GREB1L is a causative gene of a spectrum of human congenital defects, including renal agenesis. Yet the encoded protein is poorly characterised. Since the pathophysiology of congenital defects cannot be assessed in patients, it is essential to trace back origins in the embryo and identify the cellular context of the disease gene. We aim to test the hypothesis that GREB1L, as a known target of the morphogen retinoic acid, regulates mesoderm patterning, a prerequisite for organogenesis. Supported by preliminary data, our specific objectives are to define the molecular network in which GREB1L functions, dissect developmental mechanisms regulated by GREB1L in the posterior and cardiac mesoderm and investigate relevance to patients with a poorly understood heart malformation, criss-cross heart. Using an exceptional patient cohort, a unique mouse model and cutting-edge technologies in omics, organoids and quantitative 3D imaging, the PATHPATT project will provide novel insights into fundamental mechanisms of embryo patterning and retinoic acid signaling, while deciphering pathophysiological processes in the heart and kidney, potentially relevant to a broader spectrum of congenital defects. The consortium combines interdisciplinary expertise at the forefront of developmental biology, paediatric cardiology and human genetics, to comprehensively address the pathophysiology of congenital defects.

Variability in response to Ebola virus (EBOV) exposure and infection is now well-established. In particular, it was found that exposure to EBOV could result in asymptomatic or pauci-symptomatic infections, and that some highly exposed individuals could be considered as non-infected. Based on these observations, in this proposal, we formulate two main hypotheses: (1) human genetic factors play key roles in the response to EBOV infection through the control of infection after exposure and the control of pathogenesis after infection, and (2) the fine dissection of antibody profiles in healthy infected individuals and disease survivors will help understanding and defining correlates of protective immunity against EBOV infection. It takes advantage of three unique cohorts of survivors and contact persons of Ebolavirus disease (EVD) cases during the 2014-2016 and 2018-2020 EBOV outbreaks in Guinea and the Democratic Republic of Congo (DRC), respectively, established by the coordinator of the proposal. To test our hypotheses, the project is organized in two specific objectives. The first is to search for human genetic variants strongly influencing resistance to EBOV infection and those predisposing to the development of the clinical diseases using whole exome sequencing (WES) studies. Cutting edge methods will be used to analyze the WES data in three groups of individuals from the Guinean cohort: 50 highly exposed non infected contacts, 50 infected asymptomatic/pauci-symptomatic contacts, and 50 EVD survivors. These analyses will then be replicated on samples collected within the DRC cohort. The second objective is to characterize the antibody repertoires of 300 EVD survivors at inclusion, during the follow up and the final visit and in infected asymptomatic/pauci-symptomatic contact persons of EVD cases. We will use multiple antibody profiling (xMAP). We will in particular test the evolution with time of specific IgG titers and average affinities by SPR (Surface Plasmon Resonance), of the different IgG isotypes and their association with clinical severity (eg late complications) with IgG levels. Preliminary results regarding WES analyses of a first sample of 60 subjects and the evolution with time of total IgG antibodies in 543 Guinean survivors are very promising. This ambitious project is highly innovative and feasible due to the complementarity and strong expertise of the two partners in their respective fields. It will provide a refined dissection of the antibody responses among subjects who were naturally infected (with or without clinical symptoms) allowing a much better understanding of the immunological responses to EBOV infection. It should also provide new insights in the mechanisms of resistance to EBOV infection in natural conditions of infection, as well as in the pathways involved in the development of clinical disease in infected subjects. These results could open new avenues regarding the prevention of EBOV infection, and the development of novel candidate vaccines.

