Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells [BaseEditing]

Determining causal variants for autoimmune disease is an enormous challenge - 90% of autoimmune disease-associated variants are non-coding and there are often 10s-100s are in tight linkage disequilibrium with the causal variant(s), making identification of the true causal variants difficult. Using massively parallel reporter assays in a T cell line, we prioritized variants that enriched highly for likely causal variants according to statistical fine-mapping. We followed up on one of the prioritized variants, rs72928038 in the BACH2 locus, which had a high effect size, finding that it regulates Bach2 expression in a human T cell line. We created mice containing a small deletion over this non-coding variant, and have tested mutant vs. WT antigen-specific T cells for their responses during acute viral infection. In the context of rs72928038-deleted mice (termed Bach218del), we found an increase in effector T cell differentiation, which highlights a potential role for rs72928038 in modulating effector T cell differentiation in the context of autoimmune disease. Jurkat T cells were base edited with a guide RNA targeting rs72928038 or a safe harbor site and PrimeFlow RNA Label Probe was used to track BACH2 transcript expression. Base edited BACH2 PrimeFlowed cells were either not sorted (denoted by NS for sort bin) or sorted into bins according to BACH2 RNA expression.