Table_1_Genome-wide association study of SNP- and gene-based approaches to identify susceptibility candidates for lupus nephritis in the Han Chinese population.xlsx

BackgroundLupus nephritis (LN) is one of the most common and serious complications of systemic lupus erythaematosus (SLE). Genetic factors play important roles in the pathogenesis of LN and could be used to predict who might develop LN. The purpose of this study was to screen for susceptible candidates of LN across the whole genome in the Han Chinese population.
Methods592 LN patients and 453 SLE patients without renal damage were genotyped at 492,970 single nucleotide polymorphisms (SNPs) in the genome-wide association study (GWAS). Fifty-six SNPs were selected for replication in an independent cohort of 188 LN and 171 SLE without LN patients. Further quantitative real-time (qRT) PCR was carried out in 6 LN patients and 6 healthy controls. Gene-based analysis was conducted using the versatile gene-based test for GWAS. Subsequently, enrichment and pathway analyses were performed in the DAVID database.
ResultsThe GWAS analysis and the following replication research identified 9 SNPs showing suggestive correlation with LN (P<10-4). The most significant SNP was rs12606116 (18p11.32), at P=8.72×10−6. The qRT-PCR results verified the mRNA levels of LINC00470 and ADCYAP1, the closest genes to rs12606116, were significantly lower in LN patients. From the gene-based analysis, 690 genes had suggestive evidence of association (P<0.05), including LINC00470. The enrichment analysis identified the involvement of transforming growth factor beta (TGF-β) signalings in the development of LN. Lower plasma level of TGF-β1 (P<0.05) in LN patients and lower expression of transforming growth factor beta receptor 2 in lupus mice kidney (P<0.05) futher indicate the involvement of TGF-β in LN.
ConclusionsOur analyses identified several promising susceptibility candidates involved in LN, and further verification of these candidates was necessary.

研究背景：狼疮性肾炎（Lupus nephritis, LN）是系统性红斑狼疮（systemic lupus erythaematosus, SLE）最常见且严重的并发症之一。遗传因素在LN的发病机制中发挥关键作用，可用于预测个体罹患LN的风险。本研究旨在中国汉族人群全基因组范围内筛选LN易感候选位点。
研究方法：本全基因组关联研究（genome-wide association study, GWAS）对592例LN患者与453例无肾损伤的SLE患者的492970个单核苷酸多态性（single nucleotide polymorphisms, SNPs）进行基因分型。随后选取56个SNPs，在独立验证队列中进行分型验证，该队列包含188例LN患者与171例无LN的SLE患者。此外，本研究对6例LN患者及6例健康对照者开展实时定量聚合酶链式反应（quantitative real-time PCR, qRT-PCR）实验。基于基因的关联分析采用通用型GWAS基因检验方法完成。后续通过DAVID数据库进行富集分析与通路分析。
研究结果：GWAS分析及后续验证研究共筛选出9个与LN存在潜在相关性的SNPs（P<10^-4），其中最显著的位点为rs12606116（位于18p11.32区域），关联P值为8.72×10^-6。qRT-PCR结果证实，rs12606116邻近的两个基因LINC00470与ADCYAP1的mRNA表达水平在LN患者中显著降低。基于基因的关联分析共鉴定出690个存在潜在关联证据的基因（P<0.05），其中包含LINC00470。富集分析显示，转化生长因子β（transforming growth factor beta, TGF-β）信号通路参与LN的发病进程。进一步实验发现，LN患者血浆中TGF-β1水平显著降低（P<0.05），狼疮小鼠肾脏组织中转化生长因子β受体2的表达水平也显著下调（P<0.05），进一步证实了TGF-β信号通路在LN发病中的作用。
研究结论：本研究鉴定出多个与LN相关的潜在易感候选位点与基因，后续需对这些候选对象开展进一步验证工作。