Molecular Reclassification to Find Clinically Useful Biomarkers for Systemic Autoimmune Diseases: Inception Cohort

Study Overview
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Brief Summary
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Connective tissue diseases (CTD) or systemic autoimmune diseases (SADs) as they are known today are a group of chronic inflammatory conditions with autoimmune aetiology with few treatment options and difficult diagnosis.Brest team contribute to performe a new classification of the following systemic autoimmune diseases in a European Union's Seventh Framework Programme. The aim of this research consiteis to reclassify the individuals affected by SADs into molecular clusters instead of clinical entities through the determination of molecular profiles using several Omics techniques.

Detailed Description
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The overall objective of the PRECISESADS IMI project is to reclassify the individuals affected by SADs into clusters of molecular, instead of clinical entities through the determination of molecular profiles using several -omics techniques. The identification of the clusters relies on a cross sectional (CS) cohort/protocol where 2666 individuals (2000 patients and 666 controls) including a sub-study of 288 deeply characterized individuals (240 patients and 48 controls) are to be recruited. In parallel a longitudinal inception cohort/protocol will be started in order to further explore the clinical relevance of the identified clusters and their evolution over time. The objectives of the CS study and sub-study are: To identify a systemic taxonomy for patients with SADs by producing the following data in individuals with SADs and controls: genetic, epigenomic, transcriptomic, flow cytometric (from peripheral blood mononuclear cells (PBMCs)), metabolomics and proteomic in plasma and urine, exosome analysis, classical serology (antibodies and autoantibodies), and clinical data. To better characterize individual SADs at the omics level. To perform clustering analyses to determine the groups of individuals who, differentially from other groups, share specific molecular features (precision medicine). A deeper analysis will be done in a substudy of 288 individuals. The clustering process will be data-driven with the aim to find the most homogenous and differentiated clusters of diseases that clearly separate differentiate individuals from controls and other patient clusters. Aims of the Inception cohort: Specifically, this inception cohort aims at: assign individuals newly diagnosed with an systemic autoimmune disease (SAD) to any of the reclassification clusters discovered in the CS study, to study the development and modifications of OMICS signatures/clusters occurring in each individual patient in the course of the disease, including the impact of treatment on their individual pattern, and to perform deep (thorough) OMICs studies to compare their patterns of OMICS as a group, with the patterns obtained in the CS cohort. The inception cohort will have patient follow up and sample collection at baseline, month 6(±1 month) and month 18 (±1 month). As the newly diagnosed patients we plan to recruit will have minimum or no treatment, we will identify differences and similitudes to patients from the cross-sectional study that have undergone long-term treatment.

Official Title
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Molecular Reclassification to Find Clinically Useful Biomarkers for Systemic Autoimmune Diseases: Inception Cohort

Conditions
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Systemic Autoimmune Diseases

Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: · Aged 18 years or older at the time of consent Diagnosed according to prevailing criteria for one of the following systemic autoimmune diseases (see Annex 2) Rheumatoid arthritis (RA) Scleroderma or systemic sclerosis (SSc) Primary Sjögren's syndrome (SjS) Systemic lupus erythematosus (SLE) Primary antiphospholipid syndrome (PAPS) Mixed Connective Tissue Disease (MCTD) Patients with undifferentiated connective tissue disease (UCTD) for over 1 year and that do not fulfill the diagnosis of any of the above diseases. Signed the informed consent form Exclusion Criteria: · Patients unable to understand the procedures related to the protocol should not be included. The study is voluntary and patients must be able to give their informed consent. Pregnant women Neonatal lupus Drug-induced lupus Patients whose condition is so serious that they cannot take part in the study Severe nephrotic syndrome with proteinuria >=3,5 g/day Patients with stable doses of steroids >15mg/day for the last 3 months or with IV corticosteroids in the last 3 months Patients under immunosuppressants for the last 3 months prior to recruitment with: Methotrexate ≥25mg/week Azathioprine ≥2.5mg/kg/day Cyclosporine A > 3mg/kg/day Mycophenolate Mofetil > 2gr/day Treatment with cyclophosphamide (any dose or route of administration) or Belimumab in the past 6 months Patients with combined therapy of two or more immunosuppressants Patients on depletative therapy such as Rituximab in the last year Patients receiving experimental Overlap syndromes

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Gene expression in total blood | Gene expression will be done using commercial gene expression microarrays in total blood from all samples using the RNA Paxgene tube. | 2 years | 
| Flow cytometry analysis to determine cell proportions in the total blood mixture in all individuals. | 9 optimized panels of antibodies will be used to determine cell subpopulations in peripheral blood (including very minor cell populations). | 24 hours | 
| Genotyping | Genotyping will be done using a whole genome array. | 2 years | 
| Metabolite determination | Metabolite determination in plasma and urine using Nuclear Magnetic Resonance | 2 years | 
| Exosome isolation from plasma and urine | set up of the methodology for isolating exosomes in these bodily fluids for gene expression analysis | 2 years | 
| Cytokine profile determination | 88 different cytokines will be assessed with Luminex | 2 years | 
| routine autoantibodies in serum | set of serum autoantibodies will be determined in a European validated laboratory. Also, they will perform detection of antibodies against small lipid moieties i.e.antiphosphorylcholine),lupus anticoagulant and complement proteins in plasma. | 2 years | 
| Gene methylation in total blood | Methylation analysis will be done using the methylome 450k array using the DNA obtained from total blood. MicroRNA gene expression arrays using total blood. | 2 years | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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SADs, Molecular Reclassification