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Biology subjects

Tinevez, J.-Y.

Publications and source records attributed to Tinevez, J.-Y..

33 records · Page 2Linked to original sources

Insulin resistance-driven beta-cell adaptation in mice: Mechanistic characterization and 3D analysis

Aims/hypothesisPancreatic beta cells secrete insulin to control glucose homeostasis. Beta cells can also adapt their function and mass when more insulin is required, especially in situations of insulin resistance (IR). Beta-cell mass adaptation can be achieved through either beta-cell proliferation or beta-cell neogenesis, a process that involves de novo beta-cell production from precursor cells. Signals and mechanisms that control adult beta-cell neogenesis and regulate the balance between beta-cell proliferation and/or beta-cell neogenesis still need to be fully deciphered. To do so, we previously developed a mouse model of pancreatic adaptation in response to a severe insulin resistance induced by a chronic glucocorticoid (GC) treatment. We observed a massive insulin production due to beta-cell adaptation by both proliferation and neogenesis. In the present study, we aimed at further characterizing beta-cell adaptation in response to mild or severe IR by studying various GC doses, along with other pharmacological or genetic models of IR. Further, we characterized the impact of aging on pancreatic adaptation in response to GC-induced IR. Finally, we precisely quantified adult beta-cell neogenesis by developing an original 3D method of beta-cell mass analysis in toto after organ clearing. MethodsGlucose metabolism, insulin secretion and pancreatic beta-cell adaptation were studied in mice rendered IR either by adipose tissue specific invalidation of SEIPIN, by chronic treatment with the insulin receptor antagonist S961 or by chronic treatment with several doses of GC both in young and aged mice. Moreover, we developed and used an unbiased-3D analysis of beta cells on whole cleared pancreas. ResultsWe demonstrated that beta-cell neogenesis - reflected by an increase in islet density - is constantly observed in response to genetically- or pharmacology-induced (S961 or GC) IR. Next, we observed that pancreatic adaptation mechanisms are closely defined by the level of IR. Indeed, mild IR induced by low dose of GC resulted in functional adaptation solely, while more severe IR induced by higher doses of GC resulted in an increase in both islet density and mean islet size, reflecting beta-cell neogenesis and proliferation, respectively. Then, we showed that in older mice, beta-cell adaptation through neogenesis is preserved in response to IR. Finally, using a new and unbiased 3D analysis, we confirmed the increase in islet density and mean islet size after GCs treatment. Conclusions/interpretationOur results present evidence that beta-cell neogenesis is a preferential mechanism of pancreatic adaptation to increase insulin secretion in response to IR in mice. Moreover, aging does not preclude beta-cell neogenesis, suggesting that it could be triggered in elderly to compensate for IR. Finally, our innovative technique of 3D analysis of whole pancreas confirms the existence of adult beta-cell neogenesis and offers a new avenue to study islet cells and pancreas adaptation. Research in contextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIInsulin resistance can be compensated by improved insulin secretion and increased beta-cell mass. C_LIO_LINew beta cells can be formed in the pancreas of adult mice through the differentiation of precursors, a process known as neogenesis. C_LIO_LIWe previously demonstrated that glucocorticoid (GC) -induced insulin resistance leads to enhanced beta-cell proliferation and neogenesis. C_LI What is the key question?O_LIIs adaptive beta-cell neogenesis specific to GC-induced insulin resistance and persists in old mice ? C_LI What are the new findings?O_LIInsulin resistance, either genetically- or drug-induced, is a key driver to induce adaptive beta-cell neogenesis in the mouse pancreas. C_LIO_LIAging does not prevent the induction of beta-cell neogenesis in response to insulin resistance. C_LIO_LIThree-dimension analysis on cleared pancreas confirms beta-cell neogenesis in mouse models of GC-induced insulin resistance. C_LI How might this impact on clinical practice in the foreseeable future?O_LIThe mouse model of adaptive beta-cell neogenesis will be helpful to define new therapeutic targets to induce the formation of new beta cells and treat diabetes. C_LI

