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Jansen IE, Ye H, Heetveld S, Lechler MC, Michels H, Seinstra RI, Lubbe SJ, Drouet V, Lesage S, Majounie E, Gibbs JR, Nalls MA, Ryten M, Botia JA, Vandrovcova J, Simon-Sanchez J, Castillo-Lizardo M, Rizzu P, Blauwendraat C, Chouhan AK, Li Y, Yogi P, Amin N, van Duijn CM, Morris HR, Brice A, Singleton AB, David DC, Nollen EA, Jain S, Shulman JM, Heutink P. Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing. Genome Biol 2017; 18:22. [PMID: 28137300 PMCID: PMC5282828 DOI: 10.1186/s13059-017-1147-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases and 503 control participants. Candidate genes were subsequently validated for functions relevant to PD based on parallel RNA-interference (RNAi) screens in human cell culture and Drosophila and C. elegans models. RESULTS Assuming autosomal recessive inheritance, we identify 27 genes that have homozygous or compound heterozygous loss-of-function variants in PD cases. Definitive replication and confirmation of these findings were hindered by potential heterogeneity and by the rarity of the implicated alleles. We therefore looked for potential genetic interactions with established PD mechanisms. Following RNAi-mediated knockdown, 15 of the genes modulated mitochondrial dynamics in human neuronal cultures and four candidates enhanced α-synuclein-induced neurodegeneration in Drosophila. Based on complementary analyses in independent human datasets, five functionally validated genes-GPATCH2L, UHRF1BP1L, PTPRH, ARSB, and VPS13C-also showed evidence consistent with genetic replication. CONCLUSIONS By integrating human genetic and functional evidence, we identify several PD susceptibility gene candidates for further investigation. Our approach highlights a powerful experimental strategy with broad applicability for future studies of disorders with complex genetic etiologies.
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Affiliation(s)
- Iris E. Jansen
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1081HZ The Netherlands
| | - Hui Ye
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Sasja Heetveld
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Marie C. Lechler
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Graduate School of Cellular & Molecular Neuroscience, Tübingen, 72074 Germany
| | - Helen Michels
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, 9700AD The Netherlands
| | - Renée I. Seinstra
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, 9700AD The Netherlands
| | - Steven J. Lubbe
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK
- Northwestern University Feinberg School of Medicine, Ken and Ruth Davee Department of Neurology, Chicago, IL USA
| | - Valérie Drouet
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 06, UMR_S1127, Institut du Cerveau et de la Moelle épinière, Paris, France
| | - Suzanne Lesage
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 06, UMR_S1127, Institut du Cerveau et de la Moelle épinière, Paris, France
| | - Elisa Majounie
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD USA
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD USA
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Department of Medical & Molecular Genetics, King’s College London, London, UK
| | - Juan A. Botia
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Jana Vandrovcova
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Javier Simon-Sanchez
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Melissa Castillo-Lizardo
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Cornelis Blauwendraat
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Amit K. Chouhan
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
| | - Yarong Li
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
| | - Puja Yogi
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Huw R. Morris
- Department of Clinical Neuroscience, UCL Institute of Neurology, London, UK
| | - Alexis Brice
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 06, UMR_S1127, Institut du Cerveau et de la Moelle épinière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, Paris, France
| | | | - Della C. David
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Ellen A. Nollen
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, 9700AD The Netherlands
| | - Shushant Jain
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
| | - Joshua M. Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Neurology, Baylor College of Medicine, Houston, TX USA
- Department of Neuroscience and Program in Developmental Biology, Baylor College of Medicine, Houston, TX USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, 1250 Moursund St., N.1150, Houston, TX 77030 USA
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Otfried-Müller-Str. 23, Tübingen, 72076 Germany
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1081HZ The Netherlands
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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