A platform for cell type-level transcriptomic, epigenomic and spatial interrogation of Alzheimer's disease

项目摘要摘要 阿尔茨海默病(AD)进展过程中细胞类型脆弱性的空间和分子细节仍然存在 不清楚。这个项目的目标是将空间轮廓方法应用于来自多个不同捐赠者的脑组织。 阿尔茨海默病的分期描述细胞类型组成、位置和基因表达的变化 病理学的进展跨越了大脑的各个区域。空间转录学领域是高度动态和快速的 不断发展，快速发展，现在商业化，提供了更好地实现原始 该项目的目标。多重误差稳健原位杂交(MerFish)是一种能够 在组织切片中分析成百上千个基因，这使得能够从转录角度识别- 定义了细胞类型，并在不破坏组织的情况下提供了基因表达的定量评估 结构。最近，MerFish的商业开发版本已经以以下形式提供 Vizgen的MERSCOPE，它提供了能够可靠地高吞吐量的一体化系统的优势 大组织切片的空间剖面图。MERSCOPE系统代表着在 在拨款时无法获得的技术，可以极大地加速 实现我们的目标，描述与AD相关的组织微结构的变化。来自于此的试点数据 来自神经典型和受AD影响的供体脑组织的平台表明，这种方法是一种 有效和全面的方法来分析细胞类型组成和基因表达。重要的是， Vizgen MERSCOPE平台兼容基因和蛋白质表达的成像。通过组合 免疫组织化学(IHC)和水鱼这个系统，我们将能够关联病变部位 在疾病的不同阶段，与特定细胞类型接近的蛋白质聚集。我们已经开发出了IHC MERSCOPE符合MerFish的化学特性，并可将这些方法结合使用。 MERSCOPE平台将使该项目通过显著加快速度来产生更大的科学影响 最初的项目3拨款的目的是。它将使我们能够快速分析来自多个疾病阶段的组织，同时 把细胞类型和基因表达放在疾病进展和病理退变的背景下 组织。

Project Summary Abstract The spatial and molecular details of cell type vulnerability during Alzheimer’s disease (AD) progression remain unclear. The objective of this project is to apply spatial profiling methods to brain tissue from donors at multiple stages of Alzheimer’s disease to describe changes in cell type composition, location, and gene expression as pathology advances across brain regions. The field of spatial transcriptomics is highly dynamic and rapidly evolving, with rapid progress and now commercialization that offers the potential to better achieve the original aims of the project. Multiplexed Error Robust In Situ Hybridization (MERFISH) is a technique capable of profiling hundreds or thousands of genes in tissue sections, which enables identification of transcriptomically- defined cell types and provides a quantitative assessment of gene expression without disrupting tissue structure. Recently a commercially developed version of MERFISH has become available in the form of MERSCOPE by Vizgen, which provides the benefits of an all-in-one system capable of reliable high throughput spatial profiling of large tissue sections. The MERSCOPE system represents a significant advance in technology that was not available at the time of the grant’s funding and can dramatically accelerate the achievement of our aims to profile changes in tissue microarchitecture associated with AD. Pilot data from this platform derived from both neurotypical and AD-affected donor brain tissue has shown that this approach is an effective and comprehensive method for profiling cell type composition and gene expression. Importantly, the Vizgen MERSCOPE platform is compatible with imaging both gene and protein expression. By combining immunohistochemistry (IHC) and MERFISH with this system, we will be able to correlate sites of pathological protein aggregation with proximity to specific cell types at distinct stages of disease. We have developed IHC chemistry compatible with MERFISH profiling and can combine these methods for use on the MERSCOPE. The MERSCOPE platform will allow the project to deliver greater scientific impact by significantly accelerating the original Project 3 grant aims. It will enable us to profile tissue from multiple disease stages rapidly, while placing cell type and gene expression in the context of disease progression and pathological degeneration of tissue.