In mammals, the intestine is home to trillions of bacteria that cooperate with their host to establish mutualistic relationships. In humans, many emerging pathologies such as allergies, autoimmune and inflammatory disorders arise from a loss of symbiotic relationships with our microbial partners. Actually, microbial colonization during infancy shapes our intestinal immune system and recent studies have shown that microbial diversity during the first years of life is critical to the establishment of tolerance to environmental factors. Thus, exposure to antibiotics in childhood has been linked to the development of asthma and allergy and, even later in life, to the development of inflammatory bowel diseases. Microbial colonization also ensures protection against infection either directly by competition or indirectly by promoting mucosal immunity against pathogens. Therefore, understanding the mechanisms of interaction between the microbiota and the mucosal immune system is critical to imagine novel therapeutic approaches for preventing/treating inflammatory diseases or for boosting immunity against pathogens. Studies in mice have shown that the intestinal adaptive immune responses are mainly initiated in the small intestine Peyer’s patches (PPs). Microbial colonization of the intestine appears to be a crucial component of the normal maturation of these gut-associated lymphoid structures. Interestingly, mouse PPs are colonized by a specific microbiota, among which Segmented Filamentous Bacteria (SFB) profoundly influence the postnatal maturation of the mucosal immune system and promote the establishment of a physiological inflammatory environment that provides protection from enteropathogens. Our on-going work unambiguously identifies SFB in the microbiota of young children, suggesting that the biology of host-SFB interactions that we intend to describe in depth in mice will help to address the role of SFB in humans. Recently, another symbiont living close to PPs, Bifidobacterium adolescentis was associated with the stimulation of intestinal immunity. Among PP phagocytes, the monocyte-derived lysozyme-expressing dendritic cells termed LysoDC are ideally located, just below the epithelium, to interact with the commensal flora. We have shown that (i) LysoDC are responsible for the sampling of intestinal bacteria and particulate antigens; (ii) they participate in helper T cell priming and polarization. Thus, they clearly emerge as the ideal candidate to initiate adaptive immune responses against gut resident bacteria. This hypothesis is reinforced by the ability of the microbiota to modulate the differentiation state of LysoDC. The goal of our proposal is to decipher the role of the microbiota and especially of SFB and B. adolescentis in tuning up the immunological functions of PP phagocytes, notably LysoDC, and thereby in driving the maturation of gut adaptive immune responses. The project will involve the combined efforts of two scientific partners with complementary skills at the forefront of PP immunology and microbiota-host interactions. We will address the following points: (i) what is the influence of the commensal flora colonization on the phagocyte maturation state and on the initiation of the adaptive immune response in PPs? (ii) How specific individual symbionts or selected bacteria consortia are involved in this process? (iii) What is the role of LysoDC and other PP phagocytes in microbiota-driven mucosal adaptive immune response? (iv) Which bacterial-derived/induced factors are susceptible to modulate PP phagocyte functions? In summary, this project will provide valuable insights into how the microbiota influences the mucosal immune system through its interaction with PP phagocytes, which may provide new therapeutic opportunities based on targeted colonization, on the promotion of beneficial microbiota and on the strengthening/readjustment of microbiota-immune system crosstalk.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 19 (COVID-19) with symptoms ranging from mild respiratory illness to severe lung injury, multi-organ failure and ultimately death. Although SARS-CoV-2 primarily infects the lungs, gastrointestinal symptoms are frequently observed and are associated with worse COVID-19 outcomes, underlying the need to also study the infection of the intestinal mucosa. New recently identified SARS-CoV-2 variants raised particular concerns worldwide due to their high transmissibility rates. They all bear mutations in the Spike protein that binds to host cells and allows virus entry. The rapid emergence of such variants highlights the urgent need to develop highly relevant and standardized experimental models to study critical aspects of SARS-CoV-2 variant infection and replication but also to screen therapeutic candidates and assess whether drugs known to affect SARS-CoV-2 parental strain entry and replication are still efficient on these variants. Our proposal aims to monitor the ability of SARS-CoV-2 variants of concern, including South Africa, United Kingdom and Brazil ones, to infect human colonic organoid-derived cell monolayers, a model of choice to study host pathogen interaction in a standardized and reproducible way closely mimicking the in vivo situation. Our proposal also aims to study the immune response of the colonic epithelium to these variants and the impact of this response on the infection process. Finally, our project will be useful to perform a first drug screening of therapeutic candidates known to interfere with infection by the SARS-CoV-2 parental strain. In conclusion, our project will help to understand how the SARS-CoV-2 mutations affect entry and replication of the virus, and defence mechanisms of the intestinal epithelium as well as virus resistance to therapeutic candidates or to interferons. In addition, our experimental model will allow to quickly investigate other potential therapeutic candidates for other types of enteric infections, which is crucial in case of rapidly spreading pathogens, such as SARS-CoV-2.

