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. 2016 Nov 1;17(1):212.
doi: 10.1186/s13059-016-1078-x.

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

Amanda McGovern  1 , Stefan Schoenfelder  2 , Paul Martin  1 , Jonathan Massey  1 , Kate Duffus  1 , Darren Plant  1   3 , Annie Yarwood  1 , Arthur G Pratt  4 , Amy E Anderson  4 , John D Isaacs  4 , Julie Diboll  4 , Nishanthi Thalayasingam  4 , Caroline Ospelt  5 , Anne Barton  1   3 , Jane Worthington  1   3 , Peter Fraser  2 , Stephen Eyre  1 , Gisela Orozco  6
Affiliations

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

Amanda McGovern et al. Genome Biol. .

Abstract

Background: The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific assays in T and B cell lines, we provide compelling evidence that redefines causal genes at the 6q23 locus, one of the most important loci that confers autoimmunity risk.

Results: Although the function of disease-associated non-coding single nucleotide polymorphisms (SNPs) at 6q23 is unknown, the association is generally assigned to TNFAIP3, the closest gene. However, the DNA fragment containing the associated SNPs interacts through chromatin looping not only with TNFAIP3, but also with IL20RA, located 680 kb upstream. The risk allele of the most likely causal SNP, rs6927172, is correlated with both a higher frequency of interactions and increased expression of IL20RA, along with a stronger binding of both the NFκB transcription factor and chromatin marks characteristic of active enhancers in T-cells.

Conclusions: Our results highlight the importance of gene assignment for translating GWAS findings into biologically meaningful mechanisms of disease and potential therapeutic targets; indeed, monoclonal antibody therapy targeting IL-20 is effective in the treatment of rheumatoid arthritis and psoriasis, both with strong GWAS associations to this region.

Keywords: Autoimmunity; Capture Hi-C; Causal genes; Functional genomics; Genome-wide association studies (GWAS); Single nucleotide polymorphisms (SNP).

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Figures

Fig. 1
Fig. 1
Long-range interactions in the 6q23 locus. Genomic co-ordinates are shown along the top of each panel and tracks are labelled a–n. a HindIII restriction fragments. b–e Regions targeted and restriction fragments included in the Region (b, c) and Promoter (d, e) Capture experiments. f GENCODE V17 genes. g–i 1000 Genomes SNPs in LD (r2 ≥ 0.8) with the index SNPs rs6920220, associated with RA, SLE, celiac disease, T1D and IBD (g), rs7752903, associated with RA, SLE and celiac disease (h) and rs610604, associated with Ps and PsA (i). j Topologically associated domains (TADs) in GM12878 cells [20]. k–n Significant interactions identified in the Region and Promoter capture experiments in GM12878 (k, l) and Jurkat (m, n) cells. The black arrow indicates the position of the rs6927172 SNP
Fig. 2
Fig. 2
Validation of CHi-C results by 3C-qPCR in GM12878 and Jurkat cell lines. The graphs show the relative interaction frequency of (a) the 6q23 intergenic disease SNPs tagged by rs6920220, (b) the TNFAIP3 gene and (c) the IL20RA gene with their respective targets (dark grey) compared to control, non-interacting fragments (C-, light grey). Diagrams below each graph show the approximate location of the primers for the anchor, negative control (C-) and target (★) regions. Error bars indicate standard deviation of three biological replicates; * indicates t-test P value <0.05
Fig. 3
Fig. 3
eQTL effect of rs6927172 on gene expression. a Increased expression of IL20RA in primary CD4+ T-cells from 21 healthy individuals carrying the G risk allele of rs6927172, P = 0.02. b Increased expression of IL20RA in primary CD4+ T-cells from 102 early inflammatory arthritis clinic patients carrying the risk G allele of rs6927172, P = 0.03. The three different genotypes for the SNPs are displayed on the x-axis and gene expression levels on the y-axis. Error bars indicate standard deviation
Fig. 4
Fig. 4
Genotype-specific 3C showing preferential interaction of the disease risk G allele of rs6927172 with IL20RA (a) and IFNGR1 (b). –50 kb restriction fragment located 50 kb upstream of the rs6927172 containing restriction fragment, rs6927172 restriction fragment containing rs6927172, rs6920220 restriction fragment containing the top GWAS SNP in the 6q23 region, NCR non-interacting control region. Error bars indicate standard deviation of three biological replicates
Fig. 5
Fig. 5
Allele-specific ChIP in Jurkat cells, showing increased binding of H3K4me1, H3K27ac and NFκB p65 to the risk allele of rs6927172. Error bars indicate standard deviation of three biological replicates
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