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How the diversification of cell types is regulated during development to generate stereotyped tissue patterns remains a challenging question. Here we applied cell type specific translational profiling (TRAP) approach to identify gene expression signatures underlying the diversification of two muscle subsets in Drosophila . Targeting the Slou-positive muscle population, we identified Ptx1 as a new component of the ventral muscle identity code. We also generated temporal transition profiles of TRAP-enriched genes and found that a set of genes encoding regulators of the actin cytoskeleton fitted a cluster specific for lateral transverse (LT) muscles. Two of them, dCryAB and Gelsolin (Gel) , encoding actin-binding sHsp and actin-severing protein respectively, displayed LT muscle prevailing expression positively regulated by LT identity factors Lms and Apterous. In dCryAB- mutant embryos, LT muscle shapes had an irregular appearance, whereas Gel -devoid LTs occasionally developed muscle fibre splitting. Importantly, split LT muscles in Gel mutants were enlarged and bore a greater number of myonuclei, a phenotype phenocopied by overexpression of the duf fusion gene. Muscle fibre splitting is a hallmark of diseased muscle in Duchenne and other muscular dystrophies, but how muscles get split is unknown. Our analyses yield evidence that an excessive myoblast fusion could result in splitting, and suggest a deregulation of fusion machinery in dystrophic muscles. We identify new muscle identity gene Ptx1 and a new class of identity realisator genes including Gel , whose function links muscle identity in Drosophila to dystrophic muscle splitting phenotype in humans. Significance statement Key features that make two cells differ from each other are shape and size. Here, by applying translational profiling of muscle subsets in Drosophila , we identify new muscle identity realisator genes dCryAB and Gel encoding actin-binding sHsp and actin-severing protein, respectively. They both regulate growth-related properties of a subset of embryonic muscles, the LT muscles. Intriguingly, Gel- devoid LTs undergo muscle fiber splitting, a phenotype also observed in Duchenne muscular dystrophy patients. LT muscle splitting in Gel mutants is due to an excessive myoblast fusion resulting in increased muscle size, offering clues to still unknown mechanisms of pathological muscle splitting in humans.

International audience; An original immuno-regulatory strategy against inflammatory bowel diseases based on the use of 28 kDa glutathione S-transferase (P28GST), a unique schistosome protein, was recently proposed. Improvement of intestinal inflammation occurs through restoration of the immunological balance between pro-inflammatory T-helper 1 (Th1) responses and both T-helper 2 (Th2) and regulatory responses. However, detailed mechanisms explaining how P28GST prevents colitis and promotes gut homeostasis remain unknown. Considering the complex interplay between the adaptive and innate immune system and the intestinal microbiota, we raised the question of the possible role of the microbial ecosystem in the anti-inflammatory effects mediated by the helminth-derived P28GST protein. We first analyzed, by 16S rRNA sequencing, the bacterial profiles of mice fecal microbiota at several time points of the P28GST-immunomodulation period prior to trinitrobenzene sulfonic acid (TNBS)-colitis. The influence of gut microbiota in the P28GST-mediated anti-inflammatory effects was then assessed by fecal microbiota transplantation experiments from P28GST-immunized mice to either conventional or microbiota depleted naïve recipient mice. Finally, the experimental data were supplemented by the temporal fecal microbiota compositions of P28GST-treated Crohn’s disease patients from a pilot clinical study (NCT02281916). The P28GST administration slightly modulated the diversity and composition of mouse fecal microbiota while it significantly reduced experimental colitis in mice. Fecal microbiota transplantation experiments failed to restore the P28GST-induced anti-inflammatory effects. In Crohn’s disease patients, P28GST also induced slight changes in their overall fecal bacterial composition. Collectively, these results provide key elements in both the anti-inflammatory mechanisms and the safe therapeutic use of immunomodulation with such promising helminth-derived molecules.

