Systematic Study of Extracellular Vesicles and their Integrative Analysis with Parkinson's Organoids MAP

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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.