Biology subjects

Thoumine, O.

Publications and source records attributed to Thoumine, O..

9 recordsLinked to original sources

bioRxiv2026

Adaptive-optics lattice light-sheet microscopy enables correlative single-molecule imaging of endogenous proteins in native environments

Resolving molecular organization and dynamics in native environments remains challenging, as single-molecule imaging requires high sensitivity and spatiotemporal resolution while preserving 3D cellular context. Here, we present ALPINE (Adaptive-optics Lattice light-sheet microscopy for endogenous Protein Imaging in Native Environments), a modular framework for quantitative single-molecule imaging into complex biological samples. ALPINE combines adaptive-optics lattice light-sheet microscopy, programmable PSF shaping and acquisition stabilization, an engineered cell-specific labelling toolkit for endogenous cell-surface proteins and analysis pipelines assigning molecular localizations and trajectories to 3D cellular compartments. Labelling endogenous AMPA receptors in intact brain tissue, we demonstrate aberration-corrected 3D single-molecule localization and nanoscale organization within neuronal compartments. Importantly, fast optical sectioning of lattice light-sheet illumination further enables 3D single-molecule tracking in live tissue and quantification of molecular dynamics within native cellular environment. Together, ALPINE provides a modular approach to investigate how endogenous molecules are organized and dynamically regulated in complex biological systems, with components adaptable to diverse biological questions and imaging modalities.

neuroscience↗

bioRxiv2026

Neurospheres from primary rodent brain cells to probe the 3D organization and function of synapses

To improve our understanding of synapse assembly, there is a need for robust, easy-to-use, and physiologically relevant in-vitro models allowing the controllable formation of neuronal contacts in a reasonable time, whose structure and function can be investigated using advanced microscopy. To address this challenge, we engineered 3D cultures from rodent dissociated hippocampal cells, that spontaneously assemble in low attachment U-bottom wells into compact spheroids of reproducible dimensions (100-300 microns), determined by the number of seeded cells. These neurospheres contain a mix of neurons and glial cells and grow over time in culture, through the combination of cell proliferation and neurite extension. Neurospheres were immunostained in fluid phase, and/or sparsely electroporated for the multi-color visualization of synaptic proteins. Neurons extend an elaborate network of axons and dendrites, forming within 2 weeks numerous excitatory and inhibitory synapses identified at the structural level by confocal and electron microscopy, and at the functional level by electrophysiology. Periodic calcium oscillations throughout neurospheres further highlight network activity. Finally, we demonstrate the potential of neurospheres to study synaptogenesis by modulating and visualizing the adhesion protein neuroligin-1. Overall, neurospheres represent a standardized and cost-effective system to study synapse structure and function at high resolution in 3D, that should be quite appealing to the cellular neurobiology community.

neuroscience↗

bioRxiv2024

High-affinity detection of endogenously biotinylated neuroligin-1 at excitatory and inhibitory synapses using a tagged knock-in mouse strain

Neuroligins (NLGNs) are important cell adhesion molecules mediating trans-synaptic contacts between neurons. However, the high-yield biochemical isolation and visualization of endogenous NLGNs have been hampered by the lack of efficient antibodies to these proteins. Thus, to reveal their sub-cellular distribution, binding partners, and synaptic function, NLGNs have been extensively manipulated using knock-down, knock-out, or over-expression approaches, overall leading to controversial results. As an alternative to the manipulation of NLGN expression level, we describe here the generation of a new transgenic mouse strain in which native NLGN1 was N-terminally tagged with a small biotin acceptor peptide (bAP) that can be enzymatically biotinylated by the exogenous delivery of biotin ligase. After showing that knock-in mice exhibit normal behavior as well as similar synaptic number, ultrastructure, transmission properties, and protein expression levels when compared to wild type counterparts, we exploited the fact that biotinylated bAP-NLGN1 can be selectively isolated or visualized using high-affinity streptavidin conjugates. Using immunoblotting and immunofluorescence, we show that bAP-NLGN1 binds both PSD-95 and gephyrin and distributes equally well at excitatory and inhibitory synapses, challenging the historical view that NLGN1 is exclusively localized at excitatory synapses. Using super-resolution fluorescence microscopy and electron microscopy, we further highlight that bAP-NLGN1 forms in the synaptic cleft a subset of nanodomains each containing a few NLGN1 dimers, while the number of nanodomains per synapse positively scales with the post-synapse size. Overall, our study not only provides a novel, extensively characterized transgenic mouse model which will be made available to the scientific community, but also an unprecedented view of the nanoscale organization of endogenous NLGN1.

neuroscience↗

bioRxiv2021

mir124-dependent tagging of glutamatergic synapses by synaptopodin controls non-uniform and input-specific homeostatic synaptic plasticity

Homeostatic synaptic plasticity (HSP) is a process by which neurons adjust synaptic strengths to compensate for various perturbations and which allows to stabilize neuronal activity. Yet, whether the highly diverse synapses harboring a neuron respond uniformly to a same perturbation is unclear and the underlying molecular determinants remain to be identified. Here, using patch-clamp recordings, immunolabeling and imaging approaches, we report that the ability of individual synapses to undergo HSP in response to activity-deprivation paradigms depends on the local expression of the spine apparatus related protein synaptopodin (SP) acting as a synaptic tag to promote AMPA receptor synaptic accumulation and spine growth. Gain and loss-of-function experiments indicate that this process relies on the local de-repression of SP translation by miR124 which supports both non-uniform and synapse-autonomous HSP induced by global or inputspecific activity deprivation, respectively. Our findings uncover an unexpected synaptic-tagging mechanism for HSP, whose molecular actors are intriguingly shared with Hebbian plasticity and linked to multiple neurological diseases.

