Single-cell epigenomic roadmap of Alzheimer's disease

阿尔茨海默病的单细胞表观基因组路线图

• 批准号: 10390136
• 负责人: Samuel Joseph Morabito
• 金额: $ 4.19万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10390136
• 关键词: Affect; Age; Alzheimer' s Disease; Alzheimer' s disease brain; Alzheimer' s disease patient; Alzheimer' s disease risk; Amyloid beta-Protein; Atlases; Axon; Binding; Biological; Biological Assay; Biology; Brain; Brain region; CRISPR/Cas technology; Cell Nucleus; Cells; Chromatin; Cognitive; Communities; Complex; Consensus; Critical Pathways; Data; Data Set; Development; Disease; Disease associated microglia; Disease susceptibility; Distal Enhancer Elements; Enhancers; Environmental Risk Factor; Evaluation; Future; Gene Expression; Genes; Genetic Enhancer Element; Genetic Risk; Genetic Variation; Genomic Segment; Gliosis; Health; Heritability; Heterogeneity; High-Throughput Nucleotide Sequencing; Hippocampus (Brain); Impaired cognition; Knock-out; Link; Memory Loss; Meta-Analysis; Methods; Microglia; Molecular; Nerve Degeneration; Neurodegenerative Disorders; Neuroglia; Neurons; Pathology; Pathway Analysis; Pathway interactions; Pattern; Phenotype; Population; Prefrontal Cortex; Publishing; Regulator Genes; Regulatory Element; Resolution; Resources; Risk; Risk Factors; Role; Senile Plaques; Small Nuclear RNA; Specificity; Structure; Supervision; System; TREM2 gene; Techniques; Therapeutic; Transposase; Untranslated RNA; Validation; Variant; Work; brain cell; cell type; deep learning; disorder risk; entorhinal cortex; epigenome; epigenomics; experimental study; gene interaction; gene network; genetic risk factor; genetic variant; genome wide association study; healthy aging; human disease; induced pluripotent stem cell; mind control; molecular phenotype; multimodality; promoter; risk variant; single cell analysis; tau aggregation; trait; transcription factor; transcriptome; transcriptome sequencing; transcriptomics

Project Summary/Abstract Genetic variation drives phenotypic variation across many traits, including heritable risk for disease susceptibility in neurodegenerative disorders such as Alzheimer’s Disease (AD). For complex polygenic human diseases, it is difficult to unravel precisely which molecular changes are brought on by genetic risk factors. It is well known that genetic variants at the APOE locus can confer a neuroprotective status from AD, while another variant drastically increases one’s chances of developing disease. Even these well studied variants are not fully understood at the molecular level. The majority of disease-associated risk variants for AD and other disorders lie in non-coding regulatory elements and are therefore best studied using epigenomic techniques. Since previous studies have shown that AD affects different brain regions and cell types throughout its progression, I hypothesize that the mechanisms underlying genetic risk for AD act similarly in a progressive, region-specific, and cell-type-specific manner. In this proposal, we aim to generate chromatin accessibility profiles for single cells across the prefrontal cortex, the hippocampus, and the entorhinal cortex of AD patient brains, and integrate with published single cell transcriptomics data, thereby allowing us to identify enhancer- gene interactions that are disrupted by AD risk variants. Our preliminary work has shown that microglia-specific enhancers are enriched for AD genetic risk factors. Therefore, we will use CRISPR-cas9 to delete an enhancer linked to the variant rs4663105 at the BIN1 locus in induced pluripotent stem cell (iPSC) derived microglia, thereby allowing us to unravel its role in the regulatory landscape. My preliminary data from the prefrontal cortex shows that the chromatin accessibility landscape is highly cell-type specific and is significantly altered in AD patient brains, and I expect that we will find regional specificity of regulatory elements that are disrupted by AD risk variants. Aside from our specific task of identifying these disease-associated regulatory elements, an integrated study of single-cell epigenomics and single-cell transcriptomics data in AD brains will be of great value to the broader AD community to further implicate genes, networks, and pathways as targets for future studies.

项目摘要/摘要 遗传变异导致许多性状的表型变异，包括可遗传的疾病风险。 阿尔茨海默病(AD)等神经退行性疾病的易感性。对于复杂的多基因人类 对于疾病，很难准确地揭示哪些分子变化是由遗传风险因素引起的。它是 众所周知，APOE基因座上的遗传变异可以赋予AD的神经保护状态，而另一种 突变会极大地增加一个人患疾病的机会。即使是这些经过充分研究的变种也不是 在分子水平上完全被理解。AD和其他疾病的大多数相关风险变量 疾病存在于非编码的调控元件中，因此最好使用表观基因组学技术进行研究。 由于先前的研究表明，阿尔茨海默病在其整个生命周期中影响不同的大脑区域和细胞类型 进展期，我假设阿尔茨海默病遗传风险的潜在机制在进展性、 特定于区域和特定于细胞类型的方式。在这个提议中，我们的目标是产生染色质可及性 阿尔茨海默病患者前额叶皮质、海马体和内嗅觉皮质的单细胞分布 大脑，并与已发表的单细胞转录组数据相结合，从而使我们能够识别增强子- 被AD风险变种破坏的基因相互作用。我们的初步工作表明，小胶质细胞特异性 增强剂对阿尔茨海默病遗传风险因素有丰富的作用。因此，我们将使用CRISPR-Cas9删除增强子 在诱导多能干细胞(IPSC)来源的小胶质细胞中，与BIN1位点的变异rs4663105连锁， 从而使我们能够了解它在监管领域的角色。我的前额叶的初步数据 皮质显示染色质可及性景观是高度特定于细胞类型的，并且在 AD患者的大脑，我预计我们将发现调控元件的区域特异性，这些调控元件被 广告风险变种。除了我们识别这些与疾病相关的监管因素的具体任务外，还有一个 AD脑中单细胞表观基因组学和单细胞转录组学数据的综合研究将是非常有意义的 对更广泛的AD社区的价值，以进一步将基因、网络和途径作为未来的目标 学习。