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Gonzalez-Latapi P, Bustos B, Dong S, Lubbe S, Simuni T, Krainc D. Alterations in Blood Methylome as Potential Epigenetic Biomarker in Sporadic Parkinson's Disease. Ann Neurol 2024; 95:1162-1172. [PMID: 38563317 DOI: 10.1002/ana.26923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE To characterize DNA methylation (DNAm) differences between sporadic Parkinson's disease (PD) and healthy control (HC) individuals enrolled in the Parkinson's Progression Markers Initiative (PPMI). METHODS Using whole blood, we characterized longitudinal differences in DNAm between sporadic PD patients (n = 196) and HCs (n = 86) enrolled in PPMI. RNA sequencing (RNAseq) was used to conduct gene expression analyses for genes mapped to differentially methylated cytosine-guanine sites (CpGs). RESULTS At the time of patient enrollment, 5,178 CpGs were differentially methylated (2,683 hypermethylated and 2,495 hypomethylated) in PD compared to HC. Of these, 579 CpGs underwent significant methylation changes over 3 years. Several differentially methylated CpGs were found near the cytochrome P450 family 2 subfamily E member 1 (CYP2E1) gene. Additionally, multiple hypermethylated CpGs were associated with the N-myc downregulated gene family member 4 (NDRG4) gene. RNA-Seq analyses showed 75 differentially expressed genes in PD patients compared to controls. An integrative analysis of both differentially methylated sites and differentially expressed genes revealed 20 genes that exhibited hypomethylation concomitant with overexpression. Additionally, 1 gene, cathepsin H (CTSH), displayed hypermethylation that was associated with its decreased expression. INTERPRETATION We provide initial evidence of alterations in DNAm in blood of PD patients that may serve as potential epigenetic biomarker of disease. To evaluate the significance of these changes throughout the progression of PD, additional profiling at longer intervals and during the prodromal stages of disease will be necessary. ANN NEUROL 2024;95:1162-1172.
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Affiliation(s)
- Paulina Gonzalez-Latapi
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bernabe Bustos
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Siyuan Dong
- Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Steven Lubbe
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tanya Simuni
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Zhang Z, Wang R, Zhou H, Wu D, Cao Y, Zhang C, Sun H, Mu C, Hao Z, Ren H, Wang N, Yu S, Zhang J, Tao M, Wang C, Liu Y, Liu L, Liu Y, Zang J, Wang G. Inhibition of EHMT1/2 rescues synaptic damage and motor impairment in a PD mouse model. Cell Mol Life Sci 2024; 81:128. [PMID: 38472451 DOI: 10.1007/s00018-024-05176-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Epigenetic dysregulation that leads to alterations in gene expression and is suggested to be one of the key pathophysiological factors of Parkinson's disease (PD). Here, we found that α-synuclein preformed fibrils (PFFs) induced histone H3 dimethylation at lysine 9 (H3K9me2) and increased the euchromatic histone methyltransferases EHMT1 and EHMT2, which were accompanied by neuronal synaptic damage, including loss of synapses and diminished expression levels of synaptic-related proteins. Furthermore, the levels of H3K9me2 at promoters in genes that encode the synaptic-related proteins SNAP25, PSD95, Synapsin 1 and vGLUT1 were increased in primary neurons after PFF treatment, which suggests a linkage between H3K9 dimethylation and synaptic dysfunction. Inhibition of EHMT1/2 with the specific inhibitor A-366 or shRNA suppressed histone methylation and alleviated synaptic damage in primary neurons that were treated with PFFs. In addition, the synaptic damage and motor impairment in mice that were injected with PFFs were repressed by treatment with the EHMT1/2 inhibitor A-366. Thus, our findings reveal the role of histone H3 modification by EHMT1/2 in synaptic damage and motor impairment in a PFF animal model, suggesting the involvement of epigenetic dysregulation in PD pathogenesis.
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Affiliation(s)
- Zhixiong Zhang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Rui Wang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Hui Zhou
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Dan Wu
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Yifan Cao
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Chuang Zhang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Hongyang Sun
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Chenchen Mu
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Zongbing Hao
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Haigang Ren
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
- Jiangsu Provincial Medical Innovation Center of Trauma Medicine, Institute of Trauma Medicine, Soochow University, Suzhou, 215123, Jiangsu, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Nana Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Shuang Yu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Jingzhong Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Mengdan Tao
- School of Pharmacy, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Can Wang
- School of Pharmacy, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yan Liu
- School of Pharmacy, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Liu Liu
- Department of Pharmacy, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, China
| | - Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, 230026, Anhui, China
| | - Guanghui Wang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Soochow University, Suzhou, 215123, Jiangsu, China.
- Center of Translational Medicine, First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Suzhou, 215400, China.
