SUMMARY ~24 million people in the United States have an autoimmune disease, impacting quality of life and longevity of the affected individuals. While these diseases have a genetic component, as determined from high incidence in monozygotic twins, we still know very little about how genetics drives risk and progression for each disease. Genome-wide association studies have identified hundreds of autoimmune disease-associated regions of the genome, but there is often tight linkage disequilibrium between causal and non-causal variants in these regions, and most disease-associated genetic variants are in non-coding regions. Thus, determining the variants that promote disease and their effects on disease-relevant cell types is challenging. One cell type that is implicated in many autoimmune diseases is the T cell. In response to self-antigen, autoreactive T cells clonally expand and migrate to target tissues, where they cause tissue destruction. Non-coding genetic variants associated with autoimmune diseases are enriched within the accessible chromatin of T cells, suggesting that disease-causal variants alter enhancers that may affect T cell function, making them more pathogenic. We recently created a methodology to identify likely causal variants through testing variants for whether they alter regulatory region activity in allele-specific reporter assays and have used this methodology in a T cell line to discover hundreds of putatively causal variants across the genome. The next and perhaps most daunting step is to connect variants to their effect on the function of disease-relevant cell types. In this proposal, we aim to identify variants in non-coding regulatory regions that alter T cell proliferation and migration. First, we will use a novel CRISPR-interference screen to identify variant regulatory regions that regulate T cell proliferation and migration toward chemokines found in inflamed tissues. Next, we will use a single-cell screening approach in primary T cells to identify the genes modulated by variant regulatory regions. We will then determine variant regulatory regions that act synergistically or in an epistatic manner on T cell function, thereby identifying a relationship between separate genetic risk loci and their effects on T cell function. Finally, we will determine whether variants that influence T cell function are also associated with the prevalence of autoreactive T cells and disease severity using a large multiple sclerosis cohort. If successful, this work will take the first leap in directly linking hundreds of risk loci to a cellular function in an autoimmune disease-relevant cell type and it will provide insight into how genetic risk promotes disease. Our findings may therefore identify therapeutically targetable pathways for treatment of autoimmune diseases.

PROJECT NARRATIVE The goal of this project is to connect autoimmune disease genetic risk, which mostly occurs in areas outside of genes in the genome, directly to how T cells function. This will provide insight into how genetic risk for disease makes T cells more pathogenic. Our findings may therefore identify therapeutically targetable pathways for treatment of autoimmune diseases.