Takayasu arteritis risk locus in <i>IL6</i> represses the anti-inflammatory gene <i>GPNMB</i> through chromatin looping and recruiting MEF2-HDAC complex.

Abstract

Previous work has revealed a genetic association between Takayasu arteritis and a non-coding genetic variant in an enhancer region within <i>IL6</i> (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. A combination of experimental and bioinformatics tools were used to mechanistically understand the effects of the disease-associated genetic locus in <i>IL6</i>. 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 the <i>IL6</i> locus. Both cell lines and peripheral blood primary monocyte-derived macrophages were used. We identified the monocyte/macrophage anti-inflammatory gene <i>GPNMB</i>,~520 kb from <i>IL6</i>, 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. Takayasu arteritis risk locus in <i>IL6</i> might increase disease susceptibility by suppression of the anti-inflammatory gene <i>GPNMB</i> through 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.