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

大脑由数百种微妙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、运动和认知功能来自分布在这些区域的环路。因此，要了解大脑的功能，就必须了解其组成细胞类型的全球空间组织。同样，要了解认知在疾病条件下是如何崩溃的，就必须了解病理是如何影响整个大脑的电路的。阿尔茨海默病是一种毁灭性的大脑功能障碍，其社会和经济代价巨大且仍在不断增加。尽管许多研究都集中在一小部分区域(海马体和内嗅皮层)，但阿尔茨海默氏病影响整个大脑。例如，针对一个很小但非常特定的回路--基底前脑胆碱能系统的药物，是为数不多的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，但目前对这种疾病的全脑病理缺乏了解。每个大脑区域都包含许多细微区分的神经元亚型，以及其他类型的细胞，如小胶质细胞、星形胶质细胞、少突胶质细胞和血管细胞，这些细胞都可能在疾病病因学中发挥作用。关于这些细小的亚型如何参与疾病的信息非常稀少。该项目将使用一种名为原位转录学的新技术来了解大脑的全局结构，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，达到亚微米级的分辨率，在任何物种的任何组织样本中。由于不同的细胞类型表达不同的基因组合模式，平行测量细胞的基因表达谱可以实现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上，将这项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。这项技术仍处于开发阶段，目前仅在全球几个实验室发现。我们在伦敦大学学院的团队是这项技术的开发者之一。我们最近开发了它，它可以高效率地同时定位多达1000个基因，并实现自动化，以便它能够以足够高的吞吐量运行，以处理整个小鼠的大脑。我们建议在这里大规模应用这项新建立的技术，以亚微米级的分辨率制作一份完整的图谱，展示1000个精心挑选的基因在整个小鼠大脑中的表达。我们将使用它来对所有脑细胞类型进行空间定位(建立在之前的非空间转录技术的基础上)。然后，我们将把同样的方法应用于两个小鼠品系，这两个品系模拟了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-Tau22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是如何受到淀粉样蛋白和tau病理的影响的。所有数据都将免费提供，使世界各地的科学家能够使用这些数据来指导有关健康和患病大脑功能的新实验和假设。这将提供基础性信息，极大地加快了解阿尔茨海默病以及其他一系列神经和精神认知障碍的进展，例如精神分裂症、抑郁症、双相情感障碍、额颞痴呆、帕金森氏症和亨廷顿病。

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.