLVardef@a2da3borg.highwire.dtl.DTLVardef@1a58f35org.highwire.dtl.DTLVardef@5cfd1d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISmall 3D-spheroid culture promotes cell maturation C_LIO_LIStirring induces cellular stress responses & promotes ectosome release from the cytoplasmic membrane C_LIO_LIDesign of experiment efficiently enhances cell viability and EV yield with preserved immune-modulatory properties C_LIO_LIGlucose-starvation during the production phase directs insulin-sorting into extracellular vesicles C_LI

bioengineering↗

bioRxiv2023

A social-ecological geography of southern Canadian Lakes

Anthropogenic pressures, including urban and agricultural expansion, can negatively influence a lakes capacity to provide aquatic ecosystem services (ES). However, identifying lakes most at risk of losing their ES requires integrating information on lake ecological state, global change threats, and ES demand. Here, we provide a social-ecological framework that combines these features within a regional context based on an ecological evaluation of the state of 659 lakes across Canada. From deviation of impacted lakes to reference ones, we identified much higher concentrations of total nitrogen and chloride as the main indicators of altered lake ecological state in all regions identified. Lake ecological state was mapped using an additive colour model along with regional scores of threat levels and recreational ES demand. Population density and agriculture were linked to high lake vulnerability. Lakes in Southern Ontario were most concerning, being highly altered, under threat, and heavily used. Lakes near urban centers along coasts were altered and used, but less threatened, whereas those in the Prairies were altered and threatened, but less used. Our novel framework provides the first social-ecological geography of Canadian lakes, and, is a promising tool to assess lake state and vulnerability at scales relevant for management. Plan language summaryPlain language title: Assessing overall lake health across Canada to identify sites for restoration and conservation Canadians love to swim, fish, and navigate in and on the countless lakes across the country. But Canadian lakes are under a considerable amount of pressure from human activities in their watershed. The expansion of cities, intensive farming, wetland loss, and industrial development all results in the transfer of pollutants to aquatic habitats, threatening the health of lakes and the ecosystem services they provide. Where are lakes being used across Canada? What condition are they in and is their use under threat from different pressures? To answer these questions, we combined information from many different sources, including a national scale lake assessment, through the NSERC Strategic Network Cluster Lake Pulse to create the first social-ecological geography of southern Canadian lakes. Regionally specific baseline conditions were established from lakes considered healthy due to limited human activities in their watershed. When lakes with impacted watershed were compared to healthy ones within their specific region, two early warning signals of human pressure, pollution from nitrogen found in fertilizers and sewage, and chloride found in road salt, determined whether a lake was altered. We combined these two health indicators, with information on future potential lake threats and use by the population for recreational purposes. Using a colour-coded mapping technique, we were able to identify regions where lakes were altered, threatened, and used. These regions occurred primarily around dense urban areas, of southern Ontario and Quebec, and major cities on the east and west coast. Lakes were altered and threatened, but seemingly less used in the Prairie Provinces. The novel approach is very adaptable, easy to understand, and can be used at more regional levels for management to determine priority sites for conservation and restoration, as well as in science communication to describe overall lake health.

ecology↗

bioRxiv2021

IL4I1 binds to TMPRSS13 and competes with SARS-Cov2 Spike

The secreted enzyme interleukin four-induced gene 1 (IL4I1) is involved in the negative control of the adaptive immune response. IL4I1 expression in human cancer is frequent and correlates with poor survival and resistance to immunotherapy. Nevertheless, its mechanism of action remains partially unknown. Here, we identified transmembrane serine protease 13 (TMPRSS13) as an immune cell-expressed surface protein that binds IL4I1. TMPRSS13 is a paralog of TMPRSS2, whose protease activity participates in the cleavage of SARS-Cov2 Spike protein and facilitates virus induced-membrane fusion. We show that TMPRSS13 is expressed by human lymphocytes, monocytes and monocyte-derived macrophages, can cleave the Spike protein and allow Sars-Cov2 Spike pseudotyped virus entry into cells. We identify regions of homology between IL4I1 and Spike and demonstrate competition between the two proteins for TMPRSS13 binding. These findings may be relevant for both interfering with SARS-Cov2 infection and limiting IL4I1-dependent immunosuppressive activity in cancer. One-Sentence SummaryThrough binding to its newly identified receptor TMPRSS13, the enzyme IL4I1 interferes with SARS-Cov2 Spike cleavage thereby blocking viral entry into host cells.

