Biology subjects

Dupuy, A.

Publications and source records attributed to Dupuy, A..

10 recordsLinked to original sources

bioRxiv2026

Dissociated responses of vesiculogenesis and amoxicillin impact on extracellular vesicle production of first gut bacterial colonizers Bifidobacterium longum and Lactiplantibacillus plantarum

Bacterial extracellular vesicles (bEVs) have emerged as important mediators of microbiota-host interplay through the transport of active biomolecules, namely cargos, far from their release location. The neonatal period represents a critical window for the establishment of the gut microbiota and subsequent sustainable symbiotic communication. The gut primo-colonizing bacteria, including bifidobacteria and lactobacilli, likely contribute to the impact on the digestive, immune and neuron system maturation. However, exposures and experiences during this early stage may influence the development of health and diseases later on in life by altering these primo-interactions. As antibiotherapies are frequent in the postnatal period and associated to microbiota disorders, we evaluated the impact of amoxicillin on first colonizing Gram positive-derived EVs, using a robust and reproductible in-house workflow for the extraction and purification bEVs from Bifidobacterium longum and Lactiplantibacillus plantarum. The EVs production and the proteovesiculome profiles under amoxicillin treatment were compared. The results pointed out a dissociated response in the EVs release process and their regulation by amoxicillin according to strain with an enhance production of EVs for B. longum under amoxicillin. In addition, the proteovesicular analyses indicate that the vesicular protein profile was enriched and more diverse in B. longum-derived EVs from amoxicillin-treated cells than those from non-treated cells while the content shift in L. plantarum-derived EVs in amoxicillin-treated cells was in favor of protein richness loss. Overall, this study opens new avenues considering the impact of antibiotic therapies in the neonatal period on EVs derived from benefit Gram-positive gut bacteria.

microbiology↗

bioRxiv2026

A functional genomics screen identifies novel drivers of FR900359 resistance in uveal melanoma cells

Uveal melanoma (UM) is the most common form of intraocular cancer in adults and has a median survival rate of [~]1 year after metastasis occurs. Metastatic UM is largely refractory to treatment and there are no effective pharmacological therapies, resulting in poor overall survival. Activating mutations in GNAQ and GNA11 proteins (GNAQ/11) are the oncogenic initiators in >90% UM cases. While there are no targeted therapies yet identified for the GNAQ/11 oncoproteins, a natural compound called FR900359 (FR) is a selective inhibitor for both oncogenic and wild type GNAQ/11. We performed a functional genomics screen to identify drivers of FR resistance in two UM cell lines (92.1 and MEL202). The screen identified eleven genes as candidate FR resistance drivers in both cell lines. Over-expression of five of these genes (ABCB1, PLCB4, GRM1, PLCE1, PDGFRB) was predicted to provide resistance to FR treatment. Enforced expression of ABCB1 or PLCB4 did not provide immediate resistance to FR, although over-expression of either transgene led to the emergence of resistant colonies at a much higher rate than occurs spontaneously in parental cells. We show that a relatively small fraction of UM cells can tolerate the initial over-expression of PLCB4 and ABCB1, but FR treatment leads to expansion of this cell population. Expression of an ABCB1-tGFP fusion protein was used to isolate drug naive UM cells. We show that these cells are uniformly resistant to FR, unlike the bulk tumor cell population. Finally, additional experiment of the drug naive ABCB1-tGFP+ UM cells led to the observation that these cells exhibit a significantly lower rate of protein translation, like BAP1-deficient UM cells. These findings suggest that resistance to targeted GNAQ/11 inhibitors is dictated by interaction between acquired genetic alterations and epigenetic states within heterogenous UM cell populations.

cancer biology↗

bioRxiv2026

Patient-specific "Physical Twin" artery-on-chip platform reveals complex flow-dependent VWF mechanobiology and guides personalized antithrombotic therapy

