Characterization of SSc heterogeneity towards endotypes

SSc is a very heterogenous disease with a wide variety of clinical presentations and organ involvement and poor results in the recent randomized control trials. Here, we aim to identify endotypes (groups of similar patients) of SSc by performing a multidimensional integrative analysis combining health data from various sources with omics and imaging data, gathered in our different research project.

We will start by accumulating omics data in patients with SSc. The proposal of the Sclero-PROT project (which has secured 320 k€ in funding from SATT) is to characterize, using a Bruker timsTOF flex acquired thanks to CPER Resist omics, the circulating proteomic and extracellular vesicle signatures of patients with SSc compared to healthy subjects, patients with idiopathic Raynaud's, and patients with Raynaud's associated with another connective tissue disease (such as lupus). A total of 500 samples will be analyzed (300 SSc patients, 50 healthy subjects, 100 with idiopathic Raynaud's, and 50 with Raynaud's associated with another connective tissue disease). The project's strengths lie in access to a high-quality declared clinical-biological database (FHU PRECISE), collecting samples from >500 patients with SSc and Raynaud's phenomenon without SSc. This database precisely describes the severity and activity of the disease, systematically for all patients, by a reference centre. In parallel, we will study by GWAS 200 patients with SSc to look for association with disease severity (collaboration with EGID).

Then we will endotype SSc using multidimensional integrative analysis: from health data to pathogenic mechanisms focusing on humoral immunity. The clinico-biological cohort of the FHU PRECISE contains 550 highly phenotyped SSc patients for whom sera are available in a biobank at 0, 1 and 2 years. This cohort is enriched with care data from the Lille University Hospital's health data warehouse (INCLUDE), proteomic profiles (CNRS MSAP platform, analysis by Bilille platform, SCLERO-PROT project) and indirect immunofluorescence images during ANA screening (Lille University Hospital Institute of Immunology). All ethical and regulatory authorizations are already available, allowing the project to be launched immediately. The project consists in performing unsupervised clustering analyses on a population of 550 SSc patients by progressively integrating low- dimensional (clinical and biological data) and high-dimensional (proteomic profiles and indirect immunofluorescence images of ANA observed in SSc patients) health data in order to highlight endotypes. We propose an original approach to validate endotypes including clinical and biological relevance, visual aspect and temporal stability and then chemokine and inflammatory mediator profiles before selecting them to explore the pathophysiological mechanisms involved. We will focus on the role of humoral immunity in the different endotypes (as our preliminary data suggest that ANA plays a key role in SSc heterogeneity (reviewed in Chepy et al. Frontiers Immunol 2022) through confocal microscopy, pathogenic role of ANA and passive transfer of immunoglobulins in animal models. This approach will allow the development of innovative methodologies for the integration and analysis of complex health data. These contributions can be reused and applied to many other human pathologies, contributing to the dynamics of personalized medicine. It is funded by the PathOmics-SSc MESSIDORE project (1,200 KEuros) and CPER RESIST-omics (200Keuros).