Biology subjects

Pasquier, C.

Publications and source records attributed to Pasquier, C..

7 recordsLinked to original sources

bioRxiv2026

Endothelial gain of PIEZO/TRPV mechanosensors drives cavernous malformations

Vascular disease often begins as a failure to read mechanical force. Cerebral cavernous malformations (CCMs) are leaky, brain-invading capillary clusters that cause stroke and seizures and arise from endothelial loss of the CCM complex. They form exclusively in low-flow vessels but existing models cannot explain this selectivity. We previously established that CCM-mutant endothelium inverts its adhesive balance, weakening cell-cell junctions while building matrix-degrading adhesions. The mechanosensors imposing this switch are unknown. Here we show that the mechanosensitive Ca2+ channels PIEZO1, TRPV2 and TRPV4 are overexpressed in the endothelium of CCM lesions in a 42-patient cohort, and that lesion volume scales with their expression level. Mechanistically, PIEZO1 partners with TRPV4 to destabilise cell-cell junctions and with TRPV2 to reinforce cell-matrix adhesions; silencing TRPV4 restores junctional integrity and abolishes KLF4 induction, whereas silencing TRPV2 or inhibition with tranilast abolishes matrix degradation and invasion. In vivo, trpv4 knockdown or inhibition with GSK2798745 restores atrioventricular canal morphogenesis in ccm2-mutant zebrafish. Gain of mechanosensory channel function is thus a causal step in CCM pathogenesis, upstream of the KLF program. Combined therapeutic targeting of TRPV2 and TRPV4 with inhibitors validated in humans offers a route to therapy.

cell biology↗

bioRxiv2026

Single-cell transcriptomics reveals a differential response of human bronchial epithelial cell-types to cadmium chloride

Exposure of cells or tissues to chemical compounds can be analyzed through transcriptomic signatures, which can be used to classify chemical agents. This information can also enrich Adverse Outcome Pathways (AOP). Transcriptional signatures have generally been obtained using "bulk" analysis, by which the global gene expression pattern of an entire tissue is determined. Although this approach has been useful in toxicology, some information is lost, especially when tissues containing multiple cell types are considered. With the advent of single-cell transcriptomics (scRNA-seq), it is now possible to obtain higher resolution, cell type-specific responses in complex tissues. The aim of the present study was to evaluate the added value of scRNA-seq in analysis of the acute response of human bronchial epithelial cells grown at the air/liquid interface (ALI) to a known toxic compound, CdCl2, with well described transcriptional signatures of exposure. Fully differentiated mucocilliary epithelia obtained from three independent donors were exposed to 10 {micro}M CdCl2 and scRNA-seq analysis was performed on a total of 18255 cells to obtain cell type-specific signatures. Our results show that the contribution of each cell type to the overall transcriptomic bulk response varies. For example, the classical heavy metal detoxification response was only detected in multiciliated and secreting cells, while absent in basal cells. The data demonstrate that scRNA-seq provides high-resolution transcriptional signatures with unexpected features. This added information is likely to have implications for the refinement of AOPs and could serve as a basis for a new generation of tests in predictive toxicology.

pharmacology and toxicology↗

bioRxiv2025

Fatty Acid Synthase binds endogenous dsRNAs and dampens the innate immune response to exogenous dsRNAs by limiting their accumulation.

Cytoplasmic double-stranded RNA (dsRNA) is a hallmark of viral infection. It triggers innate immune responses after recognition by pathogen recognition receptors (PRRs) and leads to the production of interferons. DsRNAs arising from endogenous transcripts can also contribute to immune regulation, depending on their abundance, localization and processing. However, the mechanisms of their immunogenic potential and interactions with host proteins remain poorly understood. Fatty Acid Synthase (FASN) is a key metabolic enzyme involved in de novo lipid synthesis, implicated in the regulation of cellular growth and increasingly recognized for its pro-viral functions. Here, we investigate the impact of FASN on endogenous dsRNA dynamics in human cells and its potential role in innate immune sensing. We show that FASN depletion increases the cytoplasmic accumulation of endogenous dsRNAs and promotes their enrichment in proximity to mitochondria in HCT116 cells. Transcriptomic analyses reveal that FASN deficiency is not only associated with alterations in metabolic pathways, but also with increased expression of inflammation-related genes, such as the interferon-stimulated gene (ISG) IFIT1. Combining dsRNA pulldowns with mass spectrometry and RNA-seq demonstrates that FASN associates with a subset of cytoplasmic dsRNAs derived from nuclear-encoded transcripts under basal conditions and that its association increases when endo-dsRNA levels are experimentally elevated. FASN-deficient cells display enhanced responsiveness to exogenous dsRNA stimulation with both poly I:C and viral RNA. In addition, FASN depletion restricts replication of Sindbis virus and is associated with sustained dsRNA accumulation despite reduced viral RNA levels, supporting a link between FASN activity, dsRNA regulation and antiviral responses. Our findings identify FASN as a critical regulator of endogenous dsRNA accumulation and sensing, revealing a potential role in innate immune response modulation.

immunology↗

bioRxiv2025

Analytical Ultracentrifugation as a Tool for Exploring COSAN Assemblies.

