Impact du stress psychologique sur le remodelage de l’interactome hôte-microbiote

A la frontière entre notre milieu interne et l’environnement, le tube digestif constitue une succession d’organe spécialisé qui permet la récolte d’énergie nécessaire au fonctionnement du corps et qui assure une fonction de barrière biologique contre les pathogènes et toxines de l’environnement. Il est en relation avec le microbiome qu’il abrite, et qui complète ses fonctions grâce à son vaste métagénome. Dans les phases pré-symptologiques des maladies chroniques, une rupture de l’homéostasie est observée et reflète des défauts de cet interactome hôte-microbiote. L’étude de ces phases dynamiques qui marquent le passage de l’équilibre au déséquilibre est complexe et requiert le développement de méthodes systémiques. Dans ce travail de thèse, nous avons employé un modèle de stress psychologique (SP) pour étudier ces phases précoces des physiopathologies intestinales. Les microenvironnements intestinaux de souris soumises à un stress d’évitement de l’eau ont été caractérisé macroscopiquement et à l’échelle moléculaire pour déterminer les changements de composition du microbiote adhérent et luminal, ainsi que les modifications de l’expression des gènes de l’épithélium. Nous avons pu mettre en évidence un effet régional pro-prolifératif et pro-apoptotique du SP sur la partie distale du colon, ainsi que des changements de diversité et composition du microbiote intestinal adhérent et luminal. Enfin le développement de nouvelles analyses multi-omiques a permis l’extraction de signatures intégratives et l’identification de biomarqueurs transcriptomiques de l’épithélium intestinal et bactériens adhérents et luminaux associés à des changements d’états des barrières d’organesAt the frontier between our internal and external milieu, the digestive tract constitutes a succession of specialized organs which harvest energy from diet to fulfill our body needs and ensures a biological barrier function against pathogens and toxins from the environment. It is associated to the microbiome, which completes its functions through its vast metagenome. In the pre-symptological phases of chronic diseases, a disruption of homeostasis is observed and reflects defects in this host-microbiota interactome. The study of these dynamic phases that mark the transition from equilibrium to disequilibrium and remain complex to capture; it requires the development of systemic methods. In this thesis work, we employed a psychological stress (PS) model to study these early phases of gut pathophysiology. The gut microenvironments of mice subjected to water avoidance stress were characterized macroscopically and at the molecular level to determine changes in the composition of the adherent and luminal microbiota, as well as changes in epithelial gene expression. We were able to demonstrate a regional pro-proliferative and pro-apoptotic effect of SP on the distal part of the colon, as well as changes in the diversity and composition of the adherent and luminal intestinal microbiota. Finally, the development of new multi-omics analyses allowed the extraction of integrative signatures and the identification of transcriptomic biomarkers of the intestinal epithelium and adherent and luminal bacteria associated with changes in organ barrier state

MiBiOmics: an interactive web application for multi-omics data exploration and integration

International audienceBackground: Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows to acquire additional insights and generate novel hypotheses about a given biological system. However, it can become challenging given the often-large size of omics datasets and the diversity of existing techniques. Moreover, visualization tools for interpretation are usually non-accessible to biologists without programming skills.Results: Here, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated and interactive protocols. It implements classical ordination techniques and the inference of omics-based (multilayer) networks to mine complex biological systems, and identify robust biomarkers linked to specific contextual parameters or biological states.Conclusions: MiBiOmics provides easy-access to exploratory ordination techniques and to a network-based approach for integrative multi-omics analyses through an intuitive and interactive interface. MiBiOmics is currently available as a Shiny app at https://shiny-bird.univ-nantes.fr/app/Mibiomics and as a standalone application at https://gitlab.univ-nantes.fr/combi-ls2n/mibiomics

Expanded human CD8+CD45RClowFoxp3+ Tregs secreting IFNγ, IL-10, IL-34 and TGFβinhibit human transplant rejection

International audienceTregs play a critical role in the control of immune responses and tolerance induction; however our understanding of CD8+ Tregs is limited while they are particularly promising for therapeutic application. We previously reported that CD8+CD45RC[low] Tregs use IFNγ and IL-34 to suppress donor responses in a rat model of allotransplantation (Guillonneau et al, JCI, 2007 ; Bezieetal, JCI, 2015). Here, we aim to characterize human CD8+ Tregs to assess their potential for cell therapy in transplantation in comparison to CD4+CD25[high]CD127- Tregs

Expanded human CD8+CD45RClowFoxp3+ Tregs secreting IFNγ, IL-10, IL-34 and TGFβinhibit human transplant rejection

International audienceTregs play a critical role in the control of immune responses and tolerance induction; however our understanding of CD8+ Tregs is limited while they are particularly promising for therapeutic application. We previously reported that CD8+CD45RC[low] Tregs use IFNγ and IL-34 to suppress donor responses in a rat model of allotransplantation (Guillonneau et al, JCI, 2007 ; Bezieetal, JCI, 2015). Here, we aim to characterize human CD8+ Tregs to assess their potential for cell therapy in transplantation in comparison to CD4+CD25[high]CD127- Tregs