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Coppens G, Vanhorebeek I, Verlinden I, Derese I, Wouters PJ, Joosten KF, Verbruggen SC, Güiza F, Van den Berghe G. Assessment of aberrant DNA methylation two years after paediatric critical illness: a pre-planned secondary analysis of the international PEPaNIC trial. Epigenetics 2023; 18:2146966. [PMID: 36384393 PMCID: PMC9980627 DOI: 10.1080/15592294.2022.2146966] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Critically ill children requiring intensive care suffer from impaired physical/neurocognitive development 2 y later, partially preventable by omitting early use of parenteral nutrition (early-PN) in the paediatric intensive-care-unit (PICU). Altered methylation of DNA from peripheral blood during PICU-stay provided a molecular basis hereof. Whether DNA-methylation of former PICU patients, assessed 2 y after critical illness, is different from that of healthy children remained unknown. In a pre-planned secondary analysis of the PEPaNIC-RCT (clinicaltrials.gov-NCT01536275) 2-year follow-up, we assessed buccal-mucosal DNA-methylation (Infinium-HumanMethylation-EPIC-BeadChip) of former PICU-patients (N = 406 early-PN; N = 414 late-PN) and matched healthy children (N = 392). CpG-sites differentially methylated between groups were identified with multivariable linear regression and differentially methylated DNA-regions via clustering of differentially methylated CpG-sites using kernel-estimates. Analyses were adjusted for technical variation and baseline risk factors, and corrected for multiple testing (false-discovery-rate <0.05). Differentially methylated genes were functionally annotated (KEGG-pathway database), and allocated to three classes depending on involvement in physical/neurocognitive development, critical illness and intensive medical care, or pre-PICU-admission disorders. As compared with matched healthy children, former PICU-patients showed significantly different DNA-methylation at 4047 CpG-sites (2186 genes) and 494 DNA-regions (468 genes), with most CpG-sites being hypomethylated (90.3%) and with an average absolute 2% effect-size, irrespective of timing of PN initiation. Of the differentially methylated KEGG-pathways, 41.2% were related to physical/neurocognitive development, 32.8% to critical illness and intensive medical care and 26.0% to pre-PICU-admission disorders. Two years after critical illness in children, buccal-mucosal DNA showed abnormal methylation of CpG-sites and DNA-regions located in pathways known to be important for physical/neurocognitive development.
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Affiliation(s)
- Grégoire Coppens
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Ilse Vanhorebeek
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Ines Verlinden
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Inge Derese
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Pieter J Wouters
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Koen F Joosten
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Sascha C Verbruggen
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Fabian Güiza
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Greet Van den Berghe
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
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Harvey J, Pishva E, Chouliaras L, Lunnon K. Elucidating distinct molecular signatures of Lewy body dementias. Neurobiol Dis 2023; 188:106337. [PMID: 37918758 DOI: 10.1016/j.nbd.2023.106337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/15/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
Dementia with Lewy bodies and Parkinson's disease dementia are common neurodegenerative diseases that share similar neuropathological profiles and spectra of clinical symptoms but are primarily differentiated by the order in which symptoms manifest. The question of whether a distinct molecular pathological profile could distinguish these disorders is yet to be answered. However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. In this review, we present an overview of the clinical and pathological hallmarks of Lewy body dementias before summarizing relevant research into genetic, epigenetic, transcriptional and protein signatures in these diseases, with a particular interest in those resolving "omic" level changes. We conclude by suggesting future research directions to address current gaps and questions present within the field.
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Affiliation(s)
- Joshua Harvey
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Leonidas Chouliaras
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, UK; Specialist Dementia and Frailty Service, Essex Partnership University NHS Foundation Trust, Epping, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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Harvey J, Smith AR, Weymouth LS, Smith RG, Castanho I, Hubbard L, Creese B, Bresner K, Williams N, Pishva E, Lunnon K. Epigenetic insights into neuropsychiatric and cognitive symptoms in Parkinson's disease: A DNA co-methylation network analysis. RESEARCH SQUARE 2023:rs.3.rs-3185734. [PMID: 37790398 PMCID: PMC10543025 DOI: 10.21203/rs.3.rs-3185734/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Parkinson's disease is a highly heterogeneous disorder, encompassing a complex spectrum of clinical presentation including motor, sleep, cognitive and neuropsychiatric symptoms. We aimed to investigate genome-wide DNA methylation networks in post-mortem Parkinson's disease brain samples and test for region-specific association with common neuropsychiatric and cognitive symptoms. Of traits tested, we identify a co-methylation module in the substantia nigra with significant correlation to depressive symptoms and with ontological enrichment for terms relevant to neuronal and synaptic processes. Notably, expression of the genes annotated to the methylation loci present within this module are found to be significantly enriched in neuronal subtypes within the substantia nigra. These findings highlight the potential involvement of neuronal-specific changes within the substantia nigra with regard to depressive symptoms in Parkinson's disease.
