Systemic Lupus Erythematosus (SLE) is a multifactorial autoimmune disease affecting multiple organs that could lead to death when the kidney damage (lupus nephritis, LN) is confirmed. LN is characterized by glomerular deposits of IgM, IgG and IgA autoantibodies-containing circulating immune complexes (CIC) which lead to a chronic inflammatory renal disease resulting in kidney failure. As for many chronic inflammatory diseases, no specific treatment, early diagnostic and prognostic tools exist for SLE. Developing innovative and specific therapeutic approaches will allow a better SLE patient care and will limit the use of invasive diagnostic tests such as kidney biopsy. Basophils, representing less than 1% of circulating leukocytes, are well known for their involvement in allergic and parasitic diseases. Recent studies, including ours, demonstrated their immune regulatory role in immune memory humoral responses, in the TH2 differentiation of CD4+ T cells and during SLE development. We demonstrated in a murine model of SLE that basophils were responsible for an amplification loop of autoantibody production by promoting the TH2 differentiation of CD4+ T cells and the production of autoantibodies by plasma B cells. These functions depend on IL-4 and both total and autoreactive IgE. These results have been confirmed in SLE patients, where basophils are activated and recruited to secondary lymphoid organs (SLOs). We demonstrated that autoreactive IgE titers (able to activate basophils) are correlated with SLE disease activity (especially LN activity) and with basophil activation status. The BATTLE project is the BASILE project follow-up which was funded by the ANR in 2011. The BASILE project confirmed basophil involvement in SLE pathogenesis in several spontaneous or inducible SLE-like mouse models and in a large cohort of over 200 SLE patients, over 300 patients with various chronic kidney diseases and over 120 healthy controls. In addition the BASILE project identified SLE-specific basophil activation profiles leading to a highly promising new therapeutic approach targeting the pathway responsible for basophil accumulation in SLOs. Finally, the BASILE project established a new transgenic mouse model allowing an inducible recombinase CRE expression only in the basophil compartment. The BATTLE project aims to develop the BASILE project results in order to provide new diagnostic, prognostic and therapeutic solutions to SLE patients. The BATTLE project is subdivided into three main tasks. The first one, translational, aims to perform i) a longitudinal follow-up of SLE patients included into the BASILE cohort, ii) a transcriptome analysis of basophils from active SLE patients and healthy controls, and iii) the identification of other chronic inflammatory diseases in which basophils may be involved. The second task corresponds to a pre-clinical strategy aiming to validate the preventive and/or curative effects of the targets identified during the BASILE project in new animal models by pharmacological and/or genetic approaches. The third task, a more basic science approach, aims to generate specific tools for human and murine basophil studies and to identify two new immunoglobulin receptors detected on SLE patient basophils during the BASILE project. ANR’s support to the BATTLE project will allow my team to keep its cruising speed in a highly competitive research field that is under-represented in France and Europe. Indeed, this project will allow research and development of currently inexistent diagnostic, prognostic and therapeutic solutions for SLE.

Translational investigation of the pathophysiological role of intestinal barrier dysfunction and microbiota in juvenile idiopathic arthritis Juvenile idiopathic arthritis (JIA) is the most common childhood-onset chronic rheumatic disease. The cause of JIA remains unknown. A growing number of evidence suggests that the intestinal microbiota and intestinal barrier function are altered in JIA patient. However, a mechanistic link between alterations of intestinal immune homeostasis and JIA has not been established. Proposed study: Here we propose to investigate the functional role of the intestinal barrier and microbiota in the pathophysiology of early onset JIA. We will conduct a translational study combining ex vivo investigations using patients’ biomaterials and functional studies in murine arthritis models transplanted with human feces. Objectives: 1) Evaluation of intestinal barrier function and fecal microbiota in JIA patients versus healthy controls. 2) Identification of serum biomarkers associated to barrier dysfunction and alteration of intestinal microbiota. 3) Evaluation of the effect of the microbiota from patients and controls on the intestinal barrier function and development of arthritis in murine arthritis models transplanted with human microbiota. Feasibility: The federation of partners with strong expertise in clinical research, biomedical research and basic science guarantees the success of this project. This translational study articulates with a clinical trial. It therefore benefits from already established circuits with regard to patient recruitment, collection and processing of biomaterials. Repercussion: The demonstration that intestinal microbiota and alterations of the intestinal barrier function are the key event for the development of JIA may pave the way to new therapeutic strategies. The identified biomarkers may allow stratification of patients eligible for such treatments.

