Abstract Inflammatory bowel disease affects ∼3 million people in the US and more than 7 million people worldwide. Despite recent advances in therapeutics, there are challenges that can prevent timely diagnosis and/or adequate treatment to achieve full and sustained remission, and we currently lack strategies for disease prevention. Genome-wide association studies (GWAS) have implicated hundreds of genomic regions that associate with IBD. A recent study found that therapeutics that target genes implicated in GWAS are ∼2.6 times more likely to obtain FDA approval versus those that are not associated with GWAS. Therefore, if we could better define the genetic mechanisms that drive autoimmune diseases, we could better define the genes, cell types, and pathways involved in driving disease, which could inform the development of more effective and targeted therapeutics. A major barrier to defining IBD genetic risk mechanisms is that the genetic variants that cause IBD are often in tight linkage disequilibrium with 10s to 100s of non-causal variants, and because 90% of these variants are located within non-coding regions, making it difficult to implicate target genes, pathways, and cell types. To address this, we recently overcame technological hurdles in assaying non-coding variants in primary human T cells for their effects on the expression of nearby genes. Through testing ∼18,000 IBD and other autoimmune GWAS variants for allele-specific effects on cis-regulatory element (CRE) activities with massively parallel reporter assays (MPRAs), we identified 545 expression-modulating variants (emVars) according to differences in reporter expression between variant alleles. emVars were highly enriched for statistically fine-mapped variants with high posterior probabilities (122-fold), indicating that they are enriched for disease-causal variants. emVars had putative target genes that enriched within gene networks linked to lymphocyte activation, translation, mRNA processing and splicing, and transcriptional regulation. Using single-cell CRISPR-interference screens targeted to emVars in accessible chromatin, we linked 37 emVars to 61 genes that they regulate, including IL2RA and SLAM family members known to participate in T cell signaling and activation. Finally, to link emVars to T cell function, we used bulk CRISPR-interference screens, finding that 14 emVars within the CD28, IL2RA, OX40, and other loci control T cell proliferation. We confirmed an emVar associated with IBD modulates PPP5C expression, a gene previously unappreciated in T cell biology that modulates MAP Kinase signaling cascades, metabolic and effector expression programs, and T cell proliferation highlighting it as a putative therapeutic target. Thus, through perturbing IBD GWAS-associated variants, we have uncovered novel genes that may viable therapeutic targets for IBD.
John Ray (Thu,) studied this question.