Optimization of Calcium and RNA multiplexed activity imaging for highly parallelized evaluation of cell type functions in deep-brain structures

项目摘要 神经科学的一个中心目标是在神经元集合的信息处理特性的背景下理解动物行为。神经元是大脑信息处理网络中的回路节点，但它们也是表达数百种基因的细胞，这些基因可能对决定它们的活动模式做出重要贡献。基因表达、神经元投射、神经元活动和行为之间的关系，分别是分子和系统神经科学研究的主要途径。整合这些水平的研究将极大地促进理解分子特性对健康大脑和疾病状态下神经元信息处理特征的影响。在这个项目中，我们称之为CaRMA 2.0，我们建议开发和民主化的方法，以整合转录组学，投射组学，钙动力学和行为在大脑深部结构的测量。该提案建立在我们过去成功开发和实施钙和RNA复合活性（CaRMA）成像的基础上，该成像将这些水平的研究结合到一个大规模实验中。这是通过在行为小鼠中进行脑深部双光子钙成像来实现的，然后移除并切片大脑，将离体图像体积与体内成像的神经元对齐，然后在同一组织上进行多轮RNA荧光原位杂交（FISH）。为了可靠地产生这些高维多模态数据集，需要在本RFA-NS-18-019计划公告中指出的“神经系统大规模记录和调制的转型技术优化”方面取得重大进展。我们将开发用于深脑钙成像的改进技术，以及对相同细胞的高度多路复用基因表达分析，并将此管道应用于研究mPFC，后脑以及外侧下丘脑在饥饿，口渴和恐惧中的作用。

PROJECT SUMMARY A central goal of neuroscience is to understand animal behavior in the context of the information processing properties of neuron ensembles. Neurons are circuit nodes in the brain information processing network, but they are also cells that express hundreds of genes that may make important contributions to determining their activity patterns. The relationship between gene expression, neuron projections, neuron activity, and behavior have been, individually, major avenues for investigation in both molecular and systems neuroscience. Integrating these levels of investigation would greatly advance understanding the influence of molecular properties on neuron information processing characteristics in healthy brains and disease states. In this project, which we refer to as CaRMA 2.0, we propose to develop and democratize methodologies to integrate measurements of transcriptomics, projectomics, calcium dynamics, and behavior in deep-brain structures. This proposal builds on our past success to develop and implement Calcium and RNA Multiplexed Activity (CaRMA) imaging, which combines these levels of investigation into a single large-scale experiment. This is achieved by deep-brain two-photon calcium imaging in a behaving mouse, followed by removing and sectioning the brain, aligning the ex vivo image volume with the in vivo-imaged neurons, and then performing multiple rounds of RNA-fluorescence in situ hybridization (FISH) on the same tissue. To reliably produce these high dimensional, multi-modal datasets requires significant advancements for “Optimization of Transformative Technologies for Large Scale Recording and Modulation in the Nervous System” as indicated in this RFA-NS-18-019 program announcement. We will develop improved technologies for deep-brain calcium imaging as well as highly multiplexed gene expression analysis on the same cells and apply this pipeline to investigate the mPFC, hindbrain, and the role of the lateral hypothalamus in hunger, thirst, and fear.