Op0153 broadening Our Understanding of the Genetics of Juvenile Idiopathic Arthritis: Interrogation of Three Dimensional Chromatin Structures Within Jia-Associated Risk Loci

Abstract

BackgroundOur group has shown that, like most complex traits, the risk loci for juvenile idiopathic arthritis (JIA) identified on genome-wide association studies (GWAS) and genetic fine mapping studies are highly enriched for enhancers. Enhancers are regulatory elements that fine-tune gene expression to specific physiologic circumstances. Enhancers do not always regulate the nearest gene, and may regulate more than one gene. Enhancers typically regulate genes within the same chromatin loop, or topologically associated domain (TAD).ObjectivesTo gain a better understanding of the genetics of JIA by examining the broader chromatin architecture that encompasses the known risk haplotypes.MethodsWe used publically available chromatin conformation HiC data and the online JuiceBox software suite to query known JIA risk haplotypes for evidence of physical interactions between putative enhancers within the haplotypes and immunologically relevant genes. We specifically queried 20 haplotypes in which H3K4me1/H3K27ac marks were prominent within both lymphoid and myeloid cells. We queried data from GM12787 (B cell), K562 (lymphoblast), and THP-1 (monocyte/macrophage) cells, as well as human cord blood T cells. To identify TADs associated with specific enhancers, we used a 5KB resolution (which allowed us to visualize chromatin loops as peaks), setting the cursor at the center of each putative enhancer. We also identified the genes within the identified chromatin loop domains and used gene ontology (GO) analyses to identify functional associations among genes within the TADs incorporating the JIA risk loci.ResultsWe identified at least one chromatin loop structure in all 20 of the JIA risk haplotypes for each of the 4 cell lines we queried. These loops were not cell type specific. That is, almost identical loops structures could be seen in each of the cell lines at each of the loci, suggesting that these enhancers regulate a broad range of common leukocyte functions. The TADs incorporating the JIA haplotypes invariably included genes of immunologic interest. For example, the TAD incorporating the IL2RA haplotype including IL15R (the alpha chain of the IL15 receptor) and PKCQ, a protein kinase C-family enzyme important in both T and B cell activation. The most complex locus was C5orf56 which encompassed 23 genes (including IL3, IL4, and IL13) and 3 miRNA within 4 loops and sub-loops. Genes within the TADs were highly enriched for multiple GO terms for processes involved in leukocyte activation (e.g., MAP kinase signaling cascade), JAK-STAT responses, chemotaxis, and cytokine-mediated signaling pathways.ConclusionThese 20 JIA-associated risk loci are situated within complex chromatin regions that show similar features in both lymphoid and myeloid cells. HiC data demonstrate direct physical contacts between putative enhancers within the risk loci and multiple genes of immunologic interest. We hypothesize that at least some of the genes within the haplotype-associated TADs are the long sought “target genes” of JIA-associated genetic...