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Affiliation(s)
- Joshua Harvey
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Adam R Smith
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Luke S Weymouth
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Rebecca G Smith
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Isabel Castanho
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Leon Hubbard
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, UK
| | - Byron Creese
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Kate Bresner
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, UK
| | - Nigel Williams
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, UK
| | - Ehsan Pishva
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Katie Lunnon
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
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Tsalenchuk M, Gentleman SM, Marzi SJ. Linking environmental risk factors with epigenetic mechanisms in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:123. [PMID: 37626097 PMCID: PMC10457362 DOI: 10.1038/s41531-023-00568-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Sporadic Parkinson's disease (PD) is a progressive neurodegenerative disease, with a complex risk structure thought to be influenced by interactions between genetic variants and environmental exposures, although the full aetiology is unknown. Environmental factors, including pesticides, have been reported to increase the risk of developing the disease. Growing evidence suggests epigenetic changes are key mechanisms by which these environmental factors act upon gene regulation, in disease-relevant cell types. We present a systematic review critically appraising and summarising the current body of evidence of the relationship between epigenetic mechanisms and environmental risk factors in PD to inform future research in this area. Epigenetic studies of relevant environmental risk factors in animal and cell models have yielded promising results, however, research in humans is just emerging. While published studies in humans are currently relatively limited, the importance of the field for the elucidation of molecular mechanisms of pathogenesis opens clear and promising avenues for the future of PD research. Carefully designed epidemiological studies carried out in PD patients hold great potential to uncover disease-relevant gene regulatory mechanisms. Therefore, to advance this burgeoning field, we recommend broadening the scope of investigations to include more environmental exposures, increasing sample sizes, focusing on disease-relevant cell types, and recruiting more diverse cohorts.
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Affiliation(s)
- Maria Tsalenchuk
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK.
- Department of Brain Sciences, Imperial College London, London, UK.
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Duarte Folle A, Flores M, Kusters C, Paul K, Del Rosario I, Zhang K, Ruiz C, Castro E, Bronstein J, Ritz B, Keener A. Ethnicity and Parkinson's Disease: Motor and Nonmotor Features and Disease Progression in Latino Patients Living in Rural California. J Gerontol A Biol Sci Med Sci 2023; 78:1258-1268. [PMID: 36645401 PMCID: PMC10329232 DOI: 10.1093/gerona/glad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most common neurodegenerative disorder among older adults worldwide. Currently, studies of PD progression rely primarily on White non-Latino (WNL) patients. Here, we compare clinical profiles and PD progression in Latino and WNL patients enrolled in a community-based study in rural Central California. METHOD PD patients within 5 years of diagnosis were identified from 3 counties between 2001 and 2015. During up to 3 visits, participants were examined by movement disorders specialists and interviewed. We analyzed cross-sectional differences in PD clinical features severity at each study visit and used linear mixed models and Cox proportional hazards models to compare motor, nonmotor, and disability progression longitudinally and to assess time to death in Latinos compared to WNL patients. RESULTS Of 775 patients included, 138 (18%) self-identified as Latino and presented with earlier age at diagnosis (63.6 vs 68.9) and death (78.6 vs 81.5) than WNL. Motor (hazard ratio [HR] = 1.17 [0.71, 1.94]) and nonmotor symptoms did not progress faster in Latino versus WNL patients after accounting for differences in baseline symptom severity. However, Latino patients progressed to disability stages according to Hoehn and Yahr faster than WNL (HR = 1.81 [1.11, 2.96]). Motor and nonmotor symptoms in Latino patients were also medically managed less well than in WNL. CONCLUSIONS Our PD study with a large proportion of Latino enrollees and progression data reveals disparities in clinical features and progression by ethnicity that may reflect healthcare access and structural socioeconomic disadvantages in Latino patients with PD.
