Nada Shadia, Kahaleh Bashar, Altorok Nezam
Division of Rheumatology, University of Toledo, Toledo, OH, USA.
Department of Internal Medicine, University of Toledo, Toledo, OH, USA.
J Scleroderma Relat Disord. 2022 Feb;7(1):71-81. doi: 10.1177/23971983211033772. Epub 2021 Jul 28.
The etiology of systemic sclerosis is not clear, but there is evidence suggesting a critical role for epigenetic alterations in disease pathogenesis and clinical expression. We sought, in this study, to characterize the genome-wide DNA methylation signature in systemic sclerosis microvascular endothelial cells.
We performed a genome-wide DNA methylation study in microvascular endothelial cells derived from seven diffuse cutaneous systemic sclerosis patients compared to seven age-, sex-, and ethnicity-matched healthy controls. We paired matched samples on Illumina HumanMethylation450 (three diffuse cutaneous systemic sclerosis microvascular endothelial cells and three controls), and reproduced the results in an independent set of matched patient and controls using Illumina Infinium MethylationEPIC (four diffuse cutaneous systemic sclerosis patients and four controls) to identify differentially methylated genes.
We identified 71,353 differentially methylated CpG sites in systemic sclerosis microvascular endothelial cells using Infinium MethylationEPIC microarray in the first group (0.081% of representative probes) and 33,170 CpG sites in the second group using HumanMethylation450 microarray (0.073% of representative probes) in diffuse cutaneous systemic sclerosis microvascular endothelial cells. Among the two groups of subjects, we identified differential methylation of 2455 CpG sites, representing 1301 genes. Most of the differentially methylated CpG sites were hypermethylated (1625 CpG), corresponding to 910 genes. Common hypermethylated genes in systemic sclerosis microvascular endothelial cells include , and We also identified hypomethylation of , and in systemic sclerosis microvascular endothelial cells. Furthermore, we demonstrate significant inverse correlation between DNA methylation status and gene expression in the majority of genes evaluated. Gene ontology analysis of hypermethylated genes demonstrated enrichment of genes involved in angiogenesis ( = 0.0006). Pathway analysis of hypomethylated genes includes genes involved in vascular smooth muscle contraction ( = 0.014) and adherens junctions ( = 0.013).
Our data suggest the presence of significant genome-wide DNA methylation aberrancies in systemic sclerosis microvascular endothelial cells, and identify novel affected genes and pathways in systemic sclerosis microvascular endothelial cells.
系统性硬化症的病因尚不清楚，但有证据表明表观遗传改变在疾病发病机制和临床表现中起关键作用。在本研究中，我们试图描述系统性硬化症微血管内皮细胞全基因组DNA甲基化特征。
我们对7例弥漫性皮肤型系统性硬化症患者的微血管内皮细胞进行了全基因组DNA甲基化研究，并与7例年龄、性别和种族匹配的健康对照进行比较。我们在Illumina HumanMethylation450上对匹配样本进行配对（3例弥漫性皮肤型系统性硬化症微血管内皮细胞和3例对照），并使用Illumina Infinium MethylationEPIC在另一组独立的匹配患者和对照中重复结果（4例弥漫性皮肤型系统性硬化症患者和4例对照）以鉴定差异甲基化基因。
在第一组中，我们使用Infinium MethylationEPIC芯片在系统性硬化症微血管内皮细胞中鉴定出71353个差异甲基化的CpG位点（占代表性探针的0.081%），在第二组中，使用HumanMethylation450芯片在弥漫性皮肤型系统性硬化症微血管内皮细胞中鉴定出33170个CpG位点（占代表性探针的0.073%）。在两组受试者中，我们鉴定出2455个CpG位点的差异甲基化，代表1301个基因。大多数差异甲基化的CpG位点是高甲基化的（1625个CpG），对应910个基因。系统性硬化症微血管内皮细胞中常见的高甲基化基因包括 ，以及 。我们还在系统性硬化症微血管内皮细胞中鉴定出 、 和 的低甲基化。此外，我们证明在大多数评估基因中DNA甲基化状态与基因表达之间存在显著的负相关。高甲基化基因的基因本体分析表明参与血管生成的基因富集（ = 0.0006）。低甲基化基因的通路分析包括参与血管平滑肌收缩（ = 0.014）和黏附连接（ = 0.013）的基因。
我们的数据表明系统性硬化症微血管内皮细胞中存在显著的全基因组DNA甲基化异常，并鉴定出系统性硬化症微血管内皮细胞中受影响的新基因和通路。
