Systematic study of extracellular vesicles and their integrative analysis with Parkinson's organoids MAP

细胞外囊泡的系统研究及其与帕金森氏类器官 MAP 的综合分析

• 批准号: 10345089
• 负责人: Xianjun Dong
• 金额: $ 73.84万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-04-15 至 2027-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10345089
• 关键词: 3-Dimensional; Address; Animal Model; Area; Autopsy; Bioinformatics; Biological Markers; Biology; Biomedical Engineering; Biopsy; Blood - brain barrier anatomy; Brain; Brain Diseases; Cells; Chromosome Pairing; Clinical; Collection; Complex; Coupling; Data Set; Detection; Development; Diagnostic; Disease; Dopamine Receptor; Dyskinetic syndrome; Electrodes; Electroencephalography; Electrophysiology (science); Enhancers; Environment; Foundations; Functional disorder; Gene Cluster; Genes; Genetic; Genomics; Half-Life; Human; Interdisciplinary Study; Link; Liquid substance; Maps; Measures; Messenger RNA; Methods; MicroRNAs; Midbrain structure; Modeling; Molecular; Monitor; Movement Disorders; Nanostructures; Nature; Nerve Degeneration; Neurology; Neuronal Dysfunction; Neurosciences; Noise; Organogenesis; Organoids; Parkinson Disease; Pathogenesis; Pathology; Patients; Pattern; Perfusion; Pharmacologic Substance; Physiological; Play; Protocols documentation; Proxy; Public Health; RNA; Role; Series; Signal Transduction; Source; Synapses; System; Testing; Therapeutic; Time; Translations; Untranslated RNA; Vesicle; base; circular RNA; data modeling; design; differential expression; disorder control; dopaminergic neuron; effective therapy; exosome; extracellular vesicles; first-in-human; in vitro Model; induced pluripotent stem cell; innovation; mind control; multi-electrode arrays; multidimensional data; nervous system disorder; neural network; neuroimaging; neuron loss; neuropathology; neurophysiology; novel; risk variant; single cell analysis; single-cell RNA sequencing; therapeutic RNA; therapeutic development; three dimensional cell culture; transcriptome; transcriptome sequencing; transcriptomics; treatment response

PROJECT SUMMARY AND ABSTRACT Parkinson's disease (PD) is the most common neurological disease associated with movement abnormality. It has been 25 years since the first genetic cause of PD was identified, and yet there is still no effective treatment for the disease. One of the hinders we think is the lack of models that assess early PD pathogenesis and therapy responses in its real neurophysiological environment. This provides a significant bottleneck in our ability to make progress in this disease. Two lines of recent evidence motivate us to study PD pathogenesis in a real neurophysiological environment: (1) Human neuroimaging data and animal models both showed that synaptic disruption proceeds neuronal death, making the case that PD is a synaptopathy. (2) Many novel, regulatory, non-coding RNAs show linkage to PD pathogenesis. For instance, we found over 20,000 enhancer RNAs (or eRNAs) candidates in dopamine neurons of human post-mortem brains (Dong et al. Nature Neuroscience, 2018). They significantly co-localized with PD risk variants. The other class of novel RNAs is circular RNAs (circRNAs), which are predominantly enriched in the brain, highly specific to the synapse, and ultra-stable (e.g., 10x longer half-life than linear RNAs). We identified >11,000 circRNAs actively expressed in the dopamine neurons, many of which are significantly associated with PD pathology (Dong et al. in submission). More importantly, circRNAs can form a regulatory network with lncRNAs and miRNAs, and can be wrapped into extracellular vesicles (EV), penetrating blood-brain barriers. Based on these, we hypothesize that regulatory RNAs incl. circRNAs, eRNAs, miRNAs, lncRNAs can be detected in EV and might play a role in the synaptic dysfunction in PD pathogenesis. To test this hypothesis, we need a model to recapitulate the dynamic physiological microenvironment of PD pathogenesis. In this study, we will combine our expertise in brain organoids, PD biology, exosome analysis, single-cell omics, bioinformatics, and biomedical engineering to develop a new 3D brain organoids microphysiological analysis platform (MAP) to recapitulate the dopamine neurons' interconnectivity and study molecular neurodegeneration systematically. We will (1) first develop PD organoids and profile the transcriptome (incl. circRNAs, miRNAs, mRNAs, lncRNAs, etc.) of secreted EV and single-cell transcriptome of brain organoids, to identify PD-associated RNAs, then (2) map the pathophysiological dynamics of PD organoids in a novel, high-throughput, mini-brain-on-chip platform, and last will (3) integrate the EV-organoid temporal multi-dimensional data to infer the PD-associated RNAs and their regulatory dynamics during the PD pathogenesis. Recent breakthroughs in RNA therapeutics have led to multiple first-in-human trials and clinical approval (e.g., Moderna, Alnylam, and Ionis pharmaceuticals). circRNAs have many advantages over linear RNAs, making them potentially better suited for translation into therapeutics and diagnostics. EVs secreted from PD organoids provide a good proxy of fluid biopsy for studying PD brain's neuropathology. Thus, this interdisciplinary (neurology, biomedical engineering, computational genomics) study will set an important, highly innovative foundation for understanding PD neuropathology and exosome treatment.

