炎症体
CTCF公司
H3K4me3
KLF2
表观遗传学
增强子
全基因组关联研究
TXNIP公司
染色质免疫沉淀
染色质
Jurkat细胞
表达数量性状基因座
表观遗传学
基因表达调控
基因敲除
基因表达
遗传学
DNA甲基化
发起人
转录因子
单核苷酸多态性
T细胞
基因型
生物
基因
硫氧还蛋白
免疫系统
受体
作者
Manish Kumar Singh,Harikrishna Reddy Rallabandi,Xu‐jie Zhou,Yuanyuan Qi,Zhanzheng Zhao,Ting Gan,Hong Zhang,Loren L. Looger,Swapan K. Nath
标识
DOI:10.1136/ard-2023-224953
摘要
Objective A recent genome-wide association study linked KLF2 as a novel Asian-specific locus for systemic lupus erythematosus (SLE) susceptibility. However, the underlying causal functional variant(s), cognate target gene(s) and genetic mechanisms associated with SLE risk are unknown. Methods We used bioinformatics to prioritise likely functional variants and validated the best candidate with diverse experimental techniques, including genome editing. Gene expression was compared between healthy controls (HCs) and patients with SLE with or without lupus nephritis (LN+, LN−). Results Through bioinformatics and expression quantitative trait locus analyses, we prioritised rs4808485 in active chromatin, predicted to modulate KLF2 expression. Luciferase reporter assays and chromatin immunoprecipitation-qPCR demonstrated differential allele-specific enhancer activity and binding of active histone marks (H3K27ac, H3K4me3 and H3K4me1), Pol II, CTCF, P300 and the transcription factor PARP1. Chromosome conformation capture-qPCR revealed long-range chromatin interactions between rs4808485 and the KLF2 promoter. These were directly validated by CRISPR-based genetic and epigenetic editing in Jurkat and lymphoblastoid cells. Deleting the rs4808485 enhancer in Jurkat (KO) cells disrupted NLRP3 inflammasome machinery by reducing KLF2 and increasing CASPASE1, IL-1β and GSDMD levels. Knockout cells also exhibited higher proliferation and cell-cycle progression than wild type. RNA-seq validated interplay between KLF2 and inflammasome machinery in HC, LN+ and LN−. Conclusions We demonstrate how rs4808485 modulates the inflammasome and cellular homoeostasis through regulating KLF2 expression. This establishes mechanistic connections between rs4808485 and SLE susceptibility.
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