physiology↗

Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression

The maintenance of neural stem cells (NSCs) in the adult brain depends on their activation frequency and division mode. We use long-term intravital imaging of NSCs in the zebrafish adult telencephalon to link activation and division mode with predictive cellular and molecular parameters. We reveal that apical surface area and expression of the Notch ligand DeltaA predict NSC activation frequency, while deltaA expression marks NSC commitment to neurogenesis. We also find that deltaA-negative NSCs constitute the bona fide self-renewing NSC pool and systematically engage in asymmetric divisions generating a self-renewing deltaAneg and a neurogenic deltaApos NSC. Finally, modulation of Notch signaling during imaging indicates that the prediction of activation frequency by apical size, and the asymmetric divisions of deltaAneg NSCs, are functionally independent of Notch. These results provide dynamic qualitative and quantitative readouts of NSC lineage progression in vivo and support a hierarchical organization of NSCs in differently fated sub-populations.

neuroscience↗

ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks

Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.

biophysics↗

Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool.

Efficient tools allowing the extraction of 2D surfaces from 3D-microscopy data are essential for studies aiming to decipher the complex cellular choreography through which epithelium morphogenesis takes place during development. Most existing methods allow for the extraction of a single and smooth manifold of sufficiently high signal intensity and contrast, and usually fail when the surface of interest has a rough topography or when its localization is hampered by other surrounding structures of higher contrast. Multiple surface segmentation entails laborious manual annotations of the various surfaces separately. As automating this task is critical in studies involving tissue-tissue or tissue-matrix interaction, we developed the Zellige software, which allows the extraction of a non-prescribed number of surfaces of varying inclination, contrast, and texture from a 3D image. The tool requires the adjustment of a small set of control parameters, for which we provide an intuitive interface implemented as a Fiji plugin. As a proof of principle of the versatility of Zellige, we demonstrate its performance and robustness on synthetic images and on four different types of biological samples, covering a wide range of biological contexts.

bioinformatics↗

Neutrophils degranulate GAG-containing proteoglycofili, which block Shigella growth and degrade virulence factors

Summary paragraphNeutrophil degranulation plays a central role in their ability to kill pathogens but also to stimulate other immune cells1-3. Here we show that neutrophil degranulation, induced in hypoxia or upon Shigella infection in vitro and in vivo, leads to the release of polymers called neutrophil Proteoglycofili (PGF). PGF are mainly composed of granular proteins (myeloperoxidase, elastase, lactoferrin, cathelicidin, albumin) pre-stored in various types of granules, and chondroitin sulfate. PGF individual fibers have a diameter of 43.9 {+/-} 20.3 nm and. They secreted by viable neutrophils and do not contain DNA, as opposed to NETs which contains also granular proteins, chondroitin sulfate in addition to chromatin, released upon neutrophil disintegration and cell death. We demonstrated that PGF block the growth of Shigella and other bacteria and degrade Shigella virulence factors. The degradation of the chondroitin sulfate polymers with testes hyaluronidases destabilizes PGF ultrastructure and abolishes its antimicrobial activity. Our results provide novel insights in the neutrophil degranulation process and open new doors for the investigation of PGF contribution to cytokines concentration gradient formation and adaptive immune cells activation. Further investigations are required to better appreciate the importance of this "sterile blaster" in infectious or inflammatory diseases.

immunology↗

Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging

Intermediate filaments (IF) are involved in key cellular functions including polarization, migration, and protection against large deformations. These functions are related to their remarkable ability to extend without breaking, a capacity that should be determined by the molecular organization of subunits within filaments. However, this structure-mechanics relationship remains poorly understood at the molecular level. Here, using super-resolution microscopy (SRM), we show that vimentin filaments exhibit a ~49 nm axial repeat both in cells and in vitro. As unit-length-filaments (ULFs) were measured at ~59 nm, this demonstrates a partial overlap of ULFs during filament assembly. Using an SRM-compatible stretching device, we also provide evidence that the extensibility of vimentin is due to the unfolding of its subunits and not to their sliding, thus establishing a direct link between the structural organization and its mechanical properties. Overall, our results pave the way for future studies of IF assembly, mechanical and structural properties in cells.

biophysics↗

Bringing TrackMate in the era of machine-learning and deep-learning.

