Genome-wide Autoimmune Genetic Variant Perturbations Connect Genetic Risk to Primary T Cell Expression and Function

Abstract Text: ~24 million people in the US have an autoimmune disease, but we still lack knowledge about how disease is caused and need more effective treatments. Genome-wide association studies have identified thousands of genetic associations with autoimmune diseases, but the genetic variants that cause each disease are mostly unknown due to tight linkage disequilibrium between causal and non-causal variants and because most associations fall within enigmatic non-coding regions. To better determine variants that cause disease, we employed three approaches in primary T cells. We tested ~18,000 autoimmune variants for allele-specific effects on cis-regulatory element (CRE) activity with massively parallel reporter assays (MPRAs), identifying ~500 with allele-specific activities. These variants are enriched ~50-fold for causal variants. We next tested ~1000 variants in putative CREs for their effects T cell function using CRISPR-interference screens. We found 42 variant CREs that modulate proliferation, including several that interact with the MYC promoter, and 37 variant CREs that alter IFNg production. To directly link variants to genes they regulate, we used a single cell CRISPRi screen. 15/23 targeted variant CREs had effects on nearby gene expression including a type 1 diabetes-associated variant CRE that promotes IL2RA expression but also repressed 4 other nearby genes including IL15RA. We also identified an inflammatory bowel disease variant CRE that controls PPP5C expression and effector and metabolic expression programs. Thus, using MPRA and CRISPRi screens in primary T cells, we prioritized likely causal variants and defined their effects, which will help define mechanisms and potentially targetable pathways for autoimmune diseases.