Biology subjects

Studer, V.

Publications and source records attributed to Studer, V..

6 recordsLinked to original sources

bioRxiv2025

β-sheet stabilization of the island domain underlies ligand-induced LRR-RP activation of plant immune signaling

Leucine-rich repeat (LRR) receptor kinases (RKs) and receptor proteins (RPs) are important classes of plant pattern recognition receptors (PRRs) activating pattern-triggered immunity. While both classical and AI-based structural approaches have recently provided crucial insights into ligand-LRR-RK binding mechanisms, our understanding of ligand perception by LRR-RPs remains limited. In contrast to LRR-RKs, many LRR-RPs typically embed one or more loopout regions in their extracellular domains that are crucial for functionality. Here, we employed an AI-based approach to reveal a novel ligand-binding mechanism shared by the Arabidopsis LRR-RPs RLP23 and RLP42 - the PRRs for the short peptide ligands nlp20 and pg13, derived from NECROSIS- AND ETHYLENE-INDUCING PEPTIDE 1-like proteins (NLPs) and fungal endopolygalacturonases (PGs), respectively. This mechanism relies on a {beta}-strand interaction with the N-terminal part of the island domain (ID) loopout, which adopts an antiparallel {beta}-sheet conformation. Additionally, we investigated the larger and more complex binding interface of RLP32 - the PRR for proteobacterial TRANSLATION INITIATION FACTOR 1 (IF1), a folded protein ligand that requires its tertiary structure for recognition. Finally, we describe a mechanistic role of the ID for co-receptor recruitment conserved across LRR-RPs. Together, our results shed light on the ligand-binding mechanisms and receptor complex formation of this important class of PRRs. This opens avenues for a molecular understanding of the plant-pathogen co-evolution, as well as the engineering of plant immune receptors for crop disease resistance.

plant biology↗

bioRxiv2025

Tunable 3D Alveolosphere Model from Human Alveolar Cells: A Breakthrough Tool to Explore Emphysema Pathophysiology

RationaleThree-dimensional (3D) culture models such as alveolosphere, provide a unique tool to study emphysema mechanisms. Reducing the heterogeneity of alveolospheres which are currently mostly grown in Matrigel remains challenging. ObjectivesTo develop a tunable and reproducible 3D-alveolosphere model exclusively from human primary type II alveolar epithelial cells (AEC2) for modeling and understanding emphysema. MethodsAEC2 cells (HTII-280+) were isolated from 52 smoker and non-smoker lung samples and cultured in preformed photopolymerized hydrogel microwells of adjustable shape and size. Topological and phenotypic characterization were performed at Day (D)1, 7 and 14. Lamellar bodies (LB) were quantified using artificial intelligence (AI)-based image analysis of transmission electron microscopy (TEM) serial block face images. Emphysema was modeled through chronic exposure to 1 and 5% cigarette smoke extract (CSE) during 5 consecutive days. Measurements and Main Results3D-alveolospheres were maintained in culture for 14 days with central lumen formation observed from D7 to D14. Presence of tight junctions (TEM imaging and ZO-1 immunostaining) suggested epithelial barrier formation. AEC1 markers (p2xr4, pdpn) appeared progressively from D1 to D14 while AEC2 markers (abca3, sftpa, sftpc) persisted over time. TEM images indicated surfactant synthesis (LB, lipid bodies) and AI-driven LB quantification showed a decrease in the proportion of LB-containing cells over time. CSE exposure led to cell death, architectural disorganization, oxidative stress and inflammation. ConclusionThis standardized and adjustable 3D-alveolosphere model from human primary AEC2, reproduced key native alveolar features. CSE exposure provides an opportunity to appropriately study the pathophysiological pathways involved in emphysema.

cell biology↗

bioRxiv2024

Dissecting the binding mechanisms of synaptic membrane adhesion complexes using a micropattern based cellular model

