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.

项目总结/摘要 神经元类型的同一性是神经回路的发展和功能的核心，因为它指导神经元的发育和功能。 神经元的连接性及其突触和电生理特性。神经元的命运被认为 被称为末端选择因子的转录因子（TF）的组合控制，但知之甚少 关于基因调控机制，联系不同的TF表达特定的神经元功能。的 果蝇视觉系统，一个特征明显的大脑区域，具有类似于脊椎动物的组织 视网膜和皮质，提供了复杂性和可访问性的理想平衡，以研究这些机制。 该项目的第一个目标是破译终端选择器TF码，这些TF码建立和维护了 构成果蝇视叶的大约200种神经元类型的独特身份。使用单细胞 RNA测序（scRNA-seq）数据集，我从发育中的视叶生成，我确定了以下组合： 在每种神经元类型的分化过程中稳定维持的TF。的辅导下 Claude Desplan（K99阶段），我将通过修改这些TF作为末端选择剂发挥作用的假设来检验。 体内特定视叶神经元的TF编码，目的是可预测地将它们转分化为其他神经元。 细胞类型。这将证明末端选择子足以赋予神经元身份并有益于神经元的功能。 再生医学领域。哺乳动物系统中的保守机制可以用来诱导 将多能细胞分化为特定的神经元，可以移植来治疗失明或 神经变性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 通过结合我现有的scRNA-seq数据和新的染色质可及性， （scATAC-seq）数据。在K99阶段，我将测试预测的扰动密钥的影响 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R 00阶段通过推断所有视神经细胞的基因调控网络来推广这种方法。 在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（R 00）中执行， 利用网络模型对视觉电路进行工程精确修改。我会有选择地 将计算宽场运动的电路与检测小运动物体的电路分开。我会用 突触示踪方法以及活体钙成像，以证明功能的后果， 发育紊乱总之，这个项目将建立编码之间的直接机械联系， 神经元身份和在突触伴侣选择过程中介导细胞间相互作用的分子， 这在神经发育障碍中是常见的。德斯普兰博士对我的指导 和博诺博士，结合纽约大学令人印象深刻的资源提供了理想的环境 为我建立一个成功的独立研究项目做好准备，该项目将基因调控与大脑连接联系起来。