Gene Regulatory Networks of Synaptic Specificity

突触特异性的基因调控网络

• 批准号: 10351552
• 负责人: Mehmet Neset Ozel
• 金额: $ 12.69万
• 依托单位: NEW YORK UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10351552
• 关键词: ATAC-seq; Address; Adult; Affect; Algorithms; Award; Biological Models; Blindness; Blood Coagulation Factor VII; Brain; Brain Injuries; Brain region; Calcium; Candidate Disease Gene; Cell Surface Proteins; Cells; Chromatin; Code; Collaborations; Complex; Computational Technique; Computer Models; Data; Data Set; Defect; Detection; Development; Developmental Gene; Drosophila genus; Electrophysiology (science); Engineering; Environment; Equilibrium; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genetic study; Genomics; Goals; Human; Image; Individual; Knowledge; Lead; Learning; Link; Logic; Mediating; Mentors; Mentorship; Methods; Modeling; Modification; Molecular; Morphology; Motion; Nerve Degeneration; Nervous system structure; Neurodevelopmental Disorder; Neurons; Neurophysiology - biologic function; New York; Optic Lobe; Output; Phase; Physiological; Physiology; Process; Property; RNA; Regenerative Medicine; Regulator Genes; Research; Resources; Retina; Specificity; Synapses; System; Techniques; Testing; Time; Training; Transplantation; Universities; Visual; Visual system structure; Work; XCL1 gene; base; cell replacement therapy; cell type; effective therapy; experimental study; fly; gene regulatory network; improved; in vivo; in vivo calcium imaging; induced pluripotent stem cell; interest; machine learning framework; nerve stem cell; network models; neural circuit; neuron development; neuroregulation; novel strategies; postsynaptic; programs; relating to nervous system; response; single-cell RNA sequencing; stem cells; synaptogenesis; tool; transcription factor; transcriptome; transdifferentiation

Project Summary/Abstract Neuronal type identity is central to the development and function of neural circuits, as it instructs both the connectivity of neurons as well as their synaptic and electrophysiological properties. Neuronal fates are thought to be controlled by combinations of transcription factors (TF) known as terminal selectors, but very little is known about the gene regulatory mechanisms that link differential TF expression to specific neuronal features. The Drosophila visual system, a well-characterized brain region that has an organization analogous to the vertebrate retina and cortex, provides the ideal balance of complexity and accessibility to investigate these mechanisms. The first aim of this project will be to decipher the terminal selector TF codes that establish and maintain the unique identity of approximately 200 neuronal types that make the Drosophila optic lobes. Using a single-cell RNA sequencing (scRNA-seq) dataset I generated from developing optic lobes, I identified the combinations of TFs that are stably maintained in each neuronal type throughout their differentiation. Under the mentorship of Claude Desplan (K99 phase), I will test the hypothesis that these TFs function as terminal selectors by modifying the TF codes of specific optic lobe neurons in vivo, with the goal of predictably transdifferentiating them into other cell types. This will demonstrate the sufficiency of terminal selectors to confer neuronal identity and benefit the field of regenerative medicine. The conserved mechanisms in mammalian systems could be exploited to induce differentiation of pluripotent cells into specific neurons that could be transplanted to treat blindness or neurodegeneration. The second aim of this project will link the terminal selector TFs to their downstream targets. In collaboration with Richard Bonneau, I will learn to use the “Inferelator” algorithm to generate computational models of gene regulatory networks by combining my existing scRNA-seq data with new chromatin accessibility (scATAC-seq) data I will acquire. During the K99 phase, I will test the effects of perturbating key predicted downstream effectors on the morphology and connectivity of a select group of neurons to establish proof-of- concept. I will then generalize this approach in the R00 phase by inferring gene regulatory networks for all optic lobe neurons at multiple developmental stages. The third aim will be performed in my independent lab (R00) to utilize the network models for engineering precise modifications in visual circuits. I will seek to selectively uncouple the circuit that computes wide-field motion from the one that detects small moving objects. I will use synaptic tracing methods as well as intravital calcium imaging to demonstrate the functional consequences of developmental perturbations. Altogether, this project will establish direct mechanistic links between the encoding of neuronal identity and the molecules that mediate intercellular interactions during synaptic partner selection, which are commonly affected in neurodevelopmental disorders. The mentorship I will receive from Dr. Desplan and Dr. Bonneau, combined with the impressive resources of New York University provide the ideal environment for preparing me to build a successful independent research program that link gene regulation to brain wiring.

项目摘要/摘要 神经元类型认同是神经回路发展和功能的核心，因为它指示 神经元的连通性以及它们的突触和电生理特性。神经元的命运被认为是 被称为末端选择子的转录因子(TF)的组合控制，但人们知之甚少 关于将不同的转铁蛋白表达与特定的神经元特征联系起来的基因调控机制。这个 果蝇的视觉系统，一个具有良好特征的大脑区域，其组织结构类似于脊椎动物 视网膜和皮质，为研究这些机制提供了复杂性和可及性的理想平衡。 这个项目的第一个目标是破译终端选择器TF码，它建立和维护 形成果蝇视叶的大约200种神经元类型的独特身份。使用单个单元格 从发育中的视叶生成的RNA测序(scRNA-seq)数据集I，我确定了 在每种神经元类型的分化过程中稳定保持的转铁蛋白。在…的指导下 克劳德·德斯普兰(K99阶段)，我将测试这些TF作为末端选择器的假设，方法是修改 体内特定视叶神经元的TF编码，目的是可预测地将它们转化为其他 单元类型。这将证明末端选择器足以赋予神经元身份，并有利于 再生医学领域。哺乳动物系统中的保守机制可以被用来诱导 将多能细胞分化为特定的神经元，可移植治疗失明或 神经退行性变。该项目的第二个目标是将终端选择器TF与其下游目标联系起来。 在与Richard Bonneau的合作中，我将学习使用“Inferelator”算法来生成计算 将我现有的scRNA-seq数据与新的染色质可访问性相结合，建立基因调控网络的模型 (scatac-seq)我将获取的数据。在K99阶段，我将测试预测的扰动键的效果 下游效应器对选定的一组神经元的形态和连接性的影响，以建立- 概念。然后，我将在R00阶段通过推断所有视神经的基因调控网络来推广这种方法 处于多个发育阶段的叶神经元。第三个目标将在我的独立实验室(R00)实现 利用网络模型在视觉电路中进行精确的工程修改。我将寻求有选择地 将计算广域运动的电路与检测微小运动对象的电路分开。我会用 突触示踪方法以及活体内钙成像来展示脑缺血后的功能后果 发育紊乱。总之，这个项目将在编码之间建立直接的机械联系 神经元特性和在突触伙伴选择过程中调节细胞间相互作用的分子， 它们通常在神经发育障碍中受到影响。我将从德斯普兰博士那里得到的指导 而博诺博士与纽约大学令人印象深刻的资源相结合，提供了理想的环境 为我准备建立一个成功的独立研究项目，将基因调控与大脑连接联系起来。