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Affiliation(s)
- Aline Duarte Folle
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Marie E S Flores
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
- Altamed, Pico Rivera, California, USA
| | - Cynthia Kusters
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Irish Del Rosario
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Keren Zhang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Cristina Ruiz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Emily Castro
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Jeff Bronstein
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Adrienne M Keener
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Department of Neurology, Veterans Administration Greater Los Angeles Health Care System, Los Angeles, California, USA
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Gim JA. Integrative Approaches of DNA Methylation Patterns According to Age, Sex and Longitudinal Changes. Curr Genomics 2023; 23:385-399. [PMID: 37920553 PMCID: PMC10173416 DOI: 10.2174/1389202924666221207100513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/04/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
Background In humans, age-related DNA methylation has been studied in blood, tissues, buccal swabs, and fibroblasts, and changes in DNA methylation patterns according to age and sex have been detected. To date, approximately 137,000 samples have been analyzed from 14,000 studies, and the information has been uploaded to the NCBI GEO database. Methods A correlation between age and methylation level and longitudinal changes in methylation levels was revealed in both sexes. Here, 20 public datasets derived from whole blood were analyzed using the Illumina BeadChip. Batch effects with respect to the time differences were correlated. The overall change in the pattern was provided as the inverse of the coefficient of variation (COV). Results Of the 20 datasets, nine were from a longitudinal study. All data had age and sex as common variables. Comprehensive details of age-, sex-, and longitudinal change-based DNA methylation levels in the whole blood sample were elucidated in this study. ELOVL2 and FHL2 showed the maximum correlation between age and DNA methylation. The methylation patterns of genes related to mental health differed according to age. Age-correlated genes have been associated with malformations (anteverted nostril, craniofacial abnormalities, and depressed nasal bridge) and drug addiction (drug habituation and smoking). Conclusion Based on 20 public DNA methylation datasets, methylation levels according to age and longitudinal changes by sex were identified and visualized using an integrated approach. The results highlight the molecular mechanisms underlying the association of sex and biological age with changes in DNA methylation, and the importance of optimal genomic information management.
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Affiliation(s)
- Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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Ge X, Yao T, Zhang C, Wang Q, Wang X, Xu LC. Human microRNA-4433 (hsa-miR-4443) Targets 18 Genes to be a Risk Factor of Neurodegenerative Diseases. Curr Alzheimer Res 2022; 19:511-522. [PMID: 35929619 PMCID: PMC9906632 DOI: 10.2174/1567205019666220805120303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Neurodegenerative diseases, such as Alzheimer's disease patients (AD), Huntington's disease (HD) and Parkinson's disease (PD), are common causes of morbidity, mortality, and cognitive impairment in older adults. OBJECTIVE We aimed to understand the transcriptome characteristics of the cortex of neurodegenerative diseases and to provide an insight into the target genes of differently expressed microRNAs in the occurrence and development of neurodegenerative diseases. METHODS The Limma package of R software was used to analyze GSE33000, GSE157239, GSE64977 and GSE72962 datasets to identify the differentially expressed genes (DEGs) and microRNAs in the cortex of neurodegenerative diseases. Bioinformatics methods, such as GO enrichment analysis, KEGG enrichment analysis and gene interaction network analysis, were used to explore the biological functions of DEGs. Weighted gene co-expression network analysis (WGCNA) was used to cluster DEGs into modules. RNA22, miRDB, miRNet 2.0 and TargetScan7 databases were performed to predict the target genes of microRNAs. RESULTS Among 310 Alzheimer's disease (AD) patients, 157 Huntington's disease (HD) patients and 157 non-demented control (Con) individuals, 214 co-DEGs were identified. Those co-DEGs were filtered into 2 different interaction network complexes, representing immune-related genes and synapserelated genes. The WGCNA results identified five modules: yellow, blue, green, turquoise, and brown. Most of the co-DEGs were clustered into the turquoise module and blue module, which respectively regulated synapse-related function and immune-related function. In addition, human microRNA-4433 (hsa-miR-4443), which targets 18 co-DEGs, was the only 1 co-up-regulated microRNA identified in the cortex of neurodegenerative diseases. CONCLUSION 214 DEGs and 5 modules regulate the immune-related and synapse-related function of the cortex in neurodegenerative diseases. Hsa-miR-4443 targets 18 co-DEGs and may be a potential molecular mechanism in neurodegenerative diseases' occurrence and development.
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Affiliation(s)
- Xing Ge
- Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Tingting Yao
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Chaoran Zhang
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Qingqing Wang
- Department of Nephrology, Xuzhou Children’s Hospital, Xuzhou, Jiangsu 221000, China
| | - Xuxu Wang
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Li-Chun Xu
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China; ,Address correspondence to this author at the School of Public Health, Xuzhou Medical University, Xuzhou, 209 Tong-Shan Road, Xuzhou, Jiangsu, 221002, China; Tel: +86-516-83262650; Fax: +86-516-83262650; E-mail:
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Harvey J, Reijnders RA, Cavill R, Duits A, Köhler S, Eijssen L, Rutten BPF, Shireby G, Torkamani A, Creese B, Leentjens AFG, Lunnon K, Pishva E. Machine learning-based prediction of cognitive outcomes in de novo Parkinson's disease. NPJ Parkinsons Dis 2022; 8:150. [PMID: 36344548 PMCID: PMC9640625 DOI: 10.1038/s41531-022-00409-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
Cognitive impairment is a debilitating symptom in Parkinson's disease (PD). We aimed to establish an accurate multivariate machine learning (ML) model to predict cognitive outcome in newly diagnosed PD cases from the Parkinson's Progression Markers Initiative (PPMI). Annual cognitive assessments over an 8-year time span were used to define two cognitive outcomes of (i) cognitive impairment, and (ii) dementia conversion. Selected baseline variables were organized into three subsets of clinical, biofluid and genetic/epigenetic measures and tested using four different ML algorithms. Irrespective of the ML algorithm used, the models consisting of the clinical variables performed best and showed better prediction of cognitive impairment outcome over dementia conversion. We observed a marginal improvement in the prediction performance when clinical, biofluid, and epigenetic/genetic variables were all included in one model. Several cerebrospinal fluid measures and an epigenetic marker showed high predictive weighting in multiple models when included alongside clinical variables.