Ischemic stroke triggered by carotid atherosclerosis remains unpredictable because the thrombosis embolization is governed by patient-specific vascular geometry and hemodynamics that cannot be recapitulated in conventional models. Here, we engineered "Physical Twin" artery-on-chip platforms that reproduce individualized carotid anatomy with humanized subendothelial matrix composition and arterial endothelial phenotype under physiological flow patterns. We then established thrombotic microenvironments following laser-induced injury. Computational fluid dynamics-guided experiments across distinct patient geometries reveal that local shear dictates a mechanobiological hierarchy: high-shear bifurcations ([~]3,000 s-{superscript 1}) produce von Willebrand factor (VWF) A1-dependent thrombi suppressible by conformationally sensitive inhibitors, whereas low-shear stenoses generate fragile aggregates where VWF-integrin IIb{beta} coupling governs embolization overgrowth. Pulsatile flow suppresses thrombotic growth independent of mean shear. Molecular dynamics simulations reveal why conformationally sensitive nanobodies (caplacizumab) outperform shear-independent aptamers (ARC1172) in high-shear bifurcation flow zones. This Physical Twin platform provides a mechanistic blueprint for geometry-informed, personalized antithrombotic therapy selection.

bioengineering↗

bioRxiv2026

Ciliogenesis associated kinase 1 accumulates in its inactive form during polycystic kidney disease progression

Ciliogenesis associated kinase 1 (CILK1) deficiency in human and mice results in kidney developmental defects including cystogenesis. However, the biology of CILK1 in autosomal dominant polycystic kidney disease (ADPKD), the most common inherited kidney disease, remains to be investigated. Here, we show that CILK1 is overexpressed in dedifferentiated cells of renal tissue from ADPKD human patients in comparison to normal control tissue samples. We demonstrate that CILK1 overexpression results in protein accumulation in a non-phosphorylated inactive form. Using mouse polycystic kidney disease models, we reveal that inactive CILK1 accumulation is progressive over the course of disease progression. We show that genetic inactivation of the Polycystic Kidney Disease 1 (PKD1) gene is sufficient to trigger CILK1 accumulation. Altogether, these findings demonstrate that CILK1 regulation is altered in ADPKD and it represents a hallmark of disease progression.

biochemistry↗

bioRxiv2024

A critical role of FAK signaling in Rac1-driven melanoma cell resistance to MAPK pathway inhibition

The Rac1 P29S hotspot mutation in cutaneous melanoma is associated with resistance to MAPK pathway inhibitors (MAPKi) and worse clinical outcomes. Moreover, activation of Rac1 guanine exchange factors (GEFs) also promotes MAPKi-resistance, particularly in undifferentiated melanoma cells. Here we delineate mechanisms of Rac1-driven MAPKi-resistance and identify strategies to inhibit the growth of this class of cutaneous melanomas. We find that Rac1-driven melanomas manifest pleiotropic resistance mechanisms including (i) reduced dependence on BRAF/MEK, (ii) activation of alternative MAPK pathways utilizing Jun kinase and p38 MAP kinase, and (iii) a partial reliance on YAP/TAZ signaling. Importantly, although Rac1-driven melanoma cells display reduced dependence on BRAF/MEK, they are not completely ERK-independent. Additionally, the presence of activated Rac1 appears to create a dependency on focal adhesion kinase (FAK) signaling in undifferentiated melanoma cells. Therefore, despite the pleiotropic mechanisms of Rac1-driven MAPKi resistance, we find that combined inhibition of RAF and MEK with the RAF/MEK clamp auvotometinib and FAK with the FAK inhibitor defactinib is a promising approach for suppressing the growth of Rac1-driven melanoma cells. Thus, the avutometinib plus defactinib combination, which is currently being investigated for brain metastatic cutaneous melanoma may also have utility against Rac1-driven MAPKi-resistance in heavily pre-treated, advanced disease.

cancer biology↗

bioRxiv2024

Primary cilia promote EMT-induced triple-negative breast tumor heterogeneity and resistance to therapy