Ex Vivo Expanded Human Non-Cytotoxic CD8+CD45RClow/\textminus Tregs Efficiently Delay Skin Graft Rejection and GVHD in Humanized Mice

International audienc

Ex Vivo Expanded Human Non-Cytotoxic CD8+CD45RClow/\textminus Tregs Efficiently Delay Skin Graft Rejection and GVHD in Humanized Mice

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Expansion of natural CD8+Tregs for cell therapy

International audienceTregs play a critical role in the control of immune responses and tolerance induction; however our understanding of CD8+ Tregs is limited while they are particularly promising for therapeutic application. We previously reported that CD8+CD45RC[low] Tregs use IFNγ and IL-34 to suppress donor responses in a rat model of allotransplantation (Guillonneau et al, JCI, 2007; Bezie et al, JCI, 2015). Here, we aim to characterize human CD8+ Tregs to assess their potential for cell therapy in transplantation

Ex Vivo Expanded Human Non-Cytotoxic CD8+CD45RClow/-Tregs Efficiently Delay Skin Graft Rejection and GVHD in Humanized Mice

International audienceBoth CD4+and CD8+Tregs play a critical role in the control of immune responses and immune tolerance; however, our understanding of CD8+Tregs is limited while they are particularly promising for therapeutic application. We report here existence of highly suppressive human CD8+CD45RClow/-Tregs expressing Foxp3 and producing IFNγ, IL-10, IL-34, and TGFβ to mediate their suppressive activity. We demonstrate that total CD8+CD45RClow/-Tregs can be efficiently expanded in the presence of anti-CD3/28 mAbs, high-dose IL-2 and IL-15 and that such expanded Tregs efficiently delay GVHD and human skin transplantation rejection in immune humanized mice. Robustly expanded CD8+Tregs displayed a specific gene signature, upregulated cytokines and expansion in the presence of rapamycin greatly improved proliferation and suppression. We show that CD8+CD45RClow/-Tregs are equivalent to canonical CD4+CD25highCD127low/-Tregs for suppression of allogeneic immune responsesin vitro. Altogether, our results open new perspectives to tolerogenic strategies in human solid organ transplantation and GVHD

Ex Vivo Expanded Human Non-Cytotoxic CD8+CD45RClow/− Tregs Efficiently Delay Skin Graft Rejection and GVHD in Humanized Mice

Both CD4+ and CD8+ Tregs play a critical role in the control of immune responses and immune tolerance; however, our understanding of CD8+ Tregs is limited while they are particularly promising for therapeutic application. We report here existence of highly suppressive human CD8+CD45RClow/− Tregs expressing Foxp3 and producing IFNγ, IL-10, IL-34, and TGFβ to mediate their suppressive activity. We demonstrate that total CD8+CD45RClow/− Tregs can be efficiently expanded in the presence of anti-CD3/28 mAbs, high-dose IL-2 and IL-15 and that such expanded Tregs efficiently delay GVHD and human skin transplantation rejection in immune humanized mice. Robustly expanded CD8+ Tregs displayed a specific gene signature, upregulated cytokines and expansion in the presence of rapamycin greatly improved proliferation and suppression. We show that CD8+CD45RClow/− Tregs are equivalent to canonical CD4+CD25highCD127low/− Tregs for suppression of allogeneic immune responses in vitro. Altogether, our results open new perspectives to tolerogenic strategies in human solid organ transplantation and GVHD

Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System

International audienceAutism Spectrum Disorders (ASDs) are neurodevelopmental disorders defined by impaired social interactions and communication with repetitive behaviors, activities, or interests. Gastrointestinal (GI) disturbances and gut microbiota dysbiosis are frequently associated with ASD in childhood. However, it is not known whether microbiota dysbiosis in ASD patients also occurs in adulthood. Further, the consequences of altered gut microbiota on digestive functions and the enteric nervous system (ENS) remain unexplored. Therefore, we studied, in mice, the ability offecal supernatant (FS) from adult ASD patients to induce GI dysfunctions and ENS remodeling. First, the analyses of the fecal microbiota composition in adult ASD patients indicated a reduced α-diversity and increased abundance of three bacterial 16S rRNA gene amplicon sequence variants compared to healthy controls (HC). The transfer of FS from ASD patients (FS–ASD) to mice decreased colonic barrier permeability by 29% and 58% compared to FS–HC for paracellular and transcellular permeability, respectively. These effects are associated with the reduced expression of the tight junction proteins JAM-A, ZO-2, cingulin, and proinflammatory cytokines TNFα and IL1β. In addition, the expression of glial and neuronal molecules was reduced by FS–ASD as compared to FS-HC in particular for those involved in neuronal connectivity (βIII-tubulin and synapsin decreased by 31% and 67%, respectively). Our data suggest that changes in microbiota composition in ASD may contribute to GI alterations, and in part, via ENS remodeling