Juvenile Idiopathic Arthritis (JIA) is an heterogeneous group of inflammatory arthritis, that cripples pediatric patients, with very little information available on the potential genetic contribution, in pathophysiology and variable responses rates to available therapies. Thus, overall, JIA has very significant unmet medical needs. Among several JIA subsets, we aim to study patients with early-onset antinuclear antibody positive JIA (EO ANA+ JIA, 50% of a cohort of 1,200 JIA patients in Necker hospital) and patients with systemic JIA (sJIA, 20% of the JIA patients in Necker). Our project PREDICT-JIA, (Pathways and moleculaR analysEs to Derive multi-omIC signatures predictive to response to Treatment in JIA), aims at better understanding the molecular basis of this multifactorial disease, by performing a multi-OMIC analysis on Peripheral Blood Mononuclear Cells (PBMCs) collected before and 3 to 6 months following targeted biologic treatments by the soluble Tumor necrosis factor alpha (TNF) receptor, etanercept or the interleukin-1 (IL-1) receptor antagonist, anakinra, in EO ANA+ JIA and sJIA patients respectively. These are the most commonly used treatments at the early phase of the disease. These last years, a treat-to-target approach was recommended in JIA patients, aiming at achieving inactive disease within the first months of treatment. Based on transcriptomic, epigenomic, proteomic experiments performed at the single-cell level, combined with genomics, cellular immunophenotyping, autoantibodies and cytokines/chemokines analyses, we intend to identify and validate “pathological” cell clusters and new biomarkers, characteristic of our patients, but also predictive of responders, i.e., patients who achieve inactive disease on treatment, and non-or partial responders. By combining, in a synergistic way, our expertise in performing multi-OMICs analyses, on PBMCs, at the single-cell level (Partner 1) and in studying autoimmune/autoinflammatory responses (Partner 2), we intend to deliver new biomarkers and molecular signatures that could guide clinician in their therapeutic decisions, therefore benefit patients, but also setup new areas of research. Partners 1 and 2 are both group leaders at Imagine Institute and have been collaborating on rare genetic autoimmune/autoinflammatory diseases using single-cell multi-OMICs experiments since 2017.

Innate and cell intrinsic immune responses constitute a rapid defence system against incoming pathogens. While essential to survival, excessive activity of these responses is potentially detrimental to the host, with inborn genetic errors of these systems leading to disease. To prevent aberrant induction, while retaining effective anti-viral activity, innate immunity has to be tightly regulated. Intracellular trafficking has recently emerged as a central determinant of innate immune signalling, including in type I interferon (IFN) induction via DNA sensing, Toll-like receptor (TLR) activation and autophagy. We have identified mutations in three components of the endoplasmic reticulum (ER)-Golgi trafficking axis associated with phenotypes falling within the type I interferonopathy (T1I) spectrum i.e. monogenic diseases associated with enhanced type I IFN signalling. Currently, only limited treatment options are available for these devastating disorders, and the underlying molecular mechanisms are poorly understood. Our data indicate that COPA, ARF1 and ARFGEF1 are important for trafficking of a signalling adaptor central to DNA sensing i.e. STING. Mutations in COPA, causing COPA syndrome in humans, result in accumulation of STING at the ER-Golgi intermediate compartment (ERGIC) and chronic STING activation. Pathogenic mutations in ARF1 and ARFGEF1, causing novel T1Is, promote STING-dependent induction of type I IFN responses. Based on these preliminary data, our primary research aim is to define the precise relationship of COPA, ARF1, ARFGEF1 to each other and to STING, and thereby inform our understanding of ER-Golgi trafficking in innate immune signalling. In our first work package, we will define the mechanism of action of the novel mutations that we have identified in ARF1 and ARFGEF1, examining their impact on the localisation and activation of STING, and the consequences on downstream signalling and ARF1/ARFGEF1-dependent vesicular transport. In the second aim, we will explore the hierarchy of STING-COPA-ARF1-ARFGEF1, further dissect the mechanism(s) of STING recruitment to trafficking vesicles, and examine the mode of trafficking. As STING signalling is not the only innate immune pathway involving ER-Golgi trafficking, in a third aim, we will explore the impact of the COPA-ARF1-ARFGEF1 axis on TLR activity and autophagy. Taken together, our exploration of the molecular and cellular consequences of Mendelian disease-associated mutations will provide novel insights into the fundamental regulation of innate immunity by ER-Golgi trafficking, and characterise the key players involved. In this way, we will better understand how pathogenic, chronic immune activity is prevented, and thus inform the future treatment of both rare Mendelian disorders and more common disease states characterised by dysregulated innate immune responses.