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.