Skeletal muscles display specific features (size, shape, orientation, attachment site,number of nuclei), which are tightly controlled by the combinatorial expression of identity factors. Currently, process by which identity genes determine muscle characteristics is not fully understood. Uncovering how identity factors are interconnected and how they control network of genes specifying muscle cell fate remains a major challenge. To discover new actors of the identity code allowing the acquisition of individual muscle characteristics during Drosophila embryogenesis we optimised a genome wide cell specific approach called TRAP (Translating Ribosome Affinity Purification), which allows the isolation of mRNA engaged in translation. This method has been used on two restricted populations of muscle cells (Slou and Lms positive) and on the global musculature (Dufpositive) at three time windows covering key muscle developmental steps such as founder cell specification, myoblast fusion, attachment to the epidermis via tendon cells and the innervation by motoneurons.To assess gene expression at a global level in these muscle subsets, we performed transcriptomic analyses at targeted developmental windows by using microarray. First, a comparison of spatial gene expression allowed us to identify new potential actors of the identity code for Slou-positive muscles and the involvement of the RNA binding protein Bol in the structural organisation of muscle fibers. We also performed analyses of temporal transition profiles of genes differentially expressed in Slou- and Lms-positive muscles and identified cluster of genes enriched preferentially in the Lms population and encoding actin interacting proteins. We focused on two genes from this cluster, gel and dCryAB and determined their functions during myogenesis. These two proteins control a coordinated growth of the Lms-positive muscles by fine-tuning of both the number of fusion events and the elongation of myotubes to tendon cells. With this project, we have identified new potential actors of the identity code that govern the acquisition of individual properties of Slou and Lms muscle subsets during Drosophila embryogenesis. We hope that the newly generated data will enable to gain further knowledge on the corresponding orthologues during vertebrate myogenesis and will help to understand why particular muscles are affected in some myopathies.; Les muscles squelettiques présentent des propriétés individuelles de taille, forme, orientation, site d’attachement, nombre de noyaux, déterminées par l’expression d’une combinaison de facteurs d’identité. Les processus par lesquels ces gènes déterminent les caractéristiques finales du muscle ne sont pas pleinement compris. Découvrir comment ces régulateurs de l’identité sont connectés entre eux, à travers un réseau de gènes spécifiant le destin cellulaire de chaque type de muscle, reste un enjeu majeur. Pour identifier de nouveaux acteurs qui déterminent les caractéristiques individuelles du muscle au cours de l’embryogenèse chez la drosophile, nous avons optimisé l’approche cellule-spécifique TRAP (Translating Ribosome Affinity Purification) permettant l’isolation des ARNs messagers en cours de traduction. Cette méthode a été utilisée sur deux populations restreintes de muscles (Lms- et Slou-positives) et sur la population musculaire globale (Dufpositive) à trois fenêtres de temps ciblant des processus clés de la myogenèse tels que la spécification de cellules fondatrices, la fusion des myoblastes, l’attachement aux cellules de tendon et l’innervation par les motoneurones. Pour avoir une vue d’ensemble de l’expression des gènes dans ces différentes conditions, des analyses transcriptomiques à l’aide de puces ADNc ont été réalisées. Une étude spatiale nous a permis d’identifier de nouveaux acteurs potentiels du code d’identité nécessaires à la diversification de la population Slou ainsi que l’implication de la protéine de liaison à l’ARN, Boule, dans l’organisation des filaments d’actine au sein des fibres musculaires. Dans un second temps une analyse temporelle des données a révélé un ensemble de gènes codant pour des protéines de liaison à l’actine avec un enrichissemen tspécifique dans la population Lms positive. L’étude plus approfondie des gènes gel et dCryABa permis de déterminer leur rôle au cours de la myogenèse. Ces deux protéines participent de manière importante à la régulation de la croissance des muscles Lms positifs en régulant le nombre d’évènement de fusion, l’élongation et l’attachement des myotubes.A travers ce projet nous avons identifié de nouveaux acteurs potentiels du code d’identité, impliqués dans l’acquisition des propriétés distinctes des sous populations musculaires Slou et Lms au cours de l’embryogenèse en participant soit au contrôle de l’expression des gènes soit à l’acquisition des caractéristiques morphologiques finales. Nous espérons que les données générées permettront dans le futur d’acquérir de nouvelles connaissances sur les fonctions des orthologues de ces gènes au cours de la myogenèse desvertébrés et que cela aura un impact sur la compréhension de certaines myopathies.

International audience; The etiology of inflammatory bowel diseases remains largely unknown. We previously demonstrated that the expression of the peroxisome proliferator activated receptor-gamma (PPARγ) is downregulated in colonic epithelial cells of patients with ulcerative colitis (UC). PPARγ is a nuclear receptor that modulates inflammation. We hypothesized that its deficiency may play a role in the loss of intestinal homeostasis through the control of immunomodulatory factors. We found that thymic stromal lymphopoietin (TSLP), an epithelial cytokine with pleiotropic functions, is regulated by PPARγ. While this cytokine possesses two isoforms, only the short form (sfTSLP) was regulated by PPARγ. sfTSLP mRNA expression was decreased both in PPARγ knock-down Caco2 cells and cells treated with PPARγ antagonist, whereas PPARγ agonists induced the expression of sfTSLP in Caco2 and T-84 cells. The response element activated by PPARγ was identified in the promoter of the sfTSLP gene by chromatin immunoprecipitation and gene reporter assays. The expression of sfTSLP was significantly decreased in the colonic mucosa of UC patients compared to controls and was correlated with PPARγ expression. Our results identified sfTSLP as a new PPARγ-target gene and support the hypothesis that, in UC, PPARγ deficiency in colonic mucosa could play a role in the loss of intestinal tolerance through an impaired sfTSLP expression.