TrackMate is an automated tracking software used to analyze bioimages and distributed as a Fiji plugin. Here we introduce a new version of TrackMate rewritten to improve performance and usability, and integrating several popular machine and deep learning algorithms to improve versatility. We illustrate how these new components can be used to efficiently track objects from brightfield and fluorescence microscopy images across a wide range of bio-imaging experiments.

bioinformatics↗

Concentration of intraflagellar transport proteins at the ciliary base is required for proper train injection

Construction of cilia and flagella relies on Intraflagellar Transport (IFT). Although IFT proteins can be found in multiple locations in the cell, transport has only been reported along the axoneme. Here, we reveal that IFT concentration at the base of the flagellum of Trypanosoma brucei is required for proper assembly of IFT trains. Using live cell imaging at high resolution and direct optical nanoscopy with axially localized detection (DONALD) of fixed trypanosomes, we demonstrate that IFT proteins are localised around the 9 doublet microtubules of the proximal portion of the transition zone, just on top of the transition fibres. Super-resolution microscopy and photobleaching studies reveal that knockdown of the RP2 transition fibre protein results in reduced IFT protein concentration and turnover at the base of the flagellum. This in turn is accompanied by a 4- to 8-fold drop in the frequency of IFT train injection. We propose that the flagellum base provides a unique environment to assemble IFT trains.

cell biology↗

DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.

BO_SCPLOWACKGROUNDC_SCPLOWQuantitative imaging of epithelial tissues prompts for bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common pre-processing step consists in projecting the acquired 3D volume on a 2D plane mapping the tissue surface. Indeed, while segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in Developmental and Cell Biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement. RO_SCPLOWESULTSC_SCPLOWHere we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes, and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a user-friendly and configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools. CO_SCPLOWONCLUSIONSC_SCPLOWWe find that LocalZProjector performs well even in situations where the volume to project also contains un-wanted signal in other layers. We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs.

bioinformatics↗

Direct tracking of single proviruses reveals HIV-1/LEDGF complexes excluded from virus-induced membraneless organelles

HIV integration occurs in chromatin sites that favor the release of high levels of viral progeny, alternatively the virus is also able to discreetly coexist with the host. The viral infection perturbs the cellular environment inducing the remodeling of the nuclear landscape. Indeed, HIV-1 triggers the nuclear clustering of the host factor CPSF6, but the underlying mechanism is poorly understood. Our data indicate that HIV usurps a recently discovered biological phenomenon, called liquid-liquid phase separation (LLPS), to hijack the host cell. We observed CPSF6 clusters as part of HIV-induced membraneless organelles (HIV-1 MLOs) in macrophages, which are one of the main HIV target cells. We describe that HIV-1 MLOs follow phase separation rules and represent functional biomolecular condensates. We highlight HIV-1 MLOs as hubs of nuclear reverse transcription, while the double stranded viral DNA, once formed, rapidly migrates outside these structures. Transcription-competent proviruses localize outside, but near HIV-1 MLOs, in LEDGF-abundant regions, known to be active chromatin sites. Therefore, HIV-1 MLOs orchestrate viral events prior to the integration step and create a favorable environment for the viral replication. This study uncovers single functional host-viral complexes in their nuclear landscape, which is markedly restructured by HIV-1.

microbiology↗

Automated cell tracking using StarDist and TrackMate

The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipelines usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images.

cell biology↗

Dynamic spatiotemporal coordination of neural stem cell fate decisions through local feedback in the adult vertebrate brain

Neural stem cell (NSC) populations persist in the adult vertebrate brain over a life time, and their homeostasis is controlled at the population level. The nature and properties of these coordination mechanisms remain unknown. Here we combine dynamic imaging of entire NSC populations in their in vivo niche over weeks, pharmacological manipulations, mathematical modeling and spatial statistics, and demonstrate that NSCs use spatiotemporally resolved local feedbacks to coordinate their decision to divide. These involve a Notch-mediated inhibition from transient neural progenitors, and a dispersion effect from dividing NSCs themselves, exerted with a delay of 9-12 days. Simulations from a stochastic NSC lattice model capturing these interactions demonstrate that they are linked by lineage progression and control the spatiotemporal distribution of output neurons. These results highlight how local and temporally delayed interactions occurring between brain germinal cells generate self-propagating dynamics that maintain NSC population homeostasis with specific spatiotemporal correlations.

