Uncovering the molecular identity of retinal cell types, and their responses to nerve injury using single-cell transcriptomics

使用单细胞转录组学揭示视网膜细胞类型的分子特性及其对神经损伤的反应

• 批准号: 10132331
• 负责人: Karthik Shekhar
• 金额: $ 24.15万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-03-01 至 2023-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10132331
• 关键词: Address; Amacrine Cells; Animal Model; Axon; Behavioral; Brain; Brain region; Cell Communication; Cells; Censuses; Cerebral cortex; Cessation of life; Complex; Computer Analysis; Computing Methodologies; Custom; Data; Data Analyses; Disease; Event; Felis catus; Foundations; Functional disorder; Gene Expression; Gene Expression Profile; Genetic; Genetic Transcription; Genomics; Glaucoma; Goals; Growth; Heterogeneity; Histologic; Histology; Human; Immune; Individual; Inflammation; Intervention; Intervention Studies; Investigation; Label; Learning; Location; Macaca; Machine Learning; Maps; Measurement; Mediating; Methods; Minority; Modeling; Molecular; Molecular Genetics; Molecular Profiling; Morphology; Mus; Natural regeneration; Nerve Crush; Neuraxis; Neurons; Neurosciences; Optic Nerve; Optic Nerve Injuries; Pattern; Physiological; Physiology; Plant Roots; Recovery of Function; Reporting; Resources; Retina; Retinal Ganglion Cells; Role; Stroke; Structure; Surveys; Survival Rate; System; Taxonomy; Technology; Therapeutic; Therapeutic Intervention; Tissues; Tumor-infiltrating immune cells; Vertebrates; Vision; Visual; Work; base; cell type; central nervous system injury; design; ganglion cell; human model; in vivo; injured; injury recovery; innovation; knock-down; molecular marker; nerve injury; neuroprotection; novel marker; programs; relating to nervous system; resilience; response; retinal ganglion cell regeneration; retinal neuron; single-cell RNA sequencing; stroke-like episode; tool; transcriptomics

ABSTRACT Neurons of the central nervous system (CNS) have been historically categorized into discrete "types" based on structure, physiological responses, connectivity patterns, and molecular profiles. Heterogeneity can have other consequences- e.g. recent studies have found that some neuronal types in the retina are more resilient than other types to optic nerve injury, an event that leads to irrecoverable damage in vision. My project combines cutting-edge single-cell genomic technologies, advanced computational data analysis and molecular tools to define heterogeneity of neuronal types comprehensively, to connect molecular definitions to histology, and explore the functional consequences of this heterogeneity during nerve injury. I will focus on a tractable system, the mouse retina, which communicates visual responses to the brain. It is as complex as any other region of the brain (containing ~120 neuronal types), but benefits from having a compact, accessible structure, and experimental tools make it especially suited for detailed analyses. Building on my previous postdoctoral work, this project will, 1) Complete the census of the mouse retina, which will the first for any CNS region, by inferring molecular taxonomies of two of its most heterogenous classes (amacrines and ganglion cells) from data collected using high-throughput single-cell RNA-sequencing. Using the mouse census, initiate a similar mapping of the macaque retina, which is harder to access experimentally, but shares important features with humans that are absent in mice. 2) Conduct a systematic investigation of cell-type specific responses in the retina to optic nerve injury. This usually leads to a rapid, stereotypic death of retinal ganglion cells (RGCs), but a recent study by my colleagues reported that some RGC types are more resilient than others. Here, using 1) as a resource, I will identify factors, cell intrinsic and extrinsic, that make these RGC types resilient. 3) Selective resilience of cell types is now recognized as a feature of diseases like glaucoma and stroke. Therapies therefore need to cater to different cell types. To learn more, and derive general principles, I will examine the impact of known therapeutic interventions on the survival of different RGC types, and the underlying molecular responses, within the optic nerve injury model. Taken together, my project will derive substantial molecular information underlying neuronal heterogeneity in the mouse and macaque retina and general principles for cell-type selective resilience following CNS injury in mice. The lessons from this work will provide valuable guidance for similar studies in less accessible regions of the brain (e.g. cerebral cortex).

摘要 中枢神经系统(CNS)的神经元历来被分成不同的“类型”，基于 结构、生理反应、连接模式和分子图谱。异质性可以有其他 后果--例如，最近的研究发现，视网膜中的某些神经元类型比 其他类型的视神经损伤，这一事件导致无法恢复的视力损害。 我的项目结合了尖端的单细胞基因组技术，先进的计算数据分析和 全面定义神经元类型异质性的分子工具，将分子定义与 组织学，并探索这种异质性在神经损伤中的功能后果。我将把重点放在 易处理的系统，小鼠的视网膜，它将视觉反应传达给大脑。它和其他任何东西一样复杂 大脑的其他区域(包含约120个神经元类型)，但受益于拥有紧凑、可访问的 结构和实验工具使其特别适合于详细的分析。建立在我以前的基础上 博士后工作，这个项目将， 1)通过推断分子，完成对小鼠视网膜的普查，这将是第一次对中枢神经系统区域进行普查 它的两个最不同的类别(无核细胞和神经节细胞)的分类来自使用 高通量单细胞RNA测序。使用老鼠普查，启动类似的映射 猕猴视网膜，很难在实验中接触到，但与人类有重要的共同特征 在小鼠身上不存在。 2)系统研究视网膜对视神经损伤的细胞类型特异性反应。这 通常会导致视网膜神经节细胞(RGC)的快速、刻板的死亡，但我的同事最近的一项研究 报道称，一些研资局类型比其他类型更具弹性。在这里，使用1)作为资源，我将确定 使这些RGC类型具有弹性的细胞内在和外在因素。 3)细胞类型的选择性弹性现在被认为是青光眼和中风等疾病的一个特征。 因此，治疗需要迎合不同类型的细胞。为了了解更多，并得出一般原则，我将 研究已知的治疗干预措施对不同类型的RGC生存的影响，以及 视神经损伤模型中潜在的分子反应。 综上所述，我的项目将获得大量的分子信息，潜在的神经元异质性 小鼠和猕猴视网膜及中枢神经系统损伤后细胞类型选择性恢复的一般原理 老鼠。这项工作的经验教训将为交通不便地区的类似研究提供有价值的指导 大脑(例如大脑皮层)。