The self-assembly of the cobalta bis(dicarbollide) (COSAN) anionic boron clusters into micelles above a critical micelle concentration (cmc) of 10 - 20 mM and its behavior as "sticky nano-ions" facilitating controlled protein aggregation have been previously investigated using scattering techniques, particularly small-angle neutron and X-ray scattering. These techniques effectively provide average structural parameters but, when applied to colloidal systems, often rely on models assuming polydispersity or anisotropic shapes. Thus, complementary techniques are required to confirm or infirm the proposed analyses. Here, we employed sedimentation velocity analytical ultracentrifugation (SV-AUC), which offers the ability to resolve discrete species. We revisited two key questions: (1) the aggregation behavior of COSAN into micelles, a topic still under debate and due to its unconventional amphiphilic nature, and (2) the nature of the protein assemblies induced by COSAN, specifically their size/shape distribution and aggregation number. Our findings confirm the cmc of COSAN of 16 mM and reveal that COSAN micelles exhibit low aggregation numbers (8 in water and 14 in dilute salt), consistent with recent hypotheses. Furthermore, SV-AUC showed that COSAN promotes myoglobin aggregation into discrete oligomeric species with well-defined aggregation numbers, such as dimers, tetramers, and higher-order assemblies, depending on the COSAN-to-protein ratio. These results provide clarity on the discrete nature of COSAN micelle aggregation and protein assembly. This study highlights the complementary role of SV-AUC in understanding supramolecular assemblies, offering useful insights into the behavior of COSAN nano-ions and their interactions with biomacromolecules.

biophysics↗

bioRxiv2023

DEAD box RNA helicases 5 and 17 are new host factors for Sindbis virus infection

BackgroundRNA helicases are emerging as key factors regulating host-virus interactions. The DEAD-box ATP-dependent RNA helicase DDX5, which plays an important role in many aspects of cellular RNA biology, was also found to either promote or inhibit viral replication upon infection with several RNA viruses. Here, our aim is to examine the impact of DDX5 on Sindbis virus (SINV) infection. MethodsWe analysed the interaction between DDX5 and the viral RNA using imaging and RNA-immunoprecipitation approaches. The interactome of DDX5 in mock- and SINV-infected cells was determined by mass spectrometry. We validated the interaction with DDX17 and the viral capsid by co-immunoprecipitation in the presence or absence of an RNase treatment. We determined the subcellular localization of DDX5, its cofactor DDX17 and the viral capsid protein by co-immunofluorescence. Finally, we investigated the impact of DDX5 depletion and overexpression on SINV infection at the viral protein, RNA and infectious particle accumulation level. The contribution of DDX17 was also tested by knockdown experiments. ResultsIn this study we demonstrate that DDX5 interacts with the SINV RNA during infection. Furthermore, the proteomic analysis of the DDX5 interactome in mock and SINV-infected HCT116 cells identified new cellular and viral partners and confirmed the interaction between DDX5 and DDX17. Both DDX5 and DDX17 re-localize from the nucleus to the cytoplasm upon SINV infection and interact with the viral capsid protein. We also show that DDX5 depletion negatively impacts the viral replication cycle, while its overexpression has a pro-viral effect. Finally, we observed that DDX17 depletion reduces SINV infection, an effect which is even more pronounced in a DDX5-depleted background, suggesting a synergistic pro-viral effect of the DDX5 and DDX17 proteins on SINV. ConclusionsThese results not only shed light on DDX5 as a novel and important host factor to the SINV life cycle, but also expand our understanding of the roles played by DDX5 and DDX17 as regulators of viral infections.

microbiology↗

bioRxiv2021

Identification of active modules in interaction networks using node2vec network embedding

The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical approaches using only expression data allow the identification of genes whose expression is most altered between different conditions. However, a phenotype is rarely a direct consequence of the activity of a single gene, but rather reflects the interplay of several genes to carry out certain molecular processes. Many methods have been proposed to analyze the activity of genes in light of our knowledge of their molecular interactions. However, existing methods have many limitations that make them of limited use to biologists: they detect modules that are too large, too small, or they require the users to specify a priori the size of the modules they are looking for. We propose AMINE (Active Module Identification through Network Embedding), an efficient method for the identification of active modules. Experiments carried out on artificial data sets show that the results obtained are more reliable than many available methods. Moreover, the size of the modules to be identified is not a fixed parameter of the method and does not need to be specified; rather, it adjusts according to the size of the modules to be found. The applications carried out on real datasets show that the method enables to find important genes already highlighted by approaches solely based on gene variations, but also to identify new groups of genes of high interest. In addition, AMINE method can be used as a web service on your own data (http://amine.i3s.unice.fr).

bioinformatics↗

bioRxiv2020

SARS-CoV-2 might manipulate against its host the immunity RNAi/Dicer/Ago system

The role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive in mammals, which prompted authors to think that interferon (IFN) synthesis is essential in this clade relegating the RNAi defense strategy against viral infection as accessory function. We explore the theoretical possibilities that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction although this hypothesis seems counter intuitive. SARS-CoV-2 genome was therefore computational searched for exact intra pairing within the viral RNA and also hybrid exact pairing with human transcriptome over a minimum 20 bases length. Minimal segments of 20 bases length of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, among them mitochondrial deubiquitinase USP30, a subunit of ubiquitin protein ligase complex FBXO21 along with two long coding RNAs were retrieved. The hypothesis that viral originated RNAi might mediate degradation of messengers of the host transcriptome was corroborated by clinical observation and phylogenetic comparative analysis indicating a strong specificity of these hybrid pairing sequences for both SARS-CoV-2 and human genomes.

cell biology↗