The formation of adhesive cell-cell contacts is based on the intrinsic binding properties between specific transmembrane ligand-receptor pairs. In neurons, synaptic adhesion molecules provide a physical linkage between pre- and post-synaptic compartments, but the strength and the dynamic of these complexes in their actual membrane environments remain essentially unknown. To access such information, we developed a versatile assay to measure the affinity and binding kinetics of synaptic ligand-receptor interactions, based on the immobilization of Fc-tagged ligands on micropatterned substrates combined with live imaging of fluorescently-tagged counter receptors in heterologous cells. We applied this strategy to study the heterophilic complex formed between neurexin-1{beta} (Nrx1{beta}) and neuroligin-1 (Nlg1), compared to the homophilic SynCAM1 complex. First, the control of ligand density combined to the measurement of steady-state receptor enrichment at micropatterns demonstrates the high specificity of the matching molecular interactions and allows for the quantification of the two-dimensional affinity of the interaction in a membrane environment. Second, long-term FRAP experiments performed on the two molecular complexes and fitted with analytical models, demonstrate a diffusion-limited regime for SynCAM1 and a reaction-limited regime for Nlg1. This analysis provides a very long bond lifetime of the Nrx1{beta}-Nlg1 complex, which by comparison with a monomeric mutant of Nlg1, can be attributed to the constitutive dimerization of Nlg1. Finally, we used the stable Nrx1{beta}-Nlg1 complex as a pseudo-synaptic platform to analyze the rapid binding kinetics between the scaffolding protein PSD-95 and the intracellular domain of Nlg1, dissecting the contribution of the different PDZ domains through the use of specific PSD-95 point mutants.

neuroscience↗

bioRxiv2019

Different integrins mediate haptotaxis of T lymphocytes towards either lower or higher adhesion zones

Guidance of cells by molecules anchored on a substrate, known as haptotaxis, is arguably crucial in development, immunology and cancer, however the exact cues and mechanisms driving cell orientation in vivo are hardly identified. Adhesive haptotaxis has been described in the case of mesenchymatous cells that develop strong pulling forces with their substrates and orient via a tug of war mechanism - a competition between cells pulling edges. In the case of amoeboid cells that migrate with minimal interaction with their substrate, existence of adhesive haptotaxis remains unclear. Here, we studied the crawling of human T lymphocytes on substrates with spatially modulated adhesivity, and observed haptotaxis with surface concentrations of integrin ligands found on high endothelial veinules. Overexpression of ICAM-1 and VCAM-1 molecules observed in vivo at transmigration portals can therefore promote leukocyte recruitment. Mechanistically, we show that integrin-mediated haptotaxis of lymphocytes differ both from active chemotaxis, because no mechanotransduction was detected, and from the passive tug of war mechanism of mesenchymatous cells, because different integrins support opposite phenotypes. Cells favored more adherent zones with VLA-4 and, counterintuitively, less adherent zones with LFA-1. These results reveal that integrins control differential adhesive haptotaxis behaviors without mechanotransduction, and this smart capability may support unsuspected ways for cells path selection.

biophysics↗

bioRxiv2018

A generic widefield topographical and chemical photopatterning method for hydrogels.

3D cell culture aims at reconciliating the simplicity of in vitro models with the human like properties encountered in vivo. Soft permeable hydrogels have emerged as user-friendly materials to grow cells in more physiological conditions. With the intent on turning these homogeneous substrates into biomimetic templates, we introduce a generic solution compatible with the most biologically relevant and often frail materials. Here we take control of the chemical environment driving generic radical reactions to craft common gels with patterned light. In a simple microreactor, we harness the well-known inhibition of radicals by oxygen to enable topographical photopolymerization. Strikingly, by sustaining an oxygen rich environment, we can also induce hydrogel photo-scission which turns out to be a powerful and generic subtractive manufacturing method. We finally introduce a flexible patterned functionalization protocol based on available photo-linkers. Using these common tools on the most popular hydrogels, we tailored soft templates where cells grow or self-organize into standardized structures. The platform we describe has the potential to set a standard in future 3D cell culture experiments.

bioengineering↗

bioRxiv2018

A new approach to design artificial 3D micro-niches with combined chemical, topographical and rheological cues

The in vitro methods to recapitulate environmental cues around cells are usually optimized to test a specific property of the environment (biochemical nature or the stiffness of the extra cellular matrix (ECM), or nanotopography) for its capability to induce defined cell behaviors (lineage commitment, migration). Approaches that combine different environmental cues in 3D to assess the biological response of cells to the spatial organization of different biophysical and biochemical cues are growingly being developed. We demonstrate how the lamination of through-hole polymeric bio-functionalized membranes can be implemented to create complex bona fide micro-niches with differential 3D environmental properties using photoactive materials. Our approach enables to create micro-niches ranging in size from single cells to cell aggregates. They are bio-functionalized in 3D simultaneously with topographical featured, protein patterns and structured ECM surrogate with 1 micrometer resolution. We demonstrate how these niches extend in 3D the ability to pattern cells. We exemplify how they can be used to standardize cells shapes in 3D and to trigger the apico-basal polarization of single epithelial cells.

bioengineering↗