State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
Invest Ophthalmol Vis Sci. 2020 Nov 2;61(13):12. doi: 10.1167/iovs.61.13.12.
To identify and validate key genes that could provide a new perspective for genetic marker screening of diabetic retinopathy (DR).
The gene expression and DNA methylation profiles were obtained from the Gene Expression Omnibus. Differential expression analysis was conducted using the limma package, and then the functions of the differentially expressed genes (DEGs) were analyzed using the DAVID database, followed by protein-protein interaction (PPI) networks using Cytoscape software. We employed the Sequenom MassARRAY system to detect the promoter methylation levels of the candidate genes in peripheral blood mononuclear cells from 32 healthy individuals and 94 patients with type 2 diabetes mellitus (T2D; 64 with DR and 30 without DR) and in fibrovascular membranes (FVMs) from three proliferative DR patients and three controls with idiopathic epiretinal membranes. The mRNA levels of candidate genes were further confirmed via real-time polymerase chain reaction.
A significant enrichment of 5906 DEGs was found in immune and inflammatory responses. TGFB1, CCL2, and TNFSF2 were identified as the top three core genes associated with NLRP3 inflammation in PPI networks. These genes have relatively low levels of promoter methylation, which have been validated in peripheral blood mononuclear cells and FVMs from DR patients, and the methylation levels were found to be negative correlated with the mRNA levels and HbA1c levels in T2D patients.
Overall, these data indicate that promoter hypomethylation of NLRP3, TGFB1, CCL2, and TNFSF2 may increase the risk of DR in the Chinese Han population, indicating that these genes might serve as potential targets for the detection and treatment of DR.
鉴定和验证关键基因，为糖尿病视网膜病变（DR）的遗传标记筛选提供新视角。
从基因表达综合数据库（Gene Expression Omnibus）中获取基因表达和 DNA 甲基化谱。使用 limma 包进行差异表达分析，然后使用 DAVID 数据库分析差异表达基因（DEGs）的功能，再使用 Cytoscape 软件构建蛋白质-蛋白质相互作用（PPI）网络。我们采用 Sequenom MassARRAY 系统检测了 32 名健康个体和 94 名 2 型糖尿病患者（64 名患有 DR，30 名未患有 DR）外周血单核细胞以及 3 名增殖性 DR 患者和 3 名特发性视网膜前膜对照者纤维血管膜中候选基因的启动子甲基化水平。候选基因的 mRNA 水平通过实时聚合酶链反应进一步验证。
在免疫和炎症反应中发现了 5906 个 DEG 的显著富集。在 PPI 网络中，TGFB1、CCL2 和 TNFSF2 被鉴定为与 NLRP3 炎症相关的前三个核心基因。这些基因的启动子甲基化水平较低，在 DR 患者的外周血单核细胞和纤维血管膜中得到了验证，并且在 T2D 患者中，其甲基化水平与 mRNA 水平和 HbA1c 水平呈负相关。
总体而言，这些数据表明，NLRP3、TGFB1、CCL2 和 TNFSF2 的启动子低甲基化可能会增加中国汉族人群 DR 的发病风险，表明这些基因可能作为 DR 检测和治疗的潜在靶点。
