Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain.
Department of Gastroenterology, Hospital La Fe, Valencia, Spain.
Clin Transl Gastroenterol. 2019 Oct;10(10):e00083. doi: 10.14309/ctg.0000000000000083.
DNA methylation is an epigenetic mechanism that regulates gene expression and represents an important link between genotype, environment, and disease. It is a reversible and inheritable mechanism that could offer treatment targets. We aimed to assess the methylation changes on specific genes previously associated with Crohn's disease (CD) and to study their possible associations with the pathology.
We included 103 participants and grouped them into 2 cohorts (a first [n = 31] and a second validation [n = 72] cohort), with active CD (aCD) and inactive CD (iCD) and healthy participants (CTR). DNA was obtained from the peripheral blood and analyzed by the Agena platform. The selected genes were catalase (CAT), α-defensin 5 (DEFA5), FasR, FasL, tumor necrosis factor (TNF), TNFRSF1A, TNFRSF1B, PPA2, ABCB1, NOD2, PPARγ, and PKCζ. We used the elastic net algorithm and R software.
We studied 240 CpGs. Sixteen CpGs showed differential methylation profiles among aCD, iCD, and CTR. We selected for validation those with the greatest differences: DEFA5 CpG_11; CpG_13; CAT CpG_31.32; TNF CpG_4, CpG_12; and ABCB1 CpG_21. Our results validated the genes DEFA5 (methylation gain) and TNF (methylation loss) with P values < 0.001. In both cases, the methylation level was maintained and did not change with CD activity (aCD vs iCD). The subanalysis comparison between aCD and iCD showed significant differential methylation profiles in other CpGs: TNF, FAS, ABCB1, CAT, and TNFRS1BF genes.
The methylation status of DEFA5 and TNF genes provides a signature biomarker that characterizes patients with CD and supports the possible implication of the environment and the immune system in CD pathogenesis.
DNA 甲基化是一种调控基因表达的表观遗传机制，是基因型、环境和疾病之间的重要联系。它是一种可逆转和可遗传的机制，可为治疗提供靶点。我们旨在评估先前与克罗恩病（CD）相关的特定基因的甲基化变化，并研究它们与病理学的可能关联。
我们纳入了 103 名参与者，并将他们分为两个队列（第一队列[n=31]和第二验证队列[n=72]），包括活动期 CD（aCD）、缓解期 CD（iCD）和健康对照（CTR）。从外周血中提取 DNA，使用 Agena 平台进行分析。选择的基因有过氧化氢酶（CAT）、α-防御素 5（DEFA5）、FasR、FasL、肿瘤坏死因子（TNF）、TNFRSF1A、TNFRSF1B、PPA2、ABCB1、NOD2、PPARγ和 PKCζ。我们使用弹性网络算法和 R 软件进行分析。
我们研究了 240 个 CpG。在 aCD、iCD 和 CTR 之间，有 16 个 CpG 显示出不同的甲基化谱。我们选择了差异最大的 CpG 进行验证：DEFA5 的 CpG_11、CpG_13、CAT 的 CpG_31.32、TNF 的 CpG_4、CpG_12 和 ABCB1 的 CpG_21。我们的结果验证了基因 DEFA5（甲基化增加）和 TNF（甲基化减少）的结果，P 值均小于 0.001。在这两种情况下，甲基化水平保持不变，且不随 CD 活动（aCD 与 iCD）而改变。aCD 与 iCD 的亚组分析比较显示，在其他 CpGs（TNF、FAS、ABCB1、CAT 和 TNFRS1BF）中存在显著的差异甲基化谱。
DEFA5 和 TNF 基因的甲基化状态提供了一个特征性的生物标志物，可用于表征 CD 患者，并支持环境和免疫系统在 CD 发病机制中的可能作用。