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Affiliation(s)
- Joshua Harvey
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Rick A Reijnders
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Rachel Cavill
- Department of Advanced Computing Sciences, FSE, Maastricht University, Maastricht, The Netherlands
| | - Annelien Duits
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
- Department of Medical Psychology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sebastian Köhler
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Lars Eijssen
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
- Department of Bioinformatics-BiGCaT, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Gemma Shireby
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Byron Creese
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Albert F G Leentjens
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Katie Lunnon
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands.
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11
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Kalyakulina A, Yusipov I, Bacalini MG, Franceschi C, Vedunova M, Ivanchenko M. Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI. Gigascience 2022; 11:giac097. [PMID: 36259657 PMCID: PMC9718659 DOI: 10.1093/gigascience/giac097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND DNA methylation has a significant effect on gene expression and can be associated with various diseases. Meta-analysis of available DNA methylation datasets requires development of a specific workflow for joint data processing. RESULTS We propose a comprehensive approach of combined DNA methylation datasets to classify controls and patients. The solution includes data harmonization, construction of machine learning classification models, dimensionality reduction of models, imputation of missing values, and explanation of model predictions by explainable artificial intelligence (XAI) algorithms. We show that harmonization can improve classification accuracy by up to 20% when preprocessing methods of the training and test datasets are different. The best accuracy results were obtained with tree ensembles, reaching above 95% for Parkinson's disease. Dimensionality reduction can substantially decrease the number of features, without detriment to the classification accuracy. The best imputation methods achieve almost the same classification accuracy for data with missing values as for the original data. XAI approaches have allowed us to explain model predictions from both populational and individual perspectives. CONCLUSIONS We propose a methodologically valid and comprehensive approach to the classification of healthy individuals and patients with various diseases based on whole-blood DNA methylation data using Parkinson's disease and schizophrenia as examples. The proposed algorithm works better for the former pathology, characterized by a complex set of symptoms. It allows to solve data harmonization problems for meta-analysis of many different datasets, impute missing values, and build classification models of small dimensionality.
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Affiliation(s)
- Alena Kalyakulina
- Correspondence author. Alena Kalyakulina, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Gagarin avenue 22, Nizhny Novgorod 603022, Russia. E-mail:
| | | | | | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, 603022 Nizhny Novgorod, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, 603022 Nizhny Novgorod, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, 603022 Nizhny Novgorod, Russia
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12
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Shireby G, Dempster EL, Policicchio S, Smith RG, Pishva E, Chioza B, Davies JP, Burrage J, Lunnon K, Seiler Vellame D, Love S, Thomas A, Brookes K, Morgan K, Francis P, Hannon E, Mill J. DNA methylation signatures of Alzheimer's disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types. Nat Commun 2022; 13:5620. [PMID: 36153390 PMCID: PMC9509387 DOI: 10.1038/s41467-022-33394-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by the progressive accumulation of amyloid-beta and neurofibrillary tangles of tau in the neocortex. We profiled DNA methylation in two regions of the cortex from 631 donors, performing an epigenome-wide association study of multiple measures of AD neuropathology. We meta-analyzed our results with those from previous studies of DNA methylation in AD cortex (total n = 2013 donors), identifying 334 cortical differentially methylated positions (DMPs) associated with AD pathology including methylomic variation at loci not previously implicated in dementia. We subsequently profiled DNA methylation in NeuN+ (neuronal-enriched), SOX10+ (oligodendrocyte-enriched) and NeuN-/SOX10- (microglia- and astrocyte-enriched) nuclei, finding that the majority of DMPs identified in 'bulk' cortex tissue reflect DNA methylation differences occurring in non-neuronal cells. Our study highlights the power of utilizing multiple measures of neuropathology to identify epigenetic signatures of AD and the importance of characterizing disease-associated variation in purified cell-types.