Tumor heterogeneity and plasticity, driven by Epithelial-Mesenchymal Transition (EMT), enable cancer therapeutic resistance. We previously showed that EMT promotes primary cilia formation, which enables stemness and tumorigenesis in triple-negative breast cancer (TNBC). Here, we establish a role for primary cilia in human TNBC chemotherapeutic resistance. We developed patient-derived organoids, and showed that these recapitulated the cellular heterogeneity of TNBC biopsies. Notably, one of the identified cell states bore a quasi-mesenchymal phenotype, primary cilia, and stemness signatures. We treated our TNBC organoids with chemotherapeutics and observed partial killing. The surviving cells with organoid-reconstituting capacity showed selective enrichment for the quasi-mesenchymal ciliated cell subpopulation. Genomic analyses argue that this enrichment reflects a combination of pre-existing cells and ones that arose through drug-induced cellular plasticity. We developed a family of small-molecule inhibitors of ciliogenesis and show that these, or genetic ablation of primary cilia, suppress chemoresistance. We conclude that primary cilia help TNBC to evade chemotherapy. SignificanceCancer cells that activate EMT to acquire a quasi-mesenchymal state form primary cilia to evade chemotherapy in human triple-negative breast cancer. Pharmacological inhibition of primary ciliogenesis counteracts EMT-induced chemoresistance.

cancer biology↗

bioRxiv2023

P-Selectin promotes SARS-CoV-2 interactions with platelets and the endothelium

COVID-19 causes a clinical spectrum of acute and chronic illness and host / virus interactions are not completely understood1,2. To identify host factors that can influence SARS-CoV-2 infection, we screened the human genome for genes that, when upregulated, alter the outcome of authentic SARS-CoV-2 infection. From this, we identify 34 new genes that can alter the course of infection, including the innate immune receptor P-selectin, which we show is a novel SARS-CoV-2 spike receptor. At the cellular level expression of P-selectin does not confer tropism for SARS-CoV-2, instead it acts to suppress infection. More broadly, P-selectin can also promote binding to SARS-CoV-2 variants, SARS-CoV-1 and MERS, acting as a general spike receptor for highly pathogenic coronaviruses. P-selectin is expressed on platelets and endothelium3, and we confirm SARS-CoV-2 spike interactions with these cells are P-selectin-dependent and can occur under shear flow conditions. In vivo, authentic SARS-CoV-2 uses P-selectin to home to airway capillary beds where the virus interacts with the endothelium and platelets, and blocking this interaction can clear vascular-associated SARS-CoV-2 from the lung. Together we show for the first time that coronaviruses can use the leukocyte recruitment system to control tissue localization, and this fundamental insight may help us understand and control highly pathogenic coronavirus disease progression.

immunology↗

bioRxiv2022

Mechano-redox control of Mac-1 de-adhesion from ICAM-1 by protein disulfide isomerase promotes directional movement of neutrophils under flow

Macrophage-1 antigen or Mac-1 (CD11b/CD18, M{beta}2) is a leukocyte integrin essential for firm adhesion of neutrophils, lymphocytes and monocytes against flow when recruited to the endothelium. To migrate to the site of inflammation, leukocytes require coordinated adhesion and de-adhesion for directional movement. The vascular thiol isomerase, protein disulfide isomerase (PDI), was found by fluorescence microscopy to colocalize with high affinity Mac-1 at the trailing edge of stimulated neutrophils when adhered to ICAM-1 under fluid shear. From differential cysteine alkylation and mass spectrometry studies, PDI cleaves two allosteric disulfide bonds, C169-C176 and C224-C264, in the {beta}I domain of the {beta}2 subunit, and in mutagenesis and cell transfection studies, cleavage of the C224-C264 disulfide bond was shown to selectively control Mac-1 dis-engagement from ICAM-1 under fluid shear. Molecular dynamics simulations and binding of conformation-specific antibodies reveal that cleavage of the C224-C264 bond induces conformational change and mechanical stress in the {beta}I domain that allosterically alters exposure of an I domain epitope and shifts Mac-1 to a lower affinity state. From studies of neutrophil adherence to ICAM-1 under fluid shear, these molecular events promote neutrophil motility in the direction of flow at high shear stress. In summary, shear-dependent PDI cleavage of neutrophil Mac-1 C224-C264 disulfide bond triggers Mac-1 de-adherence from ICAM-1 at the trailing edge of the cell and enables directional movement of neutrophils during inflammation.

biochemistry↗

bioRxiv2022

"Transposon Mutagenesis Reveals RBMS3 as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis."