immunology↗

bioRxiv2021

Conditional deletion of HIF-1α provides new insight regarding the murine response to gastrointestinal infection with Salmonella Typhimurium

The hypoxia-inducible transcription factor 1 (HIF-1) has been shown to ameliorate different bacterial infections through enhancement of microbial killing. While the impact of HIF-1 on inflammatory diseases of the gut has been studied intensively, its function in bacterial infections of the intestine remains largely elusive. With the help of a publicly available gene expression data set, we could infer significant activation of the HIF-1 transcription factor after oral infection of mice with Salmonella Typhimurium. This prompted us to apply lineage-restricted deletion of the Hif1a locus in mice to examine cell type-specific functions of HIF-1 in this model. We show hypoxia-independent induction of HIF-1 activity upon Salmonella infection in the intestinal epithelium as well as in macrophages. Surprisingly, Hif1a deletion in intestinal epithelial cells impacted neither disease outcome nor inflammatory activity. The conditional knockout of Hif1a in myeloid cells enhanced the mRNA expression of the largely pro-inflammatory chemokine Cxcl2, revealing a potentially inflammatory effect of HIF-1 deficiency in myeloid cells in the gut in vivo. Again, the disease outcome was not affected. In vitro HIF-1-deficient macrophages showed an overall impaired transcription of pro-inflammatory factors, however, Salmonella bypassed direct intracellular, bactericidal HIF-1-dependent mechanisms in a Salmonella pathogenicity island (SPI)-2 independent manner. Taken together, our data suggest that HIF-1 in intestinal epithelial and myeloid cells is either dispensable or compensable in the immune defense against Salmonella Typhimurium.

microbiology↗

bioRxiv2020

Molecular and functional diversity of distinct subpopulations of extracellular vesicles from stressed pancreatic beta cells: implications for autoimmunity

Beta cell failure and apoptosis following islet inflammation have been associated with autoimmune type 1 diabetes pathogenesis. As conveyors of biological active material, extracellular vesicles (EV) act as mediators in communication with immune effectors fostering the idea that EV from inflamed beta cells may contribute to autoimmunity. Evidence accumulates that beta exosomes promote diabetogenic responses, but relative contributions of larger vesicles as well as variations in the composition of the beta cells vesiculome due to environmental changes have not been explored yet. Here, we made side-by-side comparisons of the phenotype and function of apoptotic bodies (AB), microvesicles (MV) and small EV (sEV) isolated from an equal amount of MIN6 beta cells exposed to inflammatory, hypoxic or genotoxic stressors. Under normal conditions, large vesicles represent 93% of the volume, but only 2% of the number of the vesicles. Our data reveal a consistently higher release of AB and sEV and to a lesser extent of MV, exclusively under inflammatory conditions commensurate with a 4-fold increase in the total volume of the vesiculome and enhanced export of immune-stimulatory material including the autoantigen insulin, microRNA, and cytokines. Whilst inflammation does not change the concentration of insulin inside the EV, specific Toll-like receptor-binding microRNA sequences preferentially partition into sEV. Exposure to inflammatory stress engenders drastic increases in the expression of monocyte chemoattractant protein 1 in all EV and of interleukin-27 solely in AB suggesting selective sorting towards EV subspecies. Functional in vitro assays in mouse dendritic cells and macrophages reveal further differences in the aptitude of EV to modulate expression of cytokines and maturation markers. These findings highlight the different quantitative and qualitative imprints of environmental changes in subpopulations of beta EV that may contribute to the spread of inflammation and sustained immune cell recruitment at the inception of the (auto-) immune response. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/003145v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1bf7c79org.highwire.dtl.DTLVardef@85098dorg.highwire.dtl.DTLVardef@362e33org.highwire.dtl.DTLVardef@11349ab_HPS_FORMAT_FIGEXP M_FIG C_FIG Inflammation stimulates release of a heterogeneous population of beta EV with differential expression of immunogenic substances involved in immune cell recruitment and activation. HighlightsO_LIStress engenders an up to four-fold increase in the volume of the vesiculome and enhanced auto-antigen release C_LIO_LICytokines are selectively sorted into EV subspecies C_LIO_LITLR-binding microRNAs are enriched in sEV C_LIO_LIEV from stressed beta cells promote dendritic and macrophage cell activation C_LI

immunology↗

bioRxiv2018

Analysis of cholesterol export from endo-lysosomes by Niemann Pick C2 protein using combined fluorescence and X-ray microscopy

