ABSTRACT Lupus or systemic lupus erythematosus (SLE) is a potentially fatal autoimmune disease with a substantial genetic basis. SLE is characterized by abnormal T- and B-cell responses, production of numerous pathogenic autoantibodies, and immune complex deposition, leading to various clinical manifestations including multi-organ damage (e.g., kidneys, skin). SLE has disproportionate impacts based on gender and ethnicity. Approximately 90% of those affected are women. In addition, SLE has a 3-5-fold higher prevalence in Asian, African-American, and Hispanic individuals compared to those with European ancestry, as well as more severe clinical manifesta- tions, including organ damage (e.g., nephritis). Evidence from genetics, cell biology, and animal models suggests that autophagy, a major pathway for organelle and protein turnover, plays a pivotal role in SLE pathogenesis. Autophagy is a highly conserved lysosome-mediated catabolic process that removes unwanted cytoplasmic components (e.g., long-lived and/or misfolded proteins) and damaged organelles. This process maintains cellular homeostasis and survival under metabolic stress. Recent genome-wide association studies (GWAS) have linked autoimmune diseases, including SLE, to autophagy-related genes. However, there is currently a huge gap in defining causal relationships between associated variants and molecular mechanisms underlying SLE. This lack of knowledge about pathogenic effects underlying GWAS signals hinders translating GWAS discoveries into diagnosis and treatment. To address this issue, we selected six highly ranked, well-replicated loci; four of them were initially discovered in Asian populations, two we previously reported as novel loci for SLE susceptibility. We have assembled a research team with the expertise and resources to discover and mechanistically characterize functional variants linked to SLE. We hypothesize that at each GWAS locus, both common and rare variants contribute to SLE risk by affecting expression of autophagy genes through tissue-specific regulatory elements. Aim 1 will identify SLE-predisposing variants using a comprehensive imputation-based analysis of combined novel resequencing data from SLE patients and controls in addition to our previous fine-mapping of four ethnically diverse populations. Functional variants will be prioritized by allele-specific expression, open chromatin, and 3D interaction data from immune cells. We will elucidate genetic and clinical heterogeneity of SLE by assessing association of identified variants with SLE and its clinical manifestations and autoantibody profiles. Associated variants, especially imputed and rare variants, will be validated through follow-up genotyping. Aim 2 will define the mechanistic and functional consequences of SLE-predisposing variants using appropriate functional assays, including CRISPR-based gene knock-out and base-editing in cell lines (Jurkat, Toledo, podocyte, HEK293) and primary immune cells (T- and...