Flow Cytometry (FC) is a widespread technique enabling the study of targeted cell populations in health and disease. FC is however limited in the number of assayed proteins, preventing its application for the generation of “cellular atlases” of complex tissues. In the past, I have shown that combining FC with non-linear multivariate regression Machine Learning (ML) techniques allowed to profile hundreds of proteins (>x10 compared to conventional FC) across millions of single cells, demonstrating that FC can lead to practically fruitful ML applications. This project contains three objectives aiming at applying and further developing this technique : i. Apply this technique to human inflamed or non-inflamed liver samples to obtain an exhaustive cellular profiling ii. Develop supervised classification algorithms for the automated phenotyping of FC datasets leveraging a pre-annotated reference dataset iii. Extend this technique to imaging flow cytometry datasets by using generative models to predict the cellular localisation and spatialized expression levels of hundreds of proteins This project will therefore enable both the generation of new functional hypotheses on proteins expressed by cells subsets of the human liver in the context of chronic inflammation, as well as the development of new ML applications in the context of FC and imaging FC.

Infection in the ageing population is a major public health concern. Age is independently associated with adverse outcomes in infectious diseases, with the elderly population accounting for 80% of sepsis-related deaths. The accumulation of senescent cells can drive many age-associated phenotypes. The liver has the highest proportion of age-induced senescent cells, the majority of which are liver sinusoidal endothelial cells (LSECs). LSECs are unique, highly specialised fenestrated endothelial cells that display the highest endocytosis capacity of any human cell, serve as sentinel cells to detect microbial infection through activation of pattern recognition receptors and as antigen cross-presenting cells, and thus have unique immune properties. I obtained preliminary data by analysing publicly available transcriptomic data of senescent LSECs showing that LSECs function most impacted by senescence was their immune function and in particular their interactions with lymphocytes. I have shown in vitro that senescent LSECs display a pro-inflammatory phenotype in response to antigens, when compared to young LSECs. In addition, preliminary results from in vivo infection models in mice (old and young and in a novel mouse model of LSECs-specific accelerated senescence) indicate that the aged liver response to bacterial infection is impaired and that senescent LSECs may indeed be key factors modulating the aged liver response to bacterial infection. Based on these fundings, I hypothesize that LSECs senescence impairs liver immunity during ageing and promotes excessive inflammatory responses, thereby promoting the severity of infectious diseases. I will test this hypothesis along 3 aims: 1/ Investigate the effects of senescence on LSECs on liver immune response, under basal and under infections conditions by using in vitro and in vivo experiments; 2/ Assess the consequences of senescent LSECs on infection severity using in vivo experimental models in mice with LSECs accelerated senescence (already established and validated); 3/ Explore strategies for reversing aged-induced impairment of LSECs immune function to limit infection severity, employing senolytic strategies. The consequences of age-related senescence within the liver in infectious diseases, such as sepsis, remain largely unknown. This project will provide insights into how senescent LSECs might modulate the immune response to bacterial infections and unravel impaired mechanisms and modulators induced by ageing LSECs, that could be targeted as novel therapeutic approaches to reduce the severity of sepsis in the elderly population.

Fibrotic interstitial lung diseases are a diverse group of chronic and progressive respiratory disorders, with idiopathic pulmonary fibrosis being the most common member. Evidence gleaned from animal modeling and human studies suggests that innate and adaptive immune processes can orchestrate existing fibrotic responses through a crosstalk with invading or commensal microbes in the lungs. Mucosal-Associated Invariant T cells (MAIT) are innate-like T cells recognizing bacteria-derived riboflavin precursor derivatives. In humans, MAIT cells represent a large proportion of T cells in the blood and barrier tissues, where they are anatomically close to epithelial surfaces. MAIT cells play an important role in antimicrobial immunity at mucosal sites, in particular the lung. Recent findings suggest broader functions of MAIT cells in immunity, including regulation of epithelial barrier integrity. Both human and mouse MAIT cells express a transcriptomic tissue repair signature upon stimulation. Inappropriate tissue repair ability of MAIT cells might participate in the development of pulmonary fibrosis, as observed in the liver. Based on our preliminary results, we hypothesize that MAIT cells could influence the development of pulmonary fibrosis. The main objectives of this project are 1) To characterize the role of MAIT cells in the genesis and progression of pulmonary fibrosis, 2) To study the crosstalk between MAIT cells and the lung microbiota to determine the temporal relationship between lung dysbiosis, inflammation, MAIT cell activation and fibrogenesis, and 3) To evaluate MAIT cell as a potential therapeutic target by using synthetic blocking or activating ligands. For that purpose, we will use both experimental mouse models and in vitro research on human tissues. As a perspective of interest, this may raise the possibility to use peripheral and lung MAIT cell phenotype as a novel biomarker for monitoring pulmonary fibrosis progression.