Bacterial pneumonia is a leading cause of morbidity/mortality worldwide. Antibiotics constitute the standard of care but face with the emergence of antimicrobial resistance (AMR) and the curative failure. The project aims at assessing an adjunct to antibiotic therapy as an emerging concept of overcome AMR. The project leverages (i) unique immunomodulatory flagellin that enhances airway epithelial immune defenses and increases the therapeutic outcome relative to an antibiotic, and (ii) airway-specific delivery by inhalation/nebulization. The objectives are to (1) demonstrate that flagellin strengthens the response to antibiotics in preclinical models of antibiotic-resistant pneumonia, and (2) identify host immune factors required for the gain of protection with systems biology. Outcomes include the enrichment of the pipeline of novel treatments against pneumonia, the reinforcement of the capacity to control AMR, the development of new avenues of research on the mode of action of flagellin.

Our interdisciplinary consortium aims at understanding the future evolution of the allergenic pollen grain in a context of increasing atmospheric CO2 concentration. Pollen will be collected from phleum pratense plants grown in the field under a CO2-enriched atmosphere and under drought stress. Timothy plants of various origins will be grown to observe possible evolutions of this plant favorable to adaptation to environmental stresses. The biological parameters of the pollen from these plants will be characterized (germination, quantity, size, ...). The influence of the culture conditions will be studied both on the rupture of the pollen grain and on its susceptibility to atmospheric pollution (ozone, nitrogen dioxide and particles from wood combustion). A detailed proteomic analysis is proposed with a particular attention on the importance of gibberellins in the production of allergens. Finally, the immunogenicity of pollen will be thoroughly evaluated.

The phylum Apicomplexa comprises a large group of obligate intracellular parasites of wide human and agricultural significance. Most notable is Plasmodium spp., the causative agents of malaria, and Toxoplasma gondii, one of the most common infectious agents of humans, responsible for disease of the developing fetus and immune compromised individuals. The extracellular forms of these parasites are perfectly tailored for the recognition and invasion of host cells and can be identified by the apical complex consisting of secretory organelles named micronemes (MIC) and rhoptries (ROP). These organelles are released sequentially during host cell entry and invasion. In addition to these parasite-specific organelles, the canonical eukaryotic organelles such as a central nucleus surrounded by an extensive endoplasmic reticulum (ER) and a single Golgi situated immediately anterior to the nucleus are also present in these parasites. T. gondii ROP and MIC proteins navigate through the ER, Golgi and endosome-like organelles prior to being packaged into their respective apical secretory organelles. Although it is known that in higher eukaryotic cells protein trafficking beyond the Golgi can be influenced by residues in the cytoplasmic tail of type I transmembrane receptors, the basis for initial segregation of proteins between the Golgi and the parasite secretory organelles remains unclear. We have reported that TgSORTLR, a type I transmembrane receptor localized in the Golgi cisternae and proximal vesicles of T. gondii acts as a cargo receptor likely involved in retrograde and/or anterograde transport that is necessary for the biogenesis of secretory organelles. Further, TgSORTLR is essential for host cell egress, gliding motility, cell invasion and in vivo infection, likely because of the crucial roles for the biogenesis and/or functioning of apical secretory organelles. Our findings reveal an indispensable role for T. gondii sortilin, which is the first indication that, unlike yeast and higher eukaryotes, lower branching eukaryotes such as apicomplexan parasites do not have redundant mechanisms of protein trafficking. Yet, we aim to elucidate the biological functions of retromer transport in protein trafficking and post-secretory vesicle biogenesis in T gondii. The functional networks involving the classical retromer proteins and their associated novel parasite-specific proteins will be studied by three complementary teams that are headed as follows: S. Tomavo (Team 1 at the Pasteur Institute Lille: molecular, cell biology and genetics of Apicomplexa parasites), L. Johannes (Team 2 at the Curie Institute in Paris: retrograde traffic, signalling and unconventional clathrin-independent endocytosis), and A. Van Dorsselaer (Team 3 at IPHC in Strasbourg: proteomics and biochemistry of proteins). First, we will refine the first protein network of the endolysosomal pathways and will determine how these pathways are required for organelle biogenesis in T. gondii and likely in other apicomplexan parasites. With genetically engineered parasites, we will biochemically analyze the proteome of the retrograde transport route, using a vectorial proteomics approach, a cell and model membrane reconstitution strategy, and highly sensitive quantitative proteomics, respectively. In addition, we are currently using reverse genetics to generate conditional knock out mutants for novel parasite-specific proteins that specifically bound to retromer VPS35. These mutants will be exploited to elucidate the importance of TgSORTLR and its retromer-associated components in retrograde protein trafficking and post-secretory vesicle formation. We will precisely decipher how endolysosomal-like vesicle formation and transport can be exploited to understand the biogenesis of key parasite-specific secretory organelles that are essential for parasite virulence and pathogenesis.