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Affiliation(s)
- Gemma Shireby
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L Dempster
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Stefania Policicchio
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rebecca G Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Barry Chioza
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan P Davies
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joe Burrage
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Dorothea Seiler Vellame
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Seth Love
- Dementia Research Group, University of Bristol Medical School (Translational Health Sciences), Bristol, UK
| | - Alan Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Keeley Brookes
- Biosciences, School of Science & Technology, Nottingham Trent University, Nottingham, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Paul Francis
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK.
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13
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Parkinson's disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), and NR4A2 (NURR1) in cortical neurons. NPJ Parkinsons Dis 2022; 8:120. [PMID: 36151217 PMCID: PMC9508164 DOI: 10.1038/s41531-022-00355-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 06/24/2022] [Indexed: 12/04/2022] Open
Abstract
Evidence for epigenetic regulation playing a role in Parkinson's disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this genome-wide analysis of DNA methylation in an enriched neuronal population from PD postmortem parietal cortex, we report sex-specific PD-associated methylation changes in PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), NR4A2 (NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.
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14
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Chen GK, Yan Q, Paul KC, Kusters CD, Folle AD, Furlong M, Keener A, Bronstein J, Horvath S, Ritz B. Stochastic Epigenetic Mutations Influence Parkinson's Disease Risk, Progression, and Mortality. JOURNAL OF PARKINSON'S DISEASE 2022; 12:545-556. [PMID: 34842194 PMCID: PMC9076404 DOI: 10.3233/jpd-212834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Stochastic epigenetic mutations (SEM) reflect a deviation from normal site-specific methylation patterns. Epigenetic mutation load (EML) captures the accumulation of SEMs across an individual's genome and may reflect dysfunction of the epigenetic maintenance system in response to epigenetic challenges. OBJECTIVE We investigate whether EML is associated with PD risk and time to events (i.e., death and motor symptom decline). METHODS We employed logistic regression and Cox proportional hazards regression to assess the association between EML and several outcomes. Our analyses are based on 568 PD patients and 238 controls from the Parkinson's disease, Environment and Genes (PEG) study, for whom blood-based methylation data was available. RESULTS We found an association for PD onset and EML in all genes (OR = 1.90; 95%CI 1.52-2.37) and PD-related genes (OR = 1.87; 95%CI 1.50-2.32). EML was also associated with time to a minimum score of 35 points on the motor UPDRS exam (OR = 1.28; 95%CI 1.06-1.56) and time to death (OR = 1.29, 95%CI 1.11-1.49). An analysis of PD related genes only revealed five intragenic hotspots of high SEM density associated with PD risk. CONCLUSION Our findings suggest an enrichment of methylation dysregulation in PD patients in general and specifically in five PD related genes. EML may also be associated with time to death and motor symptom progression in PD patients.
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Affiliation(s)
| | - Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Kimberly C. Paul
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Cynthia D.J. Kusters
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Aline Duarte Folle
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Melissa Furlong
- Department of Community, Environment and Policy, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA
| | - Adrienne Keener
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jeff Bronstein
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA,Correspondence to: Beate Ritz, UCLA, Epidemiology, Box 951772, Los Angeles, CA 90095, USA.
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15
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Fernández-Carrión R, Sorlí JV, Coltell O, Pascual EC, Ortega-Azorín C, Barragán R, Giménez-Alba IM, Alvarez-Sala A, Fitó M, Ordovas JM, Corella D. Sweet Taste Preference: Relationships with Other Tastes, Liking for Sugary Foods and Exploratory Genome-Wide Association Analysis in Subjects with Metabolic Syndrome. Biomedicines 2021; 10:biomedicines10010079. [PMID: 35052758 PMCID: PMC8772854 DOI: 10.3390/biomedicines10010079] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/11/2021] [Accepted: 12/29/2021] [Indexed: 12/21/2022] Open
Abstract
Taste perception and its association with nutrition and related diseases (type 2 diabetes, obesity, metabolic syndrome, cardiovascular, etc.) are emerging fields of biomedicine. There is currently great interest in investigating the environmental and genetic factors that influence sweet taste and sugary food preferences for personalized nutrition. Our aims were: (1) to carry out an integrated analysis of the influence of sweet taste preference (both in isolation and in the context of other tastes) on the preference for sugary foods and its modulation by type 2 diabetes status; (2) as well as to explore new genetic factors associated with sweet taste preference. We studied 425 elderly white European subjects with metabolic syndrome and analyzed taste preference, taste perception, sugary-foods liking, biochemical and genetic markers. We found that type 2 diabetic subjects (38%) have a small, but statistically higher preference for sweet taste (p = 0.021) than non-diabetic subjects. No statistically significant differences (p > 0.05) in preferences for the other tastes (bitter, salty, sour or umami) were detected. For taste perception, type 2 diabetic subjects have a slightly lower perception of all tastes (p = 0.026 for the combined “total taste score”), bitter taste being statistically lower (p = 0.023). We also carried out a principal component analysis (PCA), to identify latent variables related to preferences for the five tastes. We identified two factors with eigenvalues >1. Factor 2 was the one with the highest correlation with sweet taste preference. Sweet taste preference was strongly associated with a liking for sugary foods. In the exploratory SNP-based genome-wide association study (GWAS), we identified some SNPs associated with sweet taste preference, both at the suggestive and at the genome-wide level, especially a lead SNP in the PTPRN2 (Protein Tyrosine Phosphatase Receptor Type N2) gene, whose minor allele was associated with a lower sweet taste preference. The PTPRN2 gene was also a top-ranked gene obtained in the gene-based exploratory GWAS analysis. In conclusion, sweet taste preference was strongly associated with sugary food liking in this population. Our exploratory GWAS identified an interesting candidate gene related with sweet taste preference, but more studies in other populations are required for personalized nutrition.
