Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA.
Corewell Health William Beaumont University Hospital, Royal Oak, MI 48073, USA.
Int J Mol Sci. 2023 Feb 2;24(3):2876. doi: 10.3390/ijms24032876.
Precision neurology combines high-throughput technologies and statistical modeling to identify novel disease pathways and predictive biomarkers in Alzheimer's disease (AD). Brain cytochrome P450 (CYP) genes are major regulators of cholesterol, sex hormone, and xenobiotic metabolism, and they could play important roles in neurodegenerative disorders. Increasing evidence suggests that epigenetic factors contribute to AD development. We evaluated cytosine ('CpG')-based DNA methylation changes in AD using circulating cell-free DNA (cfDNA), to which neuronal cells are known to contribute. We investigated CYP-based mechanisms for AD pathogenesis and epigenetic biomarkers for disease detection. We performed a case-control study using 25 patients with AD and 23 cognitively healthy controls using the cfDNA of CYP genes. We performed a logistic regression analysis using the MetaboAnalyst software computer program and a molecular pathway analysis based on epigenetically altered CYP genes using the Cytoscape program. We identified 130 significantly (false discovery rate correction q-value < 0.05) differentially methylated CpG sites within the CYP genes. The top two differentially methylated genes identified were and . The significant molecular pathways that were perturbed in AD cfDNA were (i) androgen and estrogen biosynthesis and metabolism, (ii) C21 steroid hormone biosynthesis and metabolism, and (iii) arachidonic acid metabolism. Existing evidence suggests a potential role of each of these biochemical pathways in AD pathogenesis. Next, we randomly divided the study group into discovery and validation sub-sets, each consisting of patients with AD and control patients. Regression models for AD prediction based on CYP CpG methylation markers were developed in the discovery or training group and tested in the independent validation group. The CYP biomarkers achieved a high predictive accuracy. After a 10-fold cross-validation, the combination of cg17852385/cg23101118 + cg14355428/cg22536554 achieved an AUC (95% CI) of 0.928 (0.7871.00), with 100% sensitivity and 92.3% specificity for AD detection in the discovery group. The performance remained high in the independent validation or test group, achieving an AUC (95% CI) of 0.942 (0.9050.979) with a 90% sensitivity and specificity. Our findings suggest that the epigenetic modification of CYP genes may play an important role in AD pathogenesis and that circulating CYP-based cfDNA biomarkers have the potential to accurately and non-invasively detect AD.
精准神经学结合高通量技术和统计建模，以确定阿尔茨海默病（AD）中的新型疾病途径和预测性生物标志物。脑细胞色素 P450（CYP）基因是胆固醇、性激素和外源性化合物代谢的主要调节剂，它们可能在神经退行性疾病中发挥重要作用。越来越多的证据表明，表观遗传因素有助于 AD 的发展。我们使用已知神经元细胞会贡献的循环无细胞 DNA（cfDNA）评估 AD 中的基于胞嘧啶（'CpG'）的 DNA 甲基化变化。我们研究了 CYP 相关机制在 AD 发病机制中的作用和用于疾病检测的表观遗传生物标志物。我们使用 cfDNA 对 25 名 AD 患者和 23 名认知健康对照进行了病例对照研究。我们使用 MetaboAnalyst 软件程序进行逻辑回归分析，并使用 Cytoscape 程序基于表观遗传改变的 CYP 基因进行分子途径分析。我们在 CYP 基因内确定了 130 个差异甲基化 CpG 位点（错误发现率校正 q 值<0.05）。鉴定出的两个差异甲基化基因是 和 。AD cfDNA 中受干扰的显著分子途径是（i）雄激素和雌激素生物合成和代谢，（ii）C21 甾体激素生物合成和代谢，以及（iii）花生四烯酸代谢。现有证据表明，这些生化途径中的每一个都可能在 AD 发病机制中发挥作用。接下来，我们将研究组随机分为发现和验证子集，每个子集均由 AD 患者和对照患者组成。在发现或训练组中建立基于 CYP CpG 甲基化标记物的 AD 预测回归模型，并在独立验证组中进行测试。CYP 生物标志物具有较高的预测准确性。经过 10 倍交叉验证，组合 cg17852385/cg23101118 + cg14355428/cg22536554 在发现组中的 AUC（95%CI）为 0.928（0.7871.00），AD 检测的敏感性为 100%，特异性为 92.3%。在独立验证或测试组中，该性能仍然很高，AUC（95%CI）为 0.942（0.9050.979），敏感性和特异性均为 90%。我们的研究结果表明，CYP 基因的表观遗传修饰可能在 AD 发病机制中起重要作用，并且循环基于 CYP 的 cfDNA 生物标志物具有准确、非侵入性检测 AD 的潜力。