The Niemann-Pick C2 protein (NPC2) is a sterol transfer protein in late endosomes and lysosomes (LE/LYSs). How its capacity to transport cholesterol between membranes is linked to endo-lysosomal membrane trafficking is not known. Using quantitative fluorescence imaging combined with soft X-ray tomography (SXT); we show that NPC2 mediated sterol efflux is accompanied by large changes in distribution, size and ultrastructure of endocytic organelles. We observed clearance of intra-luminal lipid deposits, a decrease in number of autophagosomes, formation of membrane contact sites (MCSs) to the endoplasmic reticulum and extensive tubulation of LE/LYSs in three-dimensional SXT reconstructions of NPC2 treated human fibroblasts. The cells could recycle the cholesterol analog dehydroergosterol (DHE) from LE/LYSs slowly also in the absence of NPC2 protein but internalized NPC2 synchronized and accelerated this process significantly. Most fluorescent NPC2 was retained in LE/LYSs while DHE was selectively removed from these organelles, at least partially by non-vesicular exchange with other membranes. During sterol efflux LE/LYSs were reallocated to the cell periphery, where they could fuse with newly formed endosomes. Surface shedding of micro-vesicles was found, suggesting a pathway for cellular sterol release. We conclude that NPC2 mediated sterol efflux from LE/LYSs controls membrane traffic through the endo-lysosomal pathway.

cell biology↗

bioRxiv2017

Magneto-active substrates for local mechanical stimulation of living cells

Cells are able to sense and react to their physical environment by translating a mechanical cue into an intracellular biochemical signal that triggers biological and mechanical responses. This process, called mechanotransduction, controls essential cellular functions such as proliferation and migration. The cellular response to an external mechanical stimulation has been investigated with various static and dynamic systems, so far limited to global deformations or to local stimulation through discrete substrates. To apply local and dynamic mechanical constraints at the single cell scale through a continuous surface, we have developed and modelled magneto-active substrates made of magnetic micro-pillars embedded in an elastomer. Constrained and unconstrained substrates are analysed to map surface stress resulting from the magnetic actuation of the micro-pillars and the adherent cells. These substrates have a rigidity in the range of cell matrices, and the magnetic micro-pillars generate local forces in the range of cellular forces, both in traction and compression. As an application, we followed the protrusive activity of cells subjected to dynamic stimulations. Our magneto-active substrates thus represent a new tool to study mechanotransduction in single cells, and complement existing techniques by exerting a local and dynamic stimulation, traction and compression, through a continuous soft substrate.

biophysics↗

bioRxiv2017

The recombinase protein is a torque sensitive molecular switch.

How a nano-searcher finds its nano-target is a general problem in non-equilibrium statistical physics. It becomes vital when the searcher is a damaged DNA fragment trying to find its counterpart on the intact homologous chromosome. If the two copies are paired, that intact homologous sequence serves as a template to reconstitute the damaged DNA sequence, enabling the cell to survive without genetic mutations. To succeed, the search must stop only when the perfect homology is found. The biological process that ensures such a genomic integrity is called Homologous Recombination and is promoted by the Recombinase proteins. In this article, we use torque-sensitive magnetic tweezers to measure the free-energy landscape of the human Recombinase hRad51 protein assembled a DNA fragment. Based on our measurements we model the hRad51/DNA complex as an out-of-equilibrium two-state system and provide a thermodynamical description of Homologous Recombination. With this dynamical two-state model, we suggest a mechanism by which the recombinase proteins discriminate between homologous and a nonhomologous sequences.

biophysics↗