Takayasu arteritis risk locus inIL6represses the anti-inflammatory geneGPNMBthrough chromatin looping and recruiting MEF2–HDAC complex

ObjectivePrevious work has revealed a genetic association between Takayasu arteritis and a non-coding genetic variant in an enhancer region withinIL6(rs2069837 A/G). The risk allele in this variant (allele A) has a protective effect against chronic viral infection and cancer. The goal of this study was to characterise the functional consequences of this disease-associated risk locus.MethodsA combination of experimental and bioinformatics tools were used to mechanistically understand the effects of the disease-associated genetic locus inIL6. These included electrophoretic mobility shift assay, DNA affinity precipitation assays followed by mass spectrometry and western blotting, luciferase reporter assays and chromosome conformation capture (3C) to identify chromatin looping in theIL6locus. Both cell lines and peripheral blood primary monocyte-derived macrophages were used.ResultsWe identified the monocyte/macrophage anti-inflammatory geneGPNMB,~520 kb fromIL6, as a target gene regulated by rs2069837. We revealed preferential recruitment of myocyte enhancer factor 2–histone deacetylase (MEF2–HDAC) repressive complex to the Takayasu arteritis risk allele. Further, we demonstrated suppression of GPNMB expression in monocyte-derived macrophages from healthy individuals with AA compared with AG genotype, which was reversed by histone deacetylase inhibition. Our data show that the risk allele in rs2069837 represses the expression of GPNMB by recruiting MEF2–HDAC complex, enabled through a long-range intrachromatin looping. Suppression of this anti-inflammatory gene might mediate increased susceptibility in Takayasu arteritis and enhance protective immune responses in chronic infection and cancer.ConclusionsTakayasu arteritis risk locus inIL6might increase disease susceptibility by suppression of the anti-inflammatory geneGPNMBthrough chromatin looping and recruitment of MEF2–HDAC epigenetic repressive complex. Our data highlight long-range chromatin interactions in functional genomic and epigenomic studies in autoimmunity.