PROJECT SUMMARY/ABSTRACT The Mechanisms of New-Onset Autoimmunity-Longitudinal Immune Systems Analysis (MONA-LISA) will use clinical data and biospecimens obtained during performance of the clinical trial, Study of Anti-Malarials in Incomplete Lupus Erythematosus (SMILE, NCT03030118) to investigate immunological mechanisms that propel individuals who have asymptomatic or minimally symptomatic autoimmunity towards a definite diagnosis of systemic lupus erythematosus. These data and specimens are a unique resource, representing longitudinal clinical assessments, patient-reported outcomes, DNA, RNA, serum, plasma, peripheral blood mononuclear cells and urine obtained in a standardized manner before, during, and after the progression from Incomplete Lupus Erythematosus to Systemic Lupus Erythematosus (SLE) – an observation that occurred in twenty percent of the SMILE participants available for study. The overall objective of the study is to learn the underlying immunological, genomic, and metabolic differences present in individuals who progress to SLE compared to those that do not progress with goals to both develop better diagnostic and prognostic tools for health care providers as well as describe novel therapeutic targets so that individuals with early features of autoimmunity can be prevented from progressing to a state of organ damage and disability. The Specific Aims of MONA-LISA include: 1) Obtain a comprehensive, multiplex analysis of the peripheral blood immunophenotype of progressors and non-progressors in the SMILE cohort using a novel 137-plex CITE-seq analysis, sn-ATAC-seq, sc-RNA-seq and T and B cell repertoire determination to create a robust, quantitative atlas of cell-specific mRNA and epigenomic profiling in PBMC of these individuals. 2) Perform targeted genomic sequencing to categorize regulatory and structural variants of SLE risk loci to tie together the transcriptomic and epigenomic data and create novel risk assessments based on gene regulation. 3) Explore plasma and serum metabolic and lipid components that can serve as novel features that classify the risk of SMILE participants who progress towards classification with lupus. 4) Lastly, because SMILE enrolled fewer Black individuals than are represented in the epidemiology of prevalent lupus patients, we will perform a focused recruitment of non-European individuals with ILE and compare their multi-omic characterization of immunophenotypes described in Aims 1-3. This will allow more complete and generalizable conclusions to be drawn across ethnic groups and identify any ancestry-specific variations in the risk of autoimmunity progression that can explain the observed differences in lupus epidemiology. When completed, MONA-LISA will provide researchers and health care providers with better tools to predict who will develop lupus and create more effective interventional trials for disease prevention.