Macías Mónica, Alba-Linares Juan José, Acha Blanca, Blanco-Luquin Idoia, Fernández Agustín F, Álvarez-Jiménez Johana, Urdánoz-Casado Amaya, Roldan Miren, Robles Maitane, Cabezon-Arteta Eneko, Alcolea Daniel, Gordoa Javier Sánchez Ruiz de, Corroza Jon, Cabello Carolina, Erro María Elena, Jericó Ivonne, Fraga Mario F, Mendioroz Maite
Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain.
Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN CSIC), 33940 El Entrego, Spain.
Int J Mol Sci. 2025 Apr 5;26(7):3419. doi: 10.3390/ijms26073419.
Recent studies show that patients with Alzheimer's disease (AD) harbor specific methylation marks in the brain that, if accessible, could be used as epigenetic biomarkers. Liquid biopsy enables the study of circulating cell-free DNA (cfDNA) fragments originated from dead cells, including neurons affected by neurodegenerative processes. Here, we isolated and epigenetically characterized plasma cfDNA from 35 patients with AD and 35 cognitively healthy controls by using the Infinium MethylationEPIC BeadChip array. Bioinformatics analysis was performed to identify differential methylation positions (DMPs) and regions (DMRs), including ε4 genotype stratified analysis. Plasma pTau181 (Simoa) and cerebrospinal fluid (CSF) core biomarkers (Fujirebio) were also measured and correlated with differential methylation marks. Validation was performed with bisulfite pyrosequencing and bisulfite cloning sequencing. Epigenome-wide cfDNA analysis identified 102 DMPs associated with AD status. Most DMPs correlated with clinical cognitive and functional tests including 60% for Mini-Mental State Examination (MMSE) and 80% for Global Deterioration Scale (GDS), and with AD blood and CSF biomarkers. In silico functional analysis connected 30 DMPs to neurological processes, identifying key regulators such as and genes. Several DMRs were annotated to genes previously reported to harbor epigenetic brain changes in AD (, , , , , ) and were linked to ε4 genotypes. Notably, a DMR in the gene, previously shown to be hypermethylated in the AD hippocampus, was validated in cfDNA from an orthogonal perspective. These results support the feasibility of studying cfDNA to identify potential epigenetic biomarkers in AD. Thus, liquid biopsy could improve non-invasive AD diagnosis and aid personalized medicine by detecting epigenetic brain markers in blood.
最近的研究表明，阿尔茨海默病（AD）患者大脑中存在特定的甲基化标记，如果能够获取这些标记，可用作表观遗传生物标志物。液体活检能够研究源自死亡细胞（包括受神经退行性过程影响的神经元）的循环游离DNA（cfDNA）片段。在此，我们使用Infinium甲基化EPIC芯片阵列，从35例AD患者和35例认知健康对照者中分离出血浆cfDNA，并对其进行表观遗传学特征分析。进行了生物信息学分析，以鉴定差异甲基化位点（DMP）和区域（DMR），包括ε4基因型分层分析。还测量了血浆pTau181（Simoa）和脑脊液（CSF）核心生物标志物（富士瑞必欧），并将其与差异甲基化标记相关联。通过亚硫酸氢盐焦磷酸测序和亚硫酸氢盐克隆测序进行验证。全表观基因组cfDNA分析确定了102个与AD状态相关的DMP。大多数DMP与临床认知和功能测试相关，包括简易精神状态检查表（MMSE）的60%和整体衰退量表（GDS）的80%，以及与AD血液和脑脊液生物标志物相关。计算机功能分析将30个DMP与神经学过程联系起来，确定了关键调节因子，如 和 基因。几个DMR被注释到先前报道在AD中存在表观遗传脑变化的基因（ 、 、 、 、 、 ），并与ε4基因型相关。值得注意的是，先前在AD海马体中显示高甲基化的 基因中的一个DMR，从正交角度在cfDNA中得到了验证。这些结果支持了研究cfDNA以鉴定AD潜在表观遗传生物标志物的可行性。因此，液体活检可以通过检测血液中的表观遗传脑标记物来改善AD的无创诊断并辅助个性化医疗。
