Xianjun Dong, PhD APDA Research & Impact Research Investigators Xianjun Dong, PhD Investigator: Xianjun Dong, PhD Name of Institution: The Brigham and Women’s Hospital, Boston, MA Project Title: Developing RNA biomarkers of early PD pathology from brain organoids and extracellular vesicles Investigator Bio: Dr. Dong is an Assistant Professor of Neurology at Harvard Medical School in Boston, MA, and leads the Genomics and Bioinformatics Hub at Brigham and Women’s Hospital. He is a Principal Investigator in Neurology at the Ann Romney Center for Neurological Disease, and a core faculty of the APDA Center for Advanced Research at Brigham and Women’s Hospital. He received his PhD degree in Bioinformatics at the University of Bergen in Norway (supervisor: Dr. Boris Lenhard) and a Postdoctoral fellowship in Bioinformatics and Integrative Biology at the University of Massachusetts Medical School (supervisor: Dr. Zhiping Weng). He has been the Director of the Computational Neuroscience Unit of the Precision Neurology Program (Director: Clemens Scherzer, MD) at Brigham and Women’s Hospital since 2013, leading the Bioinformatics team working on neurodegenerative diseases such as Parkinson’s disease, Alzheimer’s disease, and Huntington’s disease. He is interested in developing and applying computational methods to understand the transcriptional regulation of the human genome, by integrating genomic, transcriptomic, epigenetic, and clinical data from both healthy subjects and patients with neurological diseases. Objective: Developing RNA biomarkers of early PD pathology from brain organoids and extracellular vesicles Background: When a Parkinson’s disease (PD) patient first develops motor symptoms, up to 70% of dopamine neurons in the substantia nigra have already been lost. It is therefore vital to develop biomarkers for PD that detect disease prior to onset of motor symptoms in order to investigate the early processes that occur in PD. Induced pluripotent stem cells (iPSC) from patients with penetrant familial PD mutations are a promising model for the study of these early events. 3D brain organoids have recently been generated using iPSCs to model PD. Organoids offer the advantage of providing a more physiological environment that mimics the brain, since they display an organized structure and consist of multiple cell types on a spectrum of cellular maturity. The organoid functions as a mini-brain and can be used to study potential biomarkers. One such source of potential biomarkers that is produced by the organoids are extracellular vesicles (EV) that contain ribonucleic acid (RNA). EVs are an exciting potential biomarker since they are easily recovered from blood and cerebrospinal fluids. We previously identified many RNAs upregulated in dopamine neurons from the autopsied PD brains, including enhancer RNAs and circular RNAs. We are currently investigating whether these RNAs are present in EVs which would make them promising biomarkers. Methods/Design: In this study, we will first develop midbrain organoids from iPSC derived from people with familial PD. We will then extract EVs at different development stages using our recently developed EV isolation method EXODUS (Nature Methods, 2021). We will then profile what is contained in the EVs at different stages in order to identify potential RNA biomarkers and to understand the events that lead to development of PD. Relevance to Diagnosis/Treatment of Parkinson’s disease: Our interdisciplinary study incorporating neurology, stem cell biology and computational genomics aims to 1) develop better ways of diagnosing PD, and 2) further our understanding of how PD develops.