Identification of causal genes and mechanisms by which genetic variation mediates juvenile idiopathic arthritis susceptibility using functional genomics and CRISPR-Cas9

ObjectiveGenome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with juvenile idiopathic arthritis (JIA), the majority of which are located in non-coding regions such as enhancers. This presents a challenge for pinpointing causal variants and their target genes. Interpreting these loci requires functional genomics data from disease-relevant tissues, which has been lacking for JIA. This study seeks to fill that gap and elucidate the biological mechanisms underlying JIA susceptibility. MethodsWe performed low-input whole genome promoter Capture Hi-C (PCHi-C) and ATAC-seq on CD4+ T cells from three JIA oligoarthritis patients. To link JIA-associated SNPs to potential causal genes, we integrated PCHi-C data with JIA GWAS summary statistics using our Bayesian prioritisation algorithm, Capture Hi-C Omnibus Gene Score (COGS). ATAC-seq was used to further annotate JIA GWAS loci in CD4+ T cells. We then employed CRISPR activation and interference (CRISPRa/i) in Jurkat cells to validate the prioritised SNPs and their corresponding genes. ResultsChromatin interactions between JIA-associated SNPs and gene promoters were identified in 19 of 44 non-MHC JIA loci, linking 61 known and novel target genes to the disease. Through COGS, we prioritised seven putative causal genes for JIA: RGS14, ERAP2, HIPK1, CCR4, CCRL2, CCR2, and CCR3. SNPs within promoter-interacting regions (PIRs) of these genes were further validated using CRISPRa/i to confirm their roles in regulating gene expression. ConclusionsThis study provides insights into the genetic architecture of JIA by integrating genomic and epigenomic data, identifying disease-related genes, functionally validating risk SNPs, and highlighting candidate drugs for repurposing. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSRecent genome-wide association studies in JIA have identified genetic loci associated with disease risk. However, the precise mechanisms by which these variants contribute to disease pathology remain unclear, as most do not directly alter protein-coding genes. It has been proposed that non-coding SNPs can affect genes that are important in disease through disruption of enhancer-mediated regulatory mechanisms that control their expression, with enhancers exerting their effects through chromatin interactions. Functional characterisation of risk loci is essential to delineate causal SNPs and target genes in JIA. What this study addsThis study is the first to utilise low-input Promoter Capture Hi-C to map long-range chromatin interactions in CD4+ T cells from JIA patients, alongside ATAC-seq to assess chromatin accessibility within the same samples. It identifies 61 potential target genes at JIA-associated loci and validates the regulatory roles of some of these through CRISPR activation and interference. This work enhances our understanding of how genetic variants modulate gene expression in immune cells, shedding light on key pathways involved in JIA pathogenesis. How this study might affect research, practice or policyHighlights new potential causal genes in JIA which can help understand the pathological mechanisms in JIA, and suggests the potential to repurpose CCR2/CCR5 inhibitors in JIA.