SUMMARY ACE Principal Project; PD/PI – Pascual, V. Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by breakdown of tolerance to nucleic acids (NAs) and widespread inflammation stemming from pathogenic innate and adaptive immune interactions in genetically susceptible individuals. Clinical and molecular heterogeneity represent a major challenge and contribute to the long series of failed clinical trials in SLE. Understanding major disease pathogenic drivers, identifying biomarkers to follow them in the clinical setting, and stratifying patients for targeted therapies are therefore highly significant goals to advance clinical trial design and deliver personalized patient care. This is particularly relevant to patients with childhood-onset SLE (cSLE), who present with a more aggressive phenotype and overall poorer outcome compared to adult-onset SLE. Our studies, stemming from three previous ACE cycles, uncovered molecular heterogeneity among cSLE patients which allowed their stratification based on major disease pathogenic drivers. We also described the presence in cSLE patients of a novel extra-follicular CD4+ memory T cell subset that provides B cell help independently of IL21 and CXCL13, thus expanding the spectrum of T helper pathways in this disease. We then extensively profiled the blood CD4+ T cells compartment of cSLE which uncovered transcriptomic signatures associated with disease activity (DA) and/or Lupus Nephritis (LN). Herein, we propose to deconvolute the cSLE CD4+ T cell compartment longitudinally in patients stratified according to the presence/absence of LN and the response to therapy. This will help elucidate how both standard of care and B-cell targeting therapies affect the frequency and function of CD4+ T cells and what basic mechanisms lead to amplification of T helper pathogenic pathways in SLE. Secondly, we will study functional alterations of cSLE CD4+ T regulatory cells and their potential connection with the microbiome. Results from the proposed studies will ultimately help stratify patients and identify therapeutic targets for a systemic autoimmune disease with a significant track record of clinical trial failure. Completion of the project goals will lead to a better understanding of these pathways at the phenotypic and functional levels. Additionally, these studies will identify biomarkers to characterize distinct CD4+ T cell-compartments with unprecedented granularity in blood and tissues, as well as potential targets to intervene therapeutically in selected patients.