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Schaffner SL, Wassouf Z, Lazaro DF, Xylaki M, Gladish N, Lin DTS, MacIsaac J, Ramadori K, Hentrich T, Schulze-Hentrich JM, Outeiro TF, Kobor MS. Alpha-synuclein overexpression induces epigenomic dysregulation of glutamate signaling and locomotor pathways. Hum Mol Genet 2022; 31:3694-3714. [PMID: 35567546 PMCID: PMC9616577 DOI: 10.1093/hmg/ddac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/15/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Parkinson’s disease (PD) is a neurological disorder with complex interindividual etiology that is becoming increasingly prevalent worldwide. Elevated alpha-synuclein levels can increase risk of PD and may influence epigenetic regulation of PD pathways. Here, we report genome-wide DNA methylation and hydroxymethylation alterations associated with overexpression of two PD-linked alpha-synuclein variants (wild-type and A30P) in LUHMES cells differentiated to dopaminergic neurons. Alpha-synuclein altered DNA methylation at thousands of CpGs and DNA hydroxymethylation at hundreds of CpGs in both genotypes, primarily in locomotor behavior and glutamate signaling pathway genes. In some cases, epigenetic changes were associated with transcription. SMITE network analysis incorporating H3K4me1 ChIP-seq to score DNA methylation and hydroxymethylation changes across promoters, enhancers, and gene bodies confirmed epigenetic and transcriptional deregulation of glutamate signaling modules in both genotypes. Our results identify distinct and shared impacts of alpha-synuclein variants on the epigenome, and associate alpha-synuclein with the epigenetic etiology of PD.
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Affiliation(s)
- Samantha L Schaffner
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Zinah Wassouf
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Diana F Lazaro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mary Xylaki
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Nicole Gladish
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - David T S Lin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Julia MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Katia Ramadori
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Julia M Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
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McEwen LM, O'Donnell KJ, McGill MG, Edgar RD, Jones MJ, MacIsaac JL, Lin DTS, Ramadori K, Morin A, Gladish N, Garg E, Unternaehrer E, Pokhvisneva I, Karnani N, Kee MZL, Klengel T, Adler NE, Barr RG, Letourneau N, Giesbrecht GF, Reynolds JN, Czamara D, Armstrong JM, Essex MJ, de Weerth C, Beijers R, Tollenaar MS, Bradley B, Jovanovic T, Ressler KJ, Steiner M, Entringer S, Wadhwa PD, Buss C, Bush NR, Binder EB, Boyce WT, Meaney MJ, Horvath S, Kobor MS. The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. Proc Natl Acad Sci U S A 2020; 117:23329-23335. [PMID: 31611402 PMCID: PMC7519312 DOI: 10.1073/pnas.1820843116] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The development of biological markers of aging has primarily focused on adult samples. Epigenetic clocks are a promising tool for measuring biological age that show impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several age-related phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as compared to adults. To address this gap, we aimed to develop a highly accurate, noninvasive, biological measure of age specific to pediatric samples using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032), with performance assessed in a separate test dataset (n = 689). DNAm at these 94 CpG sites was highly predictive of age in the test cohort (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.
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Affiliation(s)
- Lisa M McEwen
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Kieran J O'Donnell
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
| | - Megan G McGill
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Rachel D Edgar
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Meaghan J Jones
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Julia L MacIsaac
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - David Tse Shen Lin
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Katia Ramadori
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Alexander Morin
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Nicole Gladish
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Elika Garg
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Eva Unternaehrer
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Irina Pokhvisneva
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596
| | - Michelle Z L Kee
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School-McLean Hospital, Belmont, MA 02478
| | - Nancy E Adler
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Psychiatry, University of California, San Francisco, CA 94143
- Department of Pediatrics, University of California, San Francisco, CA 94143
| | - Ronald G Barr
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nicole Letourneau
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada T2N 4N1
- Faculty of Nursing, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Gerald F Giesbrecht
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada T2N 4N1
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - James N Reynolds
- Department of Biomedical and Molecular Sciences, School of Medicine, Queen's University, Kingston, ON, Canada K7L 3N6
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Jeffrey M Armstrong
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53706
| | - Marilyn J Essex
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53706
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 HR, Nijmegen, The Netherlands
| | - Roseriet Beijers
- Behavioural Science Institute, Radboud University, 6525 HR, Nijmegen, The Netherlands
| | - Marieke S Tollenaar
- Leiden Institute for Brain and Cognition, Institute of Psychology, Leiden University, 2300 RB, Leiden, The Netherlands
| | - Bekh Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School-McLean Hospital, Belmont, MA 02478
| | - Meir Steiner
- Department of Psychiatry and Behavioural Neurosciences, St. Joseph's Healthcare Hamilton, McMaster University, Hamilton, ON, Canada L8S 4L8
| | - Sonja Entringer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, 10117 Berlin, Germany
- Development, Health, and Disease Research Program, University of California, Irvine, CA 92617
| | - Pathik D Wadhwa
- Development, Health, and Disease Research Program, University of California, Irvine, CA 92617
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, 92617
- Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, 92617
- Department of Epidemiology, School of Medicine, University of California, Irvine, CA, 92617
| | - Claudia Buss
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, 10117 Berlin, Germany
| | - Nicole R Bush
- Department of Psychiatry, University of California, San Francisco, CA 94143
| | - Elisabeth B Binder
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - W Thomas Boyce
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Psychiatry, University of California, San Francisco, CA 94143
- Department of Pediatrics, University of California, San Francisco, CA 94143
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095;
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4;
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
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