neuroscience↗

Imaging of red-shifted photons from bioluminescent tumours using fluorescence by unbound excitation from luminescence

Early detection of tumours is today a major challenge and requires sensitive imaging methodologies coupled with new efficient probes. Bioluminescence imaging has been widely used in the field of oncology and several cancer cell lines have been genetically modified to provide bioluminescence signals. However, photons that are emitted by the majority of commonly used luciferases are usually in the blue part of the visible spectrum, where tissue absorption is still very high, making deep tissue imaging non-optimal and calling for optimised optical imaging methodologies. We have previously shown that red-shifting of bioluminescence signal by Fluorescence Unbound Excitation from Luminescence (FUEL) is a mean to increase bioluminescence signal sensitivity detection in vivo. Here, we applied FUEL to tumour detection in two different subcutaneous tumour models: the auto-luminescent human embryonic kidney (HEK293) cell line and the murine B16-F10 melanoma cell line previously transfected with the plasmid Luc2. Tumour size and bioluminescence were measured over time and tumour vascularization characterized. We then locally injected near infrared emitting Quantum Dots (NIR QDs)in the tumour site and observed a red-shifting of bioluminescence signal by (FUEL) indicating that FUEL could be used to allow deeper tumour detection.

bioengineering↗

Bidirectional intraflagellar transport is restricted to only two microtubule doublets in the trypanosome flagellum

Intraflagellar transport (IFT) is the rapid bidirectional movement of large protein complexes driven by kinesin and dynein motors along microtubule doublets of cilia and flagella. Here we used a combination of high-resolution electron and light microscopy to investigate how and where these IFT trains move within the flagellum of the protist Trypanosoma brucei. Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) analysis of trypanosomes showed that trains are found almost exclusively along two sets of doublets (3-4 and 7-8) and distribute in two categories according to their length. High-resolution live imaging of cells expressing mNeonGreen::IFT81 or GFP::IFT52 revealed for the first time IFT trafficking on two parallel lines within the flagellum. Anterograde and retrograde IFT occur on each of these lines. At the distal end, a large individual anterograde IFT train is converted in several smaller retrograde trains in the space of 3-4 seconds while remaining on the same side of the axoneme.

cell biology↗

Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking

During development coordinated cell behaviors orchestrate tissue and organ morphogenesis to suit the lifestyle of the organism. We have used here the crustacean Parhyale hawaiensis to study the cellular basis of limb development. Transgenic Parhyale embryos with fluorescently labeled nuclei were imaged at high spatiotemporal resolution with multi-view light-sheet fluorescence microscopy over several days of embryogenesis spanning appendage morphogenesis from early specification up to late differentiation stages. Cell tracking with a new tool called Massive Multi-view Tracker (MaMuT) enabled the reconstruction of the complete cell lineage of an outgrowing thoracic limb with single-cell resolution. In silico clonal analyses suggested that the limb primordium becomes subdivided from an early stage first into anterior-posterior and then into dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb bud formation is associated with the spatial modulation of cell proliferation, while limb elongation is also driven by the preferential orientation of division of epidermal cells along the proximal-distal axis of growth. Cellular reconstructions were predictive of the expression patterns of limb development genes including the Decapentaplegic (Dpp) morphogen.\n\nHIGHLIGHTSO_LIMulti-view light-sheet microscopy of crustacean embryos from species Parhyale hawaiensis are ideal for cellular-level analysis of organ morphogenesis.\nC_LIO_LILineages of 3-dimensional organs were reconstructed at single-cell resolution with the Fiji/ImageJ plugin Massive Multi-view Tracker.\nC_LIO_LIThe Parhyale limb primordium undergoes early lineage restrictions associated with particular cell behaviors and patterns of gene expression.\nC_LIO_LIDifferential rates of cell proliferation and oriented cell divisions guide appendage proximal-distal outgrowth.\nC_LI

developmental biology↗