Cellular-resolution in situ transcriptomics of the mouse brain and Alzheimer's disease models

大脑由数百种细微不同的细胞类型组成，分布在数百个不同的区域。大脑产生的感觉、运动和认知功能，都是由分布在这些区域的回路产生的。因此，要了解大脑功能，就必须了解其组成细胞类型的全局空间组织。同样，要了解认知在疾病条件下如何发生动摇，必须了解病理如何影响整个大脑的回路。阿尔茨海默病是一种破坏性的大脑功能障碍，其社会和经济成本巨大且仍在增长。虽然许多研究都集中在一小部分区域（海马和内嗅皮层），但阿尔茨海默病会影响整个大脑。例如，针对一个小但非常具体的回路，基底前脑胆碱能系统的药物是少数几种被批准用于缓解阿尔茨海默氏症症状的治疗方法之一。许多其他特定的大脑区域也可能参与其中，但目前缺乏对该疾病的全脑病理学的了解。每个大脑区域都包含许多精细区分的神经元亚型，以及其他细胞类型，如小胶质细胞，星形胶质细胞，少突胶质细胞和血管细胞，它们都可能在疾病病因中发挥作用。关于这些精细亚型如何参与疾病的信息很少。该项目将采用一种名为原位转录组学的新技术来了解大脑的整体结构，并使用小鼠模型来破坏阿尔茨海默病的病理基础。这项技术可以同时定位许多基因的表达，以亚微米的分辨率，在任何物种的任何组织样本中。因为不同的细胞类型表达不同的基因组合模式，所以细胞基因表达谱的平行测量允许精细的细胞类型分类。此外，由于细胞功能的变化几乎总是反映在基因表达的变化中，因此将该技术应用于疾病模型将使科学家能够了解每种细胞类型在病理条件下的功能变化。该技术仍在开发中，目前全球只有少数实验室发现。我们在UCL的团队是这项技术的开发者之一。我们最近已经将其开发到可以同时高效定位多达1000个基因的程度，并将其自动化，以便它可以以足够高的吞吐量运行以处理整个小鼠大脑。我们在这里建议大规模应用这种新建立的技术，以亚微米分辨率在整个小鼠大脑中产生1000个精心选择的基因表达的完整图谱。我们将使用它来空间定位所有的大脑细胞类型（建立在以前的非空间转录组技术的基础上）。然后，我们将相同的方法应用于两个小鼠系，其模拟阿尔茨海默病的两种主要病理类型：APPNL-G-F淀粉样蛋白模型和THY-Tau 22模型。这将使我们能够看到所有大脑区域的多种类型的神经元和非神经元如何受到淀粉样蛋白和tau病理的影响。所有数据都将免费提供，使世界各地的科学家能够利用这些数据指导关于健康和患病大脑功能的新实验和假设。这将提供基础信息，大大加快不仅对阿尔茨海默病而且对广泛的其他神经和精神认知障碍的理解的进展，包括例如精神分裂症、抑郁症、双相情感障碍、额颞叶痴呆、帕金森病和亨廷顿病。

The brain is composed of hundreds of subtly-different cell types, spread over hundreds of distinct regions. The sensory, motor, and cognitive functions the brain produces, arise from circuits distributed globally across these regions. To understand brain function, it is therefore essential to understand the global spatial organization of its component cell types. Similarly, to understand how cognition can falter in disease conditions, it is essential to understand how pathologies affect circuits across the whole brain.Alzheimer's disease is a devastating disorder of brain function, with a tremendous and still growing social and economic cost. Although much research has focused on a small set of regions (the hippocampus and entorhinal cortex), Alzheimer's disease affects the whole brain. For example, drugs targeting a small but very specific circuit, the basal forebrain cholinergic system, are amongst the few treatments approved for relief of Alzheimer's symptoms. Many other specific brain regions are likely to be involved also, but an understanding of the brain-wide pathology of the disease is currently lacking. Each brain region contains many finely-distinguished subtypes of neurons, as well as other cell types such as microglia, astrocytes, oligodendrocytes, and vascular cells, which all likely play a role in the disease aetiology. Precious little information is available on how these fine subtypes are involved in the disease. This project will employ a new technology, called in situ transcriptomics, to understand the global structure of the brain, and it is disrupted by the pathologies underlying Alzheimer's disease, using mouse models. This technology can localize the expression of many genes simultaneously, to sub-micrometer resolution, in samples of any tissue from any species. Because different cell types express different combinatorial patterns of genes, parallel measurement of a cell's gene expression profiles allows fine cell type classification. Furthermore, because changes in cellular function are almost always reflected in changes in gene expression, applying the technology to disease models will allow scientists to understand how the function of each cell type changes under pathological conditions.The technology is still under development, and is currently found in only a few labs worldwide. Our group at UCL are one of the developers of the technology. We have recently developed it to a point where it can localize up to 1000 genes simultaneously at high efficiency, and automated it so that it can run at high enough throughput to process an entire mouse brain. We propose here to apply this newly-established technology at scale, to produce an entire atlas of expression of 1000 carefully chosen genes, at submicron resolution, across the whole mouse brain. We will use this to spatially localize all the brain's cell types (building on work from a previous non-spatial transcriptomic technology). We will then apply the same methodology to two mouse lines, that model the two main types of pathology underlying Alzheimer's disease: the APPNL-G-F amyloid model, and the THY-Tau22 model. This will enable us to see how multiple types of neuron and non-neurons across all brain regions are affected by the amyloid and tau pathologies. All data will be made freely available, enabling scientists worldwide to use it to guide new experiments and hypotheses regarding the function of the healthy and diseased brain. This will provide foundational information, greatly accelerating progress towards understanding not only Alzheimers but also a wide range of other neurological and psychiatric disorders of cognition including for example schizophrenia, depression, bipolar disorder, frontotemporal dementia, Parkinson's disease, and Huntington's disease.