项目概要和摘要 帕金森病（PD）是与运动异常相关的最常见的神经系统疾病。已经25了 自第一个帕金森病的遗传原因被发现以来已经有很多年了，但仍然没有有效的治疗方法。之一 我们认为的障碍是缺乏评估早期 PD 发病机制和真实治疗反应的模型 神经生理环境。这给我们在这种疾病方面取得进展的能力带来了重大瓶颈。 最近的两方面证据促使我们在真实的神经生理环境中研究 PD 发病机制：(1) 人类 神经影像数据和动物模型都表明突触破坏会导致神经元死亡，这证明了这一点 PD是一种突触病。 (2) 许多新型、调节性、非编码 RNA 显示与 PD 发病机制的联系。例如， 我们在人类死后大脑的多巴胺神经元中发现了超过 20,000 个增强子 RNA（或 eRNA）候选者（Dong 等人） 等人。自然神经科学，2018）。它们与 PD 风险变异明显共存。另一类新型 RNA 是 环状 RNA (circRNA)，主要富集于大脑中，对突触具有高度特异性，并且超稳定 （例如，半衰期比线性 RNA 长 10 倍）。我们鉴定出超过 11,000 个 circRNA 在多巴胺神经元中活跃表达， 其中许多与 PD 病理学显着相关（Dong 等人提交）。更重要的是，circRNA可以 与lncRNA和miRNA形成调控网络，可以包裹到细胞外囊泡（EV）中，穿透 血脑屏障。基于这些，我们假设调节 RNA 包括。 circRNA、eRNA、miRNA、lncRNA 可以在 EV 中检测到，并且可能在 PD 发病机制中的突触功能障碍中发挥作用。 为了检验这一假设，我们需要一个模型来概括 PD 发病机制的动态生理微环境。 在这项研究中，我们将结合我们在脑类器官、PD生物学、外泌体分析、单细胞组学、 生物信息学和生物医学工程开发新型3D脑类器官微生理分析平台 (MAP) 概括多巴胺神经元的互连性并研究分子神经变性 系统地。我们将 (1) 首先开发 PD 类器官并分析转录组（包括 circRNA、miRNA、mRNA、 lncRNA等）分泌的EV和脑类器官的单细胞转录组，以鉴定PD相关RNA，然后（2） 在新型、高通量、微型脑芯片平台中绘制 PD 类器官的病理生理动态图，最后 (3) 整合 EV 类器官时间多维数据来推断 PD 相关 RNA 及其调控 PD发病机制中的动态变化。 最近 RNA 疗法的突破导致了多项首次人体试验和临床批准（例如，Moderna、 Alnylam 和 Ionis 制药）。 circRNA 比线性 RNA 有许多优势，使其可能更好 适合转化为治疗学和诊断学。 PD 类器官分泌的 EV 提供了良好的液体代理 用于研究 PD 脑神经病理学的活检。因此，这个跨学科（神经病学、生物医学工程、 计算基因组学）研究将为理解帕金森病神经病理学奠定重要的、高度创新的基础 和外泌体治疗。