Biology subjects

Valitutti, S.

Publications and source records attributed to Valitutti, S..

5 recordsLinked to original sources

bioRxiv2024

Highly adaptable deep-learning platform for automated detection and analysis of vesicle exocytosis

Vesicle exocytosis is a fundamental component of intercellular communication, in all organisms. It has been studied for decades, using various imaging tools. Nevertheless, exocytosis research is still limited by the lack of reliable automated analysis procedures. To address this, we developed the Intelligent Vesicle Exocytosis Analysis Platform (IVEA), a nearly universal solution for analyzing exocytosis acquired with live cell imaging. IVEA is applicable to a wide variety of experimental model systems, microscopes and reporter fluorophores. IVEA combines state-of-the-art deep-learning and computer vision regimes to enable fully automated analysis of large data. IVEA runs as a FIJI plugin and does not require prior training or human intervention. IVEA is 60 times faster than manual analysis and is able to detect rare events often missed by the human eye. Overall, IVEA represents a breakthrough in the analysis of cellular secretory mechanisms and has a transformative potential for the exocytosis imaging field.

bioengineering↗

bioRxiv2024

Pore formation at the lytic synapse triggers the canonical pyroptotic cell death pathway

Prokaryotic pore-forming toxins drive inflammasome activation and pyroptosis through K+-dependent activation of the canonical NLRP3/caspase-1/gasdermin D signaling axis. In this study, we hypothesized that perforin, a eukaryotic pore-forming protein released into the lytic synapse by antigen-specific cytotoxic T lymphocytes (CTLs) upon cognate antigen recognition, mimics the pro-pyroptotic activity of ancestral pore-forming toxins, complementing its role as a conduit for granzymes. Utilizing imaging and molecular approaches, we demonstrate that perforation of target cells upon CTL attack elicits swift K+ efflux followed by NLRP3-dependent activation of proinflammatory caspase-1 and its major substrate, the pyroptotic executioner gasdermin D (GSDMD). Acute target cell death upon CTL attack is gasdermin-dependent and demonstrates morphological and molecular features of pyroptosis, including pyroptotic body formation, cell bloating, plasma membrane rupture, and release of intracellular contents. Perforation of target cells by soluble perforin is sufficient to trigger rapid K+ efflux, caspase-1 activation, and pyroptosis. By contrast, sustained interaction with CTLs unmasks a delayed apoptotic phenotype in the remaining target cells. Interestingly, exposure of target cells to exogenous supramolecular attack particles (SMAPs) recapitulates this apoptotic phenotype, suggesting that soluble perforin and SMAPs play dichotomous roles in target cell death. Our results reveal a novel mechanism for engagement of pyroptotic machinery upon CTL attack, in which perforin itself can autonomously engage programmed cell death (PCD), highlighting the complexity and diversity of the CTL lytic arsenal.

immunology↗

bioRxiv2023

ISiCell: involving biologists in the design process of agent-based models in cell biology

Agent-based models are commonly used in biology to study tissue-scale phenomena by reproducing the individual behavior of the cells. They offer the possibility to study cellular biology at the individual cell scale to explore the basic behavior of cells which are responsible of the emergence of more complex phenomena at the tissue scale. Additionally, they can produce a predictive tool that will help taking decisions for biologic experiments based on in silico simulations. However these models require a good intercomprehension between the biologists and the modelers and thus it may take weeks or months to end up providing a usable prototype. To address this limitation, we propose a new methodology to facilitate the dialog between biologists and modelers and improve biologists involvement in the design of the model. For this purpose, UML diagrams, in particular, state-transition and activity diagrams, are used. They allow a better comprehension of the model for the biologists and offer a general frame for structuring models. Visualization of simulations is also used to have qualitative feedbacks from the biologist on the model. They are instrumental to validate or refine the prototype before exploring it. Alongside this methodology, we propose a web platform that enables to build state-transition and activity diagrams to describe a model and translate them into code. The generated code is then compiled on-the-fly and simulations are ready to visualize and explore. The platform also disposes of tools to directly visualize and manually explore the model. These tools allow for qualitative validation of the model and additional interaction with the biologists. Finally in this article, we show the capacity of our platform to reproduce models from the literature and to build new models starting from workshops with biologists. Its range of application is wide and includes immunology, oncology or cell biology. Author summaryWe developed a methodology based on diagrams to facilitate the dialog between computer scientists and biologists when building in silico models. The main idea is to limit misunderstandings and improve the involvement of the biologists in the prototyping process. For this purpose, we use visual methods to simplify the modeling phase. Alongside this methodology, we propose a web platform, called ISiCell, which enables to visually code thanks to diagrams that will be translated into code. The platform allows for compiling the generated code on the fly and to visualize and explore the model directly with the platform. The strong advantage of the platform is that one day workshop biologist/modeler allows to build new models. Additionally, we were able to reproduce models from the literature within the modeling platform showing the versatility of the tool. Our long-term objective is to use our methodology and platform in new contexts to develop new models. We intend the make the platform more user friendly in order to expand the community of users. Involving biologists in the conception of in silico models might improve their acceptability in the community.

systems biology↗

bioRxiv2021

T helper cell-licensed mast cells promote inflammatory Th17 cells

CD4+ T helper cells (Th) infiltrate sites of inflammation and orchestrate the immune response by instructing local leukocytes. Mast cells (MCs) are tissue sentinel cells particularly abundant in skin and mucosa. Here, we analyzed the interplay between human MCs and Th cells and, through the application of RNAseq and functional assays, showed that Th cells induced a specific transcriptomic program in helped MCs (named here MCTH) driving them toward an inflammatory phenotype. The gene signature of MCTH indicated that MCs helped by Th cell acquired in turn the capacity to regulate effector T cell response through wide-range of soluble and membrane ligands. Accordingly, we showed that MCTH promoted Th17 cells and notably an inflammatory subset of Th17, producing both IFN-{gamma} and GM-CSF, through a PGE2 and IL-1{beta} axis. Our findings demonstrate that activated effector/memory CD4+ T cells activate and instruct resting MCs toward a specific differentiated pro-inflammatory phenotype endowed with the capacity to speak back to effector T cells and to mold their functions.

immunology↗

bioRxiv2020

Stochastic asymmetric repartition of lytic machinery in dividing human CD8+ T cells generates heterogeneous killing behavior

Cytotoxic immune cells are endowed with a high degree of heterogeneity in their lytic function, but how this heterogeneity is generated is still an open question. We therefore investigated if human CD8+ T cells could segregate their lytic components during telophase, using imaging flow cytometry, confocal microscopy and live cell imaging. We show that CD107a+-intracellular vesicles, perforin and granzyme B unevenly segregate in a constant fraction of telophasic cells during each division round. Mathematical modeling posits that unequal lytic molecule inheritance by daughter cells results from the random distribution of lytic granules on the two sides of the cleavage furrow. Finally, we establish that the level of lytic compartment in individual CTL dictates CTL killing capacity. Together, our results show the stochastic asymmetric distribution of effector molecules in dividing CD8+ T cells. They propose uneven mitotic repartition of pre-packaged lytic components as a mechanism generating non-hereditary functional heterogeneity in CTL.

immunology↗