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.

项目摘要和摘要 帕金森氏病（PD）是与运动异常有关的最常见神经系统疾病。已经25岁了 自确定了PD的第一个遗传原因以来，仍未对该疾病进行有效治疗。之一 我们认为的阻碍是缺乏评估早期PD发病机理和治疗反应的模型 神经生理环境。这为我们在这种疾病中取得进展的能力提供了重要的瓶颈。 最近的两条证据促使我们在实际神经生理环境中研究PD发病机理：（1）人类 神经影像学数据和动物模型都表明突触中断会导致神经元死亡，使情况 该PD是一种突触病。 （2）许多新型的调节性，非编码RNA显示与PD发病机理的联系。例如， 我们在人类验尸大脑的多巴胺神经元中发现了20,000多个增强子RNA（或ERNAS）候选者（Dong et eT al。自然神经科学，2018年）。它们与PD风险变体大大共定位。另一类的小说RNA是 圆形RNA（CIRCRNA），主要富含大脑，高度特异性与突触，并且超稳 （例如，比线性RNA长10倍。我们确定了在多巴胺神经元中积极表达的11,000个CircrNA， 其中许多与PD病理学显着相关（Dong等人在提交中）。更重要的是，circrnas可以 与LNCRNA和miRNA形成一个调节网络，可以包裹成细胞外囊泡（EV），穿透 血脑屏障。基于这些，我们假设该调节性RNA含有。 Circrnas，Ernas，mirnas，lncrnas 可以在EV中检测到，并可能在PD发病机理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发病机理的动态生理微环境。 在这项研究中，我们将结合我们在脑器官，PD生物学，外泌体分析，单细胞OMICS上的专业知识， 生物信息学和生物医学工程，以开发新的3D脑器官微生物生理分析平台 （MAP）概括多巴胺神经元的互连和研究分子神经退行性 系统地。我们将（1）首先开发PD器官并介绍转录组（包括Circrnas，miRNA，mRNA，MRNA， 分泌的EV和脑器官单细胞转录组的lncRNA等，以鉴定与PD相关的RNA，然后（2） 在一个新颖的高通量，小脑芯片平台和最后一个新颖的，高通量的PD器官的病理生理动力学绘制 将（3）整合EV-型时间多维数据以推断与PD相关的RNA及其调节 PD发病机理期间的动力学。 RNA疗法的最新突破导致了多次人类试验和临床批准（例如Moderna， Alnylam和Ionis Pharmaceuticals）。 circrnas比线性RNA具有许多优势，使其可能更好 适合转化为治疗和诊断。从PD器官分泌的电动汽车提供了良好的液体代理 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PD神经病理学设定一个重要的，高度创新的基础 和外泌体治疗。