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Affiliation(s)
- Rebeca Fernández-Carrión
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
| | - Jose V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellon, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
| | - Carolina Ortega-Azorín
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
| | - Rocío Barragán
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Sleep Center of Excellence, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division of General Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ignacio M. Giménez-Alba
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
| | - Andrea Alvarez-Sala
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
| | - Montserrat Fitó
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Cardiovascular Risk and Nutrition Research Group (CARIN), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Jose M. Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA;
- Nutritional Genomics and Epigenomics Group, IMDEA Alimentación, 28049 Madrid, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Correspondence: ; Tel.: +34-96-386-4800
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16
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Meng J, Wang F, Ji L, Liang Y, Nian W, Song L, Zhu A. Comprehensive methylation profile of CSF cfDNA revealed pathogenesis and diagnostic markers for early-onset Parkinson's disease. Epigenomics 2021; 13:1637-1651. [PMID: 34664993 DOI: 10.2217/epi-2021-0176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background: Early-onset Parkinson's disease (EOPD) is one uncommon Parkinson's disease subtype with characteristic clinicopathological features. The full epigenomic profile of EOPD is largely unknown. Methods: We performed the first study to investigate the EOPD full methylation profile of cerebrospinal fluid (CSF) cell-free DNA (cfDNA) from 26 EOPD patients and 10 control patients. Results: 2220 differentially methylated genes were identified in EOPD. Hypermethylation far outweighed hypomethylation in gene numbers. Clustering and enrichment analyses identified aberrant neuronal function and immune response. Weighted correlation network analysis demonstrated significant correlation between methylation signatures and clock drawing test (CDT), mini-mental state examination (MMSE), education, working status, alcohol drinking history and Hamilton anxiety scale (HAMA). Several key networking genes in EOPD aberrant methylation were also identified. Conclusions: The methylation profile and signatures of CSF cfDNA were revealed for the first time in EOPD. Aberrant methylation signatures were correlated with education, working status, alcohol drinking history, CDT, MMSE and HAMA.
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Affiliation(s)
- Jie Meng
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China.,Department of Neurology & State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, & Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Fenglin Wang
- Department of genetics and cell biology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Lei Ji
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Yuhua Liang
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Wei Nian
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Lele Song
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China.,Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, 100091, PR China
| | - Aiqin Zhu
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
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17
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Paul KC, Binder AM, Horvath S, Kusters C, Yan Q, Rosario ID, Yu Y, Bronstein J, Ritz B. Accelerated hematopoietic mitotic aging measured by DNA methylation, blood cell lineage, and Parkinson's disease. BMC Genomics 2021; 22:696. [PMID: 34565328 PMCID: PMC8474781 DOI: 10.1186/s12864-021-08009-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Aging and inflammation are important components of Parkinson's disease (PD) pathogenesis and both are associated with changes in hematopoiesis and blood cell composition. DNA methylation (DNAm) presents a mechanism to investigate inflammation, aging, and hematopoiesis in PD, using epigenetic mitotic aging and aging clocks. Here, we aimed to define the influence of blood cell lineage on epigenetic mitotic age and then investigate mitotic age acceleration with PD, while considering epigenetic age acceleration biomarkers. RESULTS We estimated epigenetic mitotic age using the "epiTOC" epigenetic mitotic clock in 10 different blood cell populations and in a population-based study of PD with whole-blood. Within subject analysis of the flow-sorted purified blood cell types DNAm showed a clear separation of epigenetic mitotic age by cell lineage, with the mitotic age significantly lower in myeloid versus lymphoid cells (p = 2.1e-11). PD status was strongly associated with accelerated epigenetic mitotic aging (AccelEpiTOC) after controlling for cell composition (OR = 2.11, 95 % CI = 1.56, 2.86, p = 1.6e-6). AccelEpiTOC was also positively correlated with extrinsic epigenetic age acceleration, a DNAm aging biomarker related to immune system aging (with cell composition adjustment: R = 0.27, p = 6.5e-14), and both were independently associated with PD. Among PD patients, AccelEpiTOC measured at baseline was also associated with longitudinal motor and cognitive symptom decline. CONCLUSIONS The current study presents a first look at epigenetic mitotic aging in PD and our findings suggest accelerated hematopoietic cell mitosis, possibly reflecting immune pathway imbalances, in early PD that may also be related to motor and cognitive progression.
