We present a methodological development for glycomics - a field which lags far behind its counterparts genomics and proteims in terms of available analytical tools. The proposed method will focus on profiling glycans epitopes (acetylated sialic acid and sulfatated extremities) which is currently beyond the state of the art of analytical chemistry and impairs the comprehensive characterisation of glycosylation profiles of proteins. The original concept underlying the proposition is the use of IR ion spectroscopy coupled with three dimension of separation (LC, IMS and MS) to resolve all existing isomeric patterns present in a heterogeneous mixture. The project brings together an interdisciplinary consortium of acknowledged experts in the fields of glycomics, ion spectroscopy, glycan synthesis and immunology.?To demonstrate the future impact of the method for glycosciences, we propose a case study: the early diagnostic of rheumatoid arthritis.

Clostridioides difficile, an anaerobic Gram-positive spore-forming bacterium, is responsible for a wide spectrum of infections ranging from diarrhea to life-threatening pseudomembranous colitis. The use of antibiotic therapy raises concerns about the selection of antibiotic-resistant bacteria at hospitals. New therapeutic targets should be investigated as alternatives to antibiotic treatments. Polysaccharides (PS) biosynthesis enzymes are encoded in a PS locus where most genes are essential for bacterial viability. We propose therefore the enzymes involved in PS biosynthesis as new therapeutic targets. Moreover, vaccines currently under development target the toxins and may not prevent C. difficile colonization and dissemination. We also propose in this project to evaluate PSII and/or LTA as vaccine component(s) of a vaccine that may prevent C. difficile colonization and dissemination. To that aim, the project will (i) define if either one or both PSII and LTA are essential for bacterial viability, ii) identify specific enzymes involved in PSII or LTA biosynthesis, (iii) target them with inhibitors and (iv) test PSII and LTA as vaccine candidates using an innovative approach. We recently developed a new genetic conditional lethal mutant system and have already obtained antibodies directed against PSII. Using these tools, we showed that the PSII seems to be essential for bacterial viability. The project will be divided into three tasks. The first will determine whether PSII, its anchoring and/or LTA are essential and define at least two enzymes as new therapeutic targets, one of each involved in each PS biosynthesis. The second task will look for inhibitors able to target these specific enzymes, using in silico models and a chemistry approach. The last task will test PSII and LTA as vaccine candidates. This project aims to combat C. difficile infections and prevent them using vaccination.

Despite decades of lipid lowering drug delivery, prevention strategies and efforts in research, cardiovascular diseases, mainly caused by atherosclerosis, are still the leading cause of death worldwide. New therapies are then mandatory to reduce the residual cardiovascular risk and to prevent atherothrombotic events. Atherosclerosis is a chronic inflammatory disease of the vascular wall triggered by low density lipoprotein internalisation within the subendothelial space. More than the obstruction of the arterial lumen, instability and rupture of the plaque are now recognized as the most deleterious events. Among processes triggering plaque instability, intraplaque neovascularization accelerates plaque progression, induces plaque rupture and attenuates statin benefit in human. Our preliminary data identified the nuclear receptor Rev-erb-a as a putative inhibitor of intraplaque neovascularization in human and mouse plaques in vivo as well as in vitro in endothelial cells. We then hypothesize that Rev-erb-a represents a new anti-atherogenic target that prevents intraplaque neovascularization by inhibiting the angiogenic activity of endothelial cells. This proposal will be the first to address the role of Rev-erba in angiogenesis and intraplaque neovascularization. This project will involve original available mouse models, innovative validated whole organ imaging techniques, in combination with cellular omics and mechanistic studies and a translational clinical part addressing the relevance of experimental results to human disease. We anticipate to identify Rev-erb-a as a novel therapeutic target to reduce intraplaque neovascularization and cardiovascular diseases.

Esophageal Atresia (EA) is a rare developmental defect of the foregut that presents with or without a Tracheo-Esophageal Fistula (TEF). The prevalence of EA/TEF over time and around the world has been relatively stable (> 165 new EA/year on average in France). EA/TEF is manifested in a broad spectrum of anomalies: in some patients it manifests as an isolated atresia, but in more than 60% of the cases it affects several organ systems. While the associated malformations are often those of the VACTERL spectrum (Vertebral, Anorectal, Cardiac, Tracheo-Esophageal, Renal and Limb), many patients are affected by other malformations, such as anomalies of the genitourinary, respiratory and gastrointestinal systems. Though EA/TEF is a genetically heterogeneous condition, recurrent genes and loci are sometimes affected. Trachea-Esophageal (TE) defects are in fact a variable feature in several known single gene disorders and in patients with specific recurrent Copy Number Variations and structural chromosomal aberrations. At present, a causal genetic aberration can be identified in less than 10% of patients. In most, EA/TEF is a sporadic finding; the familial recurrence rate is low (1%). As this suggests that epigenetic and environmental factors also contribute to the disease, non-syndromic EA/TEF is generally believed to be a multifactorial condition. Several population-based studies and case reports describe a wide range of associated risks, including age, diabetes, drug use, herbicides, smoking and fetal alcohol exposure. The phenotypical and genetic heterogeneity seen in EA/TEF patients indicates not one underlying cause, but several. In this project we will combine the French register of EA and multiomic studies in order to elucidate new causes or mechanisms in the etiology within specific sub-populations. Improved knowledge of predictive factors and molecular mechanisms may improve prediction and parental counseling and prevent co-morbidity. In this context, state of the art multi-omics will be performed from esophageal biopsies. Systemic/integrative biology will be then undertaken to establish predictive networks. Validation of EA pathways will be investigated using cross link coupled to mass spectrometry (XL-MS) and with BioID in order to evaluate the protein-protein partner involved in networks to better understand physiopathological mechanisms occurring in EA etiology. Integration of all the data using robust bioinformatics and biostatistics will give hypotheses for EA etiology. Based on these fundamental knowledges acquired on the EA pathology, a translational research step will be launched. Multi-omics analyses will be then performed on extracellular vesicles (EVs) issued from amniotic liquid. EVs have raised interest as a potential source of biomarker discovery because of the resemblance of their molecular content to that of the releasing cells. EVs in amniotic liquid will be the mirror of the EA pathology occurring in course of fetus development. Thus, multi-omic analyses of these EVs will be the first steps to improve the prenatal EA/TEF diagnostic.

In species with separate sexes, sex chromosomes are believed to play a major role in reproductive isolation. We will test this hypothesis on a group of four plant species belonging to the Otites section of the genus Silene where two XY and ZW systems occur. Through interspecies crosses, QTL mapping and transcriptomics, we will assess the occurence of Haldane's rule (stronger impact on the heterogametic sex), the relative involvement of X/Z chromosomes in reproductive isolation. A population genomics approach will complete the analysis in order to establish the best scenarii of speciation of the four species.