In this project, we aim to take an important step toward identifying novel targets of therapy in juvenile idiopathic arthritis (JIA). To do this, we will use genetic information that has been generated from genome- wide association studies (GWAS) and genetic fine mapping studies. These studies have shown that much of the genetic risk for JIA lies within genomic regions that are highly enriched for enhancer function, a feature that JIA shares with almost every other autoimmune disease. The underlying premise of this work is that, by identifying genetic risk variants that alter enhancer function, and then identifying the genes whose expression levels change when enhancer function is altered, we will identify promising new therapeutic targets. In this proof-of-concept project, we will focus on IL2RA, an important risk locus for JIA and multiple other autoimmune diseases. We have previously shown that the IL2RA locus contains an intronic enhancer whose function is attenuated by genetic variants that we initially identified on whole genome sequencing of children with the polyarticular form of JIA.
We aim to identify the target genes of these genetic variants, i.e., the genes whose expression levels are altered when function of the intronic enhancer is attenuated. To accomplish this aim, we rely on the fact that, while enhancers may not always regulate the nearest gene, they typically regulate genes within the same chromatin loop or topologically associated domain (TAD). We will use RNA-guided epigenome editing with a deactivated nuclease coupled to an epigenome editing enzyme, Krppel associated box (KRAB) repressor (dCAS-KRAB). We will then use conventional rtPCR approaches to identify which of the 12 genes that are incorporated within the TAD that contains the IL2RA enhancer show changes in expression level when that enhancer is attenuated. If successful, we will have established as proof-of-concept the utility of using the broader chromatin architecture that incorporates the JIA risk haplotypes and RNA-guided epigenome editing as a strategy for identify therapeutic targets in JIA. We expect that completion of this work will lead quickly to a larger project aimed at identifying all the target genes of genetically altered enhancers within the JIA risk loci. Furthermore, successful completion will also lead to the development of partnerships with key industry leaders to rapidly translate these findings to the clinical setting. !
In this project, we aim to identify promising drug targets for juvenile idiopathic arthritis (JIA), on of the most common chronic diseases of children. We will use state-of-the-art techniques to change interactions between DNA and proteins in a region of the genome that we already know contributes to genetic risk in JIA. We will then examine how those changes alter the expression of genes in that region, as those genes whose expression is altered are likely to be promising targets of therapy. !
