Identification of a specific APOE transcript and functional elements associated with Alzheimer’s disease

IF 14.9 1区 医学 Q1 NEUROSCIENCES Molecular Neurodegeneration Pub Date : 2024-08-29 DOI:10.1186/s13024-024-00751-7
Qiang Chen, Luis Aguirre, Guoming Liang, Huanhuan Zhao, Tao Dong, Felix Borrego, Itziar de Rojas, Qichan Hu, Christopher Reyes, Ling-Yan Su, Bao Zhang, James D. Lechleiter, Harald H. H. Göring, Philip L. De Jager, Joel E. Kleinman, Thomas M. Hyde, Pan P. Li, Agustín Ruiz, Daniel R. Weinberger, Sudha Seshadri, Liang Ma
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Abstract

The APOE gene is the strongest genetic risk factor for late-onset Alzheimer’s Disease (LOAD). However, the gene regulatory mechanisms at this locus remain incompletely characterized. To identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with multi-omics data from human postmortem brains including 2,179 RNA-seq samples from 3 brain regions and two ancestries (European and African), 667 DNA methylation samples, and ChIP-seq samples. Additionally, we plotted the expression trajectory of APOE transcripts in human brains during development. We identified an AD-linked APOE transcript (jxn1.2.2) particularly observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features, cognitive impairment, and the presence of the APOE4 allele in DLPFC. We prioritized two independent functional SNPs (rs157580 and rs439401) significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. These SNPs are located within active chromatin regions and affect brain-related transcription factor-binding affinities. The two SNPs shared effects on the jxn1.2.2 transcript between European and African ethnic groups. The novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease etiology.
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鉴定与阿尔茨海默病相关的特定 APOE 转录本和功能要素
APOE 基因是晚发性阿尔茨海默病(LOAD)最强的遗传风险因素。然而,该基因位点的基因调控机制仍未完全定性。为了在 APOE 基因座中发现新的与阿兹海默症相关的功能元件,我们将 SNP 变异与来自人类死后大脑的多组学数据(包括来自 3 个大脑区域和两个血统(欧洲人和非洲人)的 2,179 份 RNA-seq 样本、667 份 DNA 甲基化样本和 ChIP-seq 样本)进行了整合。此外,我们还绘制了人脑发育过程中 APOE 转录物的表达轨迹。我们发现了一种与 AD 相关的 APOE 转录本(jxn1.2.2),该转录本尤其可见于背外侧前额叶皮层(DLPFC)。APOE jxn1.2.2 转录本与脑神经病理学特征、认知障碍以及 DLPFC 中 APOE4 等位基因的存在有关。我们优先选择了两个与 jxn1.2.2 转录本丰度和 DNA 甲基化水平显著相关的独立功能 SNPs(rs157580 和 rs439401)。这两个 SNP 位于活跃的染色质区域,影响脑相关转录因子的结合亲和力。这两个SNP对欧洲和非洲族群的jxn1.2.2转录本具有共同的影响。新的 APOE 功能元件提供了潜在的治疗靶点,并从机理上揭示了疾病的病因。
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来源期刊
Molecular Neurodegeneration
Molecular Neurodegeneration 医学-神经科学
CiteScore
23.00
自引率
4.60%
发文量
78
审稿时长
6-12 weeks
期刊介绍: Molecular Neurodegeneration, an open-access, peer-reviewed journal, comprehensively covers neurodegeneration research at the molecular and cellular levels. Neurodegenerative diseases, such as Alzheimer's, Parkinson's, Huntington's, and prion diseases, fall under its purview. These disorders, often linked to advanced aging and characterized by varying degrees of dementia, pose a significant public health concern with the growing aging population. Recent strides in understanding the molecular and cellular mechanisms of these neurodegenerative disorders offer valuable insights into their pathogenesis.
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