Mutationally-activated BRAFV600E is detected in ~2% of all human non-small cell lung cancers (NSCLC), and serves as a predictive biomarker for treatment of patients with FDA-approved pathway-targeted therapies that inhibit signaling by the BRAFV600E oncoprotein kinase. In genetically engineered mouse (GEM) models, expression of BRAFV600E in alveolar type 2 (AT2) pneumocytes initiates the development of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinomas. To identify genes that might cooperate with BRAFV600E for malignant lung cancer progression we employed Sleeping Beauty (SB)-mediated transposon mutagenesis, which dramatically accelerated the onset of lethal lung adenocarcinomas. Amongst the diverse group of genes identified by this in vivo screen was Rbms3 (RNA binding motif single-stranded interacting protein 3), an RNA-binding protein implicated as a possible tumor suppressor. Using CRISPR/CAS9 gene editing we confirmed that RBMS3 silencing cooperated with BRAFV600E to promote progression of malignant lung cancer with a distinct micropapillary architecture. Moreover, RBMS3 silencing also cooperated with BRAFV600E to promote the growth of lung organoids in vitro. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of b-catenin (CTNNB1), suggesting that RBMS3 silencing may result in elevated signaling through the WNT>CTNNB1>c-MYC pathway. Finally, analyses of patient samples in The Cancer Genome Atlas (TCGA) revealed that the region of chromosome 3 encompassing RBMS3 is frequently lost in NSCLC and correlates with poor patient prognosis. Collectively, SB-mediated transposon mutagenesis has revealed the ability of a novel tumor suppressor, RBMS3, to cooperate with BRAFV600E to promote lung carcinogenesis, and suggests that RBMS3 silencing may contribute to malignant progression of numerous human lung cancers. SIGNIFICANCEThe BRAFV600E oncoprotein kinase is a potent initiator of benign lung tumorigenesis, but is insufficient to elicit malignant lung adenocarcinoma without additional cooperating alterations. Sleeping Beauty-mediated transposon mutagenesis has revealed a number of genes that cooperate with BRAFV600E to promote lung cancer progression, in particular Rbms3, which encodes an RNA binding protein. Hence, this genetic screen provides a deeper understanding of the molecular mechanisms underlying BRAFV600E-driven lung carcinogenesis, and is an important step improving our ability to successfully target this disease.

cancer biology↗

bioRxiv2018

Translocator Protein Localises To CD11b+ Macrophages In Atherosclerosis

BackgroundAtherosclerosis is characterized by lipid deposition, monocyte infiltration and foam cell formation in the artery wall. Translocator protein (TSPO) is abundantly expressed in lipid rich tissues. Recently, TSPO has been identified as a potential diagnostic tool in cardiovascular disease. The purpose of this study was to determine if the TSPO ligand, 18F-PBR111, can identify early atherosclerotic lesions and if TSPO expression can be used to identify distinct macrophage populations during lesion progression.\n\nMethods and ResultsApoE-/- mice were maintained on a high-fat diet for 3 or 12 weeks. C57BL/6J mice maintained on chow diet served as controls. Mice were administered 18F-PBR111 intravenously and PET/CT imaged. After euthanasia, aortas were isolated, fixed and optically cleared. Cleared aortas were immunostained with DAPI, and fluorescently labelled with antibodies to-TSPO, the tissue resident macrophage marker F4/80 and the monocyte-derived macrophage marker CD11b. TSPO expression and the macrophage markers were visualised in fatty streaks and mature lesions by light sheet microscopy. While tissue resident F4/80+ macrophages were evident in the arteries of animals without atherosclerosis, no CD11b+ macrophages were observed in these animals. In contrast, mature plaques had high CD11b and low F4/80 expression. A ~3-fold increase in the uptake of 18F-PBR111 was observed in the aortas of atherosclerotic mice relative to controls.\n\nConclusionsImaging of TSPO expression is a new approach for studying atherosclerotic lesion progression and inflammatory cell infiltration. The TSPO ligand, 18F-PBR111, is a potential clinical diagnostic tool for the detection and quantification of atherosclerotic lesion progression in humans.

pathology↗