目的:5mC甲基化和羟甲基化(5hmC)与阿尔茨海默病(AD)相关。然而,以前的研究受到缺乏5hmC计算的限制。本研究旨在寻找与AD相关的预测因子和潜在的治疗化学品,使用生物信息学方法整合5mC,5hmC,和表情变化,和AD小鼠模型。
方法:基因表达微阵列和5mC和5hmC测序数据集从GEO库下载。142例AD和52例正常内嗅皮层标本。来自氧化亚硫酸氢盐测序(oxBS)处理的样品的数据,仅代表5mC,用于计算5hmC水平。功能分析,随机森林监督分类和甲基化验证。CMap预测了潜在的化学物质。莫里斯水迷宫,使用FAD4TAD小鼠模型进行Y迷宫和新物体识别行为测试。分离皮质和海马组织进行免疫组织化学染色。
结果:C1QTNF5,UBD,ZFP106,NEDD1,AKT3和MBP基因涉及13个具有5mc的启动子CpG位点,5hmC甲基化和表达差异进行鉴定。AKT3和MBP在患者和小鼠模型中均下调。AKT3和MBP中的三个CpG位点在验证时显示出显著的甲基化差异。FAD4TAD小鼠显示脑功能衰退,皮质和海马中AKT3表达降低。预测十种化学物质作为AD的潜在治疗方法。
结论:AKT3和MBP可能与AD病理有关,可作为生物标志物。这十种预测的化学物质可能会提供新的治疗方法。我们的发现可能有助于识别新的标志物和促进对AD机制的理解。
OBJECTIVE: 5 mC methylation and hydroxymethylation (5hmC) are associated with Alzheimer\'s disease (AD). However, previous studies were limited by the absence of a 5hmC calculation. This study aims to find AD associated predictors and potential therapeutic chemicals using bioinformatics approach integrating 5 mC, 5hmC, and expression changes, and an AD mouse model.
METHODS: Gene expression microarray and 5 mC and 5hmC sequencing datasets were downloaded from GEO repository. 142 AD and 52 normal entorhinal cortex specimens were enrolled. Data from oxidative bisulfite sequencing (oxBS)-treated samples, which represent only 5 mC, were used to calculate 5hmC level. Functional analyses, random forest supervised classification and methylation validation were applied. Potential chemicals were predicted by CMap. Morris water maze, Y maze and novel object recognition behavior tests were performed using FAD4T AD mice model. Cortex and hippocampus tissues were isolated for immunohistochemical staining.
RESULTS: C1QTNF5, UBD, ZFP106, NEDD1, AKT3, and MBP genes involving 13 promoter CpG sites with 5mc, 5hmC methylation and expression difference were identified. AKT3 and MBP were down-regulated in both patients and mouse model. Three CpG sites in AKT3 and MBP showed significant methylation difference on validation. FAD4T AD mice showed recession in brain functions and lower AKT3 expression in both cortex and hippocampus. Ten chemicals were predicted as potential treatments for AD.
CONCLUSIONS: AKT3 and MBP may be associated with AD pathology and could serve as biomarkers. The ten predicted chemicals might offer new therapeutic approaches. Our findings could contribute to identifying novel markers and advancing the understanding of AD mechanisms.