Environmental impact assessment of goods and services is nowadays a major challenge for both economic and ethical reasons. Life Cycle Assessment provides a well accepted methodology for modeling environmental impacts of human activities. This methodology relies on the decomposition of a studied system into interdependent processes in a step called Life Cycle Inventory. Every process has several environmental impacts and the composition of those processes provides the cumulated environmental impact for the studied human activities. Several organizations provide processes databases containing several thousands of processes with their interdependency links that are used by LCA practitioners to do an LCA study. Understanding and audit of those databases requires to analyze a huge amount of processes and their dependency relations. But those databases can contain thousands of processes linked together. We identified two problems that the experts faces using those databases: - organize the processes and their dependency relations to improve the comprehensibility; - calculate the impacts and, if it is not possible, find why it is not feasible. In this thesis, we: - show that there are some semantic similarities between the processes and their dependency relations and propose a new way to model the dependency relations in an inventory database. In our approach, we semantically index the processes using an ontology and we use a multi-layers model of the dependency relations. We also study a declarative approach of this multi-layers approach; - propose a method to calculate the environmental impacts of the processes based on linear algebra and graph theory, and we study the conditions of the feasibility of this calculation when we have a cyclic model. We developed a prototype based on this approach that showed some convincing results on different use cases. We tested our prototype on a case study based on a data set extracted from the National Renewable Energy restricted to the electricity production in the United-States., L'analyse des impacts environnementaux de la production de biens et de services est aujourd'hui devenue un enjeu majeur. L'analyse en cycle de vie est la méthode consacrée pour modéliser les impacts environnementaux des activités humaines. L'inventaire en cycle de vie, qui est l'une des étapes de cette méthode, consiste à décomposer les activités économiques en processus interdépendants. Chaque processus a des impacts environnementaux et la composition de ces processus nous donne l'impact cumulé des activités étudiées. Plusieurs entreprises et agences gouvernementales fournissent des bases de données d'inventaires en cycle de vie pour que les experts puissent réutiliser des processus déjà étudiés lors de l'analyse d'un nouveau système. L'audit et la compréhension de ces inventaires nécessite de s'intéresser à un très grand nombre de processus et à leurs relations d'interdépendance. Ces bases de données peuvent comporter plusieurs milliers de processus et des dizaines de milliers de relations de dépendance. Pour les experts qui utilisent les bases de données d'inventaire en cycle de vie, deux problèmes importants sont clairement identifiés : - organiser les processus pour avoir une meilleure compréhensibilité du modèle ; - calculer les impacts d'une modélisation (composition de processus) et, le cas échéant, détecter les raisons de la non convergence du calcul. Dans cette thèse, nous : - mettons en évidence de l'existence de similarités sémantiques entre les processus et leurs relations d'interdépendance et proposons une nouvelle approche pour modéliser les relations d'interdépendance entre les processus d'une base de données d'inventaire. Elle se base sur un étiquetage sémantique des processus à l'aide d'une ontologie et une modélisation multi-niveaux des relations d'interdépendance entre les processus. Nous étudions aussi deux approches déclaratives d'interaction avec ce modèle multi-niveau. - étudions les différentes méthodes de calcul des impacts basées sur des notions classiques d'algèbre linéaire et de théorie des graphes. Nous étudions aussi les conditions de non convergence de ces méthodes en présence de cycle dans le modèle des relations de dépendances. Un prototype implémentant cette approche a montré des résultats probants sur les cas étudiés. Nous avons réalisé une étude de cas de ce prototype sur les processus de production d'électricité aux États-Unis extraits de la base de données d'inventaire en cycle de vie de l'agence environnementale américaine. Ce prototype est à la base d'une application opérationnelle utilisée par l'entreprise.

National audience; Environmental impact assessment of goods and services is nowadays a major chal-lenge for both economic and ethical reasons. Life Cycle Assessment (LCA) provides a well-accepted methodology for modelling environmental impacts of human activities. One stage of the LCA methodology is Life Cycle Inventory (LCI), which consists of decomposing economic activities as elementary processes linked together through interdependency relations. A global analysis of economic activities requires considering a huge amount of elementary processes and interdependency links, making the model difficult to understand. In this paper, we propose a semantic approach for the modelling of LCI databases. The method has the advantage of offering a more comprehensible model. We explain our model and illustrate it with LCI data for the U.S. electricity production.