Cell-type Specific Interrogation of Variant Function in Alzheimer's Disease

摘要 阿尔茨海默病（AD）影响全球超过2600万人，但治疗选择有限。这 这在很大程度上是由于AD的分子机制尚不清楚。全基因组关联研究 （GWAS）已经确定了与AD相关的基因组区域，但确定确切的致病变体 基因仍然是一个重大挑战。高通量基因组技术的最新发展 令人难以置信的潜力，功能上表征这些因果特征，但必须适用于正确的细胞 类型神经元、星形胶质细胞和小胶质细胞都被认为在AD的病因学中起关键作用，但获得了 可以理解的是，用于这些实验的可存活的原代人脑细胞是非常困难的。因此，最近 将人类诱导多能干细胞快速分化为各种脑细胞类型的方案提供了巨大的 有望成为破译AD遗传基础的工具，并指导未来的治疗工作。 该项目的目标是确定哪些AD风险变体改变人类的转录调控能力， 并将它们映射到它们所调控的基因。为了了解哪些变体在小胶质细胞中起作用， 星形胶质细胞和神经元，我将在人类诱导多能干细胞中进行大规模平行报告分析。 细胞（hiPSC）分化成每种细胞类型（Aim 1）。为了识别AD风险基因，我将使用公开可用的 hiPSC衍生的小胶质细胞、星形胶质细胞和神经元中的Hi-C、ATAC-seq和RNA-seq将变体与基因联系起来 (Aim 2A）。我将在功能上验证一系列具有CRISPR抑制作用的假定变异基因对（Aim 2B）。 这项工作的结果将确定细胞类型特定的因果变异，以及它们调节的基因。这 将产生积极的影响，因为确切了解AD中哪些基因与哪些细胞类型有关， 将阐明疾病病因的分子机制。这项研究中发现的基因可以作为 未来研究的目标和治疗设计的候选人。

Abstract Alzheimer’s Disease (AD) affects over 26 million people worldwide, yet the treatment options are limited. This is in large part due to the unclear molecular mechanisms underlying AD. Genome-wide association studies (GWAS) have identified genomic regions that are associated with AD, but determining the exact causal variants and genes remains a major challenge. Recent developments in high throughput genomic technologies have incredible potential to functionally characterize these causal features, but must be applied to the correct cell types. Neurons, astrocytes, and microglia are all thought to play key roles in the etiology of AD but obtaining viable primary human brain cells for these experiments is understandably very difficult. Therefore, recent protocols to rapidly differentiate human induced pluripotent stem cells into various brain cell types offer great promise as tools to decipher the genetic basis of AD and guide future therapeutic efforts. The goal of this project is to identify which AD risk variants alter transcriptional regulatory capacity in human brain cells and to map them to the genes they regulate. To understand which variants are functional in microglia, astrocytes, and neurons, I will perform massively parallel reporter assays in human induced pluripotent stem cells (hiPSCs) differentiated into each cell type (Aim 1). To identify AD risk genes, I will use publicly available Hi-C, ATAC-seq, and RNA-seq in hiPSC-derived microglia, astrocytes, and neurons to link variants to genes (Aim 2A). I will functionally validate a selection of putative variant-gene pairs with CRISPR inhibition (Aim 2B). The results of this work will identify cell-type specific causal variants, and the genes that they regulate. This will have a positive impact because understanding exactly which genes are involved in which cell types in AD will elucidate the molecular mechanisms of the disease etiology. The genes identified in this study can act as targets for future studies and candidates for therapeutic design.