neuroscience↗

bioRxiv2020

Iterative inhibition of commissural growth cone exploration, not post-crossing barrier, ensures forward midline navigation through SlitC-PlxnA1 signaling

Sensitization to Slits and Semaphorin (Sema)3B floor plate repellents after midline crossing is thought to be the mechanism expelling commissural axons contralaterally and preventing their back-turning. We studied the role of Slit-C terminal fragment sharing with Sema3B the Plexin (Plxn) A1 receptor, newly implicated in midline guidance. We generated a knock-in mouse strain baring PlxnA1Y1815F mutation altering SlitC but not Sema3B responses and observed recrossing phenotypes. Using fluorescent reporters, we found that Slits and Sema3B form clusters decorating an unexpectedly complex mesh of ramified FP glia basal processes spanning the entire navigation path. Time-lapse analyzes revealed that impaired SlitC sensitivity destabilized axon trajectories by inducing high levels of growth cone exploration from the floor plate entry, increasing risk of aberrant decisions. Thus, FP crossing is unlikely driven by post-crossing sensitization to SlitC. Rather, SlitC limits growth cone plasticity and exploration through reiterated contacts, continuously imposing a straight and forward-directed trajectory.

developmental biology↗

bioRxiv2020

FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins

Fluorescence live-cell and super-resolution microscopy methods have considerably advanced our understanding of the dynamics and mesoscale organization of macro-molecular complexes that drive cellular functions. However, different imaging techniques can provide quite disparate information about protein motion and organization, owing to their respective experimental ranges and limitations. To address these limitations, we present here a unified computer program that allows one to model and predict membrane protein dynamics at the ensemble and single molecule level, so as to reconcile imaging paradigms and quantitatively characterize protein behavior in complex cellular environments. FluoSim is an interactive real-time simulator of protein dynamics for live-cell imaging methods including SPT, FRAP, PAF, and FCS, and super-resolution imaging techniques such as PALM, dSTORM, and uPAINT. The software, thoroughly validated against experimental data on the canonical neurexin-neuroligin adhesion complex, integrates diffusion coefficients, binding rates, and fluorophore photo-physics to calculate in real time the distribution of thousands of independent molecules in 2D cellular geometries, providing simulated data of protein dynamics and localization directly comparable to actual experiments.

biophysics↗

bioRxiv2019

Optogenetic control of excitatory post-synaptic differentiation through neuroligin-1 tyrosine phosphorylation

Neuroligins (Nlgs) are adhesion proteins mediating trans-synaptic contacts in neurons. However, conflicting results around their role in synaptic differentiation arise from the various techniques used to manipulate Nlg expression. Orthogonally to these approaches, we triggered here the phosphorylation of endogenous Nlg1 in CA1 hippocampal neurons using a photoactivatable tyrosine kinase receptor (optoFGFR1). Light stimulation for 24 h selectively increased dendritic spine density and AMPA receptor-mediated EPSCs in wild-type neurons, but not in Nlg1 knock-out neurons or when endogenous Nlg1 was replaced by a non-phosphorylatable mutant (Y782F). Moreover, light stimulation of optoFGFR1 partially occluded LTP. Combined with computer simulations, our data support a model by which Nlg1 tyrosine phosphorylation promotes the assembly of an excitatory post-synaptic scaffold that captures surface AMPA receptors. This optogenetic strategy thus highlights the impact of Nlg1 intracellular signaling in synaptic differentiation and potentiation, while enabling an acute control of these mechanisms.\n\nImpact StatementOrthogonal to the traditional paradigms used to manipulate neuroligin expression level, the optogenetic trigger of tyrosine phosphorylation supports a strong role of endogenous neuroligin-1 in excitatory synaptic differentiation and potentiation.

neuroscience↗

bioRxiv2019

Spatial and temporal profiling of receptor membrane insertion controls commissural axon responses to midline repellents

Accurate perception of guidance cues is crucial for axonal pathfinding. During their initial navigation in the spinal cord, commissural axons are kept insensitive to midline repellents. Through yet unclear mechanisms acting during midline crossing in the floor plate, they switch on responsiveness to various repulsive signals, that establish a permanent midline barrier and propel the axons for exit. Whether these gains of response are coupled to occur in synchrony or rather are independently activated through signaling-specific programs is fully unknown. We set-up a paradigm for live imaging and super resolution analysis of guidance receptor dynamics during commissural growth cone navigation in chick and mouse embryos. We uncovered a remarkable program of delivery and allocation of receptors at the growth cone surface, generating receptor-specific spatial and temporal profiles. This reveals a mechanism whereby commissural growth cones can discriminate coincident repulsive signals that they functionalize at different time points of their navigation.

developmental biology↗

bioRxiv2017

Pre-post synaptic alignment through neuroligin tunes synaptic transmission efficiency

The nanoscale organization of neurotransmitter receptors relative to pre-synaptic release sites is a fundamental determinant of both the amplitude and reliability of synaptic transmission. How modifications in the alignment between pre- and post-synaptic machineries affect synaptic current properties has only been addressed with computer modeling, and therefore remains hypothetical. Using dual-color single molecule based super-resolution microscopy, we found a strong spatial correlation between AMPA receptor (AMPAR) nanodomains and the post-synaptic adhesion protein neuroligin-1 (NLG1). Expression of a C-terminal truncated form of NLG1 disrupted this correlation without affecting the intrinsic organization of AMPAR nanodomains. Moreover, this NLG1 dominant-negative mutant significantly shifted the pre-synaptic release machinery from AMPAR synaptic clusters. Electrophysiology and computer modeling show that this physical shift is sufficient to induce a significant decrease in synaptic transmission. Thus, our results suggest the necessity for synapses to release glutamate in front of AMPAR nanodomains, to maintain a high efficiency of synaptic responses.

neuroscience↗