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Fernández-Santiago R, Merkel A, Castellano G, Heath S, Raya Á, Tolosa E, Martí MJ, Consiglio A, Ezquerra M. Whole-genome DNA hyper-methylation in iPSC-derived dopaminergic neurons from Parkinson's disease patients. Clin Epigenetics 2019; 11:108. [PMID: 31337434 PMCID: PMC6651999 DOI: 10.1186/s13148-019-0701-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
Background Parkinson’s disease (PD) is characterized by the loss of midbrain dopaminergic neurons (DAn). Previously, we described the presence of DNA hyper- and hypo-methylation alterations in induced pluripotent stem cells (iPSC)-derived DAn from PD patients using the Illumina 450K array which prominently covers gene regulatory regions. Methods To expand and contextualize previous findings, we performed the first whole-genome DNA bisulfite sequencing (WGBS) using iPSC-derived DAn from representative PD subjects: one sporadic PD (sPD) patient, one monogenic LRRK2-associated PD patient (L2PD), and one control. Results At the whole-genome level, we detected global DNA hyper-methylation in the PD which was similarly spread across the genome in both sPD and L2PD and mostly affected intergenic regions. Conclusion This study implements previous epigenetic knowledge in PD at a whole genome level providing the first comprehensive and unbiased CpG DNA methylation data using iPSC-derived DAn from PD patients. Our results indicate that DAn from monogenic or sporadic PD exhibit global DNA hyper-methylation changes. Findings from this exploratory study are to be validated in further studies analyzing other PD cell models and patient tissues. Electronic supplementary material The online version of this article (10.1186/s13148-019-0701-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rubén Fernández-Santiago
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.
| | - Angelika Merkel
- Statistical Genomics Team at the Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Giancarlo Castellano
- Dept. of Anatomic Pathology, Pharmacology and Microbiology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Spain
| | - Simon Heath
- Statistical Genomics Team at the Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ángel Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, 08908, Barcelona, Spain.,Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Eduard Tolosa
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.,Movement Disorders Unit, Dept. of Neurology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Spain
| | - María-José Martí
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.,Movement Disorders Unit, Dept. of Neurology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Spain
| | - Antonella Consiglio
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona, 08907, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), 08028, Barcelona, Spain.,Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Mario Ezquerra
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.
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