Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3.
Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3.
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DOI：
10.3389/fgene.2022.1011965
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发表时间：
2022
影响因子：
3.7
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中科院分区：
文献类型：
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TNFAIP3/A20是一个重要的自身免疫性疾病风险位点，与半形TNFAIP3表达相关，具有复杂的染色质结构，有超过30个预测的增强子。该研究旨在对系统性红斑狼疮（SLE）风险单倍型指数SNP rs10499197标记的TNFAIP3启动子上游约55 kb的增强子进行功能表征。采用EMSA和/或荧光素酶报告基因法检测rs10499197、rss58905141和rs9494868在免疫细胞类型中的等位基因效应。对无风险或SLE风险TNFAIP3单倍型的患者源性EBV B细胞进行共免疫沉淀、ChIP-qPCR和3C-qPCR，以评估单倍型对转录因子结合和TNFAIP3位点染色质调控的特异性影响。本研究发现，TNFAIP3位点具有一个复杂的染色质调控网络，从IL20RA的启动子区到TNFAIP3的3 '非翻译区跨越约1M bp。增强子的功能分析表明，RelA/p65和CEBPB结合基序的共同依赖性，通过上下动态的远程相互作用，在TNFAIP3 SLE风险单倍型中增加IL20RA和IFNGR1的表达，降低TNFAIP3的表达。对rs10499197连锁不平衡（D ' = 1.0）的SNP检测发现，rs9494868是一个功能性SNP，在体外核因子结合和增强子激活方面存在等位基因特异性增加的风险。总之，本研究表明，携带在~ 109 kb SLE风险单倍型上的snp促进了IL20RA和IFNGR1的高表型表达，同时抑制了TNFAIP3的表达，增加了这一在自身免疫性疾病病理中至关重要的位点的机制潜力。
TNFAIP3/A20 is a prominent autoimmune disease risk locus that is correlated with hypomorphic TNFAIP3 expression and exhibits complex chromatin architecture with over 30 predicted enhancers. This study aimed to functionally characterize an enhancer ∼55 kb upstream of the TNFAIP3 promoter marked by the systemic lupus erythematosus (SLE) risk haplotype index SNP, rs10499197. Allele effects of rs10499197, rs58905141, and rs9494868 were tested by EMSA and/or luciferase reporter assays in immune cell types. Co-immunoprecipitation, ChIP-qPCR, and 3C-qPCR were performed on patient-derived EBV B cells homozygous for the non-risk or SLE risk TNFAIP3 haplotype to assess haplotype-specific effects on transcription factor binding and chromatin regulation at the TNFAIP3 locus. This study found that the TNFAIP3 locus has a complex chromatin regulatory network that spans ∼1M bp from the promoter region of IL20RA to the 3′ untranslated region of TNFAIP3. Functional dissection of the enhancer demonstrated co-dependency of the RelA/p65 and CEBPB binding motifs that, together, increase IL20RA and IFNGR1 expression and decreased TNFAIP3 expression in the context of the TNFAIP3 SLE risk haplotype through dynamic long-range interactions up- and downstream. Examination of SNPs in linkage disequilibrium (D’ = 1.0) with rs10499197 identified rs9494868 as a functional SNP with risk allele-specific increase in nuclear factor binding and enhancer activation in vitro. In summary, this study demonstrates that SNPs carried on the ∼109 kb SLE risk haplotype facilitate hypermorphic IL20RA and IFNGR1 expression, while suppressing TNFAIP3 expression, adding to the mechanistic potency of this critically important locus in autoimmune disease pathology.