There are three major autoimmune liver diseases (AILD): autoimmune hepatitis (AIH), primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). Around thirty thousand persons are affect by one of the three AILD in France with three thousand new cases per year. They are characterized by an immune attack of the hepatocytes, the intrahepatic bile ducts and the extrahepatic bile ducts, respectively. A strong genetic association of AILD with class II HLA genes in the Major Histocompatibility Complex (MHC) is observed, and specific and non-specific autoantibodies are present and used for diagnosis. The class II HLA gene predisposition and the presence of autoantibodies targeting specific self-antigens are consistent with the hypothesis of a central pathogenic involvement of self-antigen-specific CD4 T lymphocytes in AILD pathogenesis. However, the specific signature and role of autoreactive CD4 T cells are poorly understood in AILD. In general, identification and characterization of autoreactive CD4 T cells remain difficult in patient’s blood. There is also an enormous need for innovative treatment and for biomarker to help clinicians in the management of these diseases. Although AIH patients have a good response to immunosuppressive (IS) treatment (corticosteroids and azathioprine), the risk of relapse upon treatment withdrawal is high (>60%). For PBC and PSC no efficient IS treatment exists and non-response to the standard treatment is linked to poor outcome. Moreover, it is difficult to predict clinical outcome at presentation, upon treatment and before complete withdrawal. The main objective of the DISTAL project is to establish the molecular signature of autoimmune self-antigen-specific T cells in AILD, with three aims: 1- to get new insights into the mechanisms of autoimmunity in the liver, 2- to use autoreactive T cells as new targets for the development of specific therapeutic strategies, as alternative to the non-specific IS treatments, 3- to identify an immune biomarker to help clinicians in their management of patients with AILD. To fulfill these ambitious goals, three tasks will be undertaken, based on original preliminary results. In Task#1 we will establish the molecular atlas of autoreactive CD4 T cells from the blood of AILD patients, at the single-cell level, to characterize their transcriptional profile; Task#2 will identify the peptide sequences of the dominant T cell epitopes from liver self-antigens, to track autoreactive T cells in patients and to develop future personalized peptide-immunotherapy; Task#3 will identify a clinically relevant “autoimmune T cell signature” in the blood of patients to be used for diagnostic and prognostic assessment of AILD. This original project will benefit from our access to a bio-collection (Bio-HAI, CHU-Nantes) of AILD blood and liver samples unique in France (more than 140 patients to date), the HEPATIMGO network (8 hospitals in the Western part of France: Angers, Brest, La Roche Sur Yon, Nantes, Orléans, Poitier, Rennes, Tours), the capacity to identify self-antigen specific memory CD4 T cell by the in vitro restimulation assay developed in the lab by Dr. Amédée RENAND (CRTI, Nantes) and from the recent development of a novel state-of-the-art integrative single-cell RNAseq (scRNAseq) method to analyze autoreactive CD4 T cells at the single-cell level (P. MILPIED, CIML, Marseille). The impact of the DISTAL project is high and has the ambition to: 1)-identify immune biomarkers to facilitate patients’ stratification (risk of non-response to treatment, risk of relapse); 2)-understand the role of immune cell subsets in the pathogenesis of the disease; and 3)-characterize self-antigen specific CD4 T cells and the epitopes they recognize, to serve as a basis for the development of an innovative personalized therapy, as an alternative to non-specific immunosuppression.