The discovery of novel classes of antibiotics for Enterobacteriaceae, A. baumannii and P. aeruginosa (the most critically classed pathogens on the WHO priority list), is particularly obstructed by their efficient and promiscuous xenobiotic efflux pumps that prevent the efficacy of new chemical entities. The upregulation of these pumps in clinical strains also results in resistance to current antibiotics. It is therefore clear that developing inhibitors to these efflux systems, as well as enriching our knowledge of the basic biology of these pumps will be a major step forward in breaking the xenobiotic defence system of these bacteria. Efflux pump inhibitors (EPIs) previously discovered have thus far not been developed into clinical candidates but have greatly helped understand the mechanism by which the pumps work, and proven the druggability of these targets. It is clear that strengthening and expanding this basic knowledge on efflux pumps to bacteria such as A. baumannii is fundamental and synergistic to the development of novel EPIs to help fight Gram-negative infections. Through a fragment-screening we have identified a small water soluble compound able to boost the activity of a broad spectrum of AcrAB-TolC efflux pump substrates in both E. coli and K. pneumoniae. Preliminary data within the EFFORT partnership show that this EPI may bind the “hydrophobic trap” of AcrB, a critical pocket important for pump inhibition. In A. baumannii, this EPI was found to boost the activity of chloramphenicol. By drawing similarities with E. coli, the new EPI may therefore also be a novel inhibitor for efflux in A. baumannii. The EFFORT consortium will aim to pinpoint the binding pocket of the new EPI in E. coli, K. pneumonia and A. baumannii, and investigate its ability to act as a chemical scaffold for inhibiting other efflux pumps in A. baumannii and P. aeruginosa (such as silent efflux pumps). This whole effort will be supported by structural studies to define the exact binding position of the inhibitors in E. coli AcrB, in K. pneumoniae AcrB and in the to be uncovered A. baumannii efflux pump. The structural biology will be supported by both X-ray crystallography and state-of-the-art Cryo-EM imaging that will maximise the likelihood of enriching out knowledge in efflux pump biology and EPIs. The size and chemical properties of the novel EPI make it very accommodating for easy chemical diversification, rationally guided by structural biology data, molecular dynamics simulations and biological activities, that will aim to improve the potency of the EPI. The physico-chemical and pharmacokinetic properties of the compounds will also be monitored to rapidly identify optimised molecules ready to be tested for in vivo efficacy. Overall EFFORT will both enlighten the basic structural biology of efflux pumps in Gram-negative bacteria by state of the art techniques, and develop a promising EPI.

The eradication of viral infections is an ongoing challenge in the medical field, not only due to the problem of spreading but also to virus ability to evolve by genetic mutations. In contrast to bacterial infections which are mostly treated using antibiotics, antiviral treatment development is difficult and immunization against viral infections is not always possible. These considerations apply also to respiratory diseases caused by human coronavirus (HCoV) infections. Initially, Middle-East Respiratory Syndrome coronavirus (MERS-CoV) infections occurred sporadically; however, horizontal infection among human patients observed particularly in hospital and nosocomial settings has raised concerns about the pandemic potential of MERS-CoV. The main goal of the NanoMERS project is the identification of specific and efficient nanomaterials derived anti-MERS-CoV agents effectively inhibiting viral entry and their in vitro and in vivo testing. This multi-disciplinary project involves 3 teams (IEMN-University Lille, Institut Galien Paris-Sud; Center for Infection & Immunity of Lille) that are highly complementary due to the technical pre-existing know-how of each partner. The focus will be on the use of carbon based nanostructures, notably modified C-dots and graphene-dots and nanoparticle formulations of poly(D, L-lactide-co-glycolide) (PLGA). Identification of most promising anti-MERS-CoV nanostructures using in vitro tests, determination of the pharmacokinetic of the best nanostructures, the possibility of pulmonary delivery using nebulization of mice as well as testing of most promising anti-MERS structures in MERS-CoV infected 3D reconstituted human respiratory epitheliums are the main objectives.