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Affiliation(s)
- Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.
| | - Alexandra M Binder
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Cynthia Kusters
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Irish Del Rosario
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Yu Yu
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
| | - Jeff Bronstein
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Beate Ritz
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
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18
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Fonseca Cabral G, Schaan AP, Cavalcante GC, Sena-dos-Santos C, de Souza TP, Souza Port’s NM, dos Santos Pinheiro JA, Ribeiro-dos-Santos Â, Vidal AF. Nuclear and Mitochondrial Genome, Epigenome and Gut Microbiome: Emerging Molecular Biomarkers for Parkinson's Disease. Int J Mol Sci 2021; 22:9839. [PMID: 34576000 PMCID: PMC8471599 DOI: 10.3390/ijms22189839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is currently the second most common neurodegenerative disorder, burdening about 10 million elderly individuals worldwide. The multifactorial nature of PD poses a difficult obstacle for understanding the mechanisms involved in its onset and progression. Currently, diagnosis depends on the appearance of clinical signs, some of which are shared among various neurologic disorders, hindering early diagnosis. There are no effective tools to prevent PD onset, detect the disease in early stages or accurately report the risk of disease progression. Hence, there is an increasing demand for biomarkers that may identify disease onset and progression, as treatment-based medicine may not be the best approach for PD. Over the last few decades, the search for molecular markers to predict susceptibility, aid in accurate diagnosis and evaluate the progress of PD have intensified, but strategies aimed to improve individualized patient care have not yet been established. CONCLUSIONS Genomic variation, regulation by epigenomic mechanisms, as well as the influence of the host gut microbiome seem to have a crucial role in the onset and progress of PD, thus are considered potential biomarkers. As such, the human nuclear and mitochondrial genome, epigenome, and the host gut microbiome might be the key elements to the rise of personalized medicine for PD patients.
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Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ana Paula Schaan
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Giovanna C. Cavalcante
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Tatiane Piedade de Souza
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Natacha M. Souza Port’s
- Laboratório de Neurofarmacologia Molecular, Universidade de São Paulo, São Paulo 05508-000, Brazil;
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará–R. dos Mundurucus, Belém 66073-000, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
| | - Amanda F. Vidal
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
- ITVDS—Instituto Tecnológico Vale Desenvolvimento Sustentável–R. Boaventura da Silva, Belém 66055-090, Brazil
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He S, Huang L, Shao C, Nie T, Xia L, Cui B, Lu F, Zhu L, Chen B, Yang Q. Several miRNAs derived from serum extracellular vesicles are potential biomarkers for early diagnosis and progression of Parkinson's disease. Transl Neurodegener 2021; 10:25. [PMID: 34315539 PMCID: PMC8317324 DOI: 10.1186/s40035-021-00249-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/08/2021] [Indexed: 12/21/2022] Open
Abstract
Background Blood-based test for predicting disease progression and early diagnosis of Parkinson’s disease (PD) is an unmet need in the clinic. The profiles of microRNAs (miRNAs) are regarded as potential diagnostic biomarkers for human diseases, whereas miRNAs in the periphery are susceptible to the influence of various components. MiRNAs enriched in serum extracellular vesicles (EVs) have demonstrated disease-specific advantages in diagnosis due to their high abundance, stability and resistance to degradation. This study was aimed to screen differentially expressed EV-derived miRNAs between healthy controls and PD patients to aid in diagnosis of PD. Methods A total of 31 healthy controls and 72 patients with a diagnosis of PD at different Hoehn and Yahr stages in Tangdu Hospital were included. In total, 185 differentially expressed miRNAs were obtained through RNA sequencing of serum EVs as well as edgeR and t-test analyses. Subsequently, the weighted gene co-expression network analysis (WGCNA) was utilized to identify the commonly expressed miRNAs in all stages of PD by constructing connections between modules, and specifically expressed miRNAs in each stage of PD by functional enrichment analysis. After aligning these miRNAs with PD-related miRNAs in Human miRNA Disease Database, the screened miRNAs were further validated by receiver operating characteristic (ROC) curves and quantitative real-time polymerase chain reaction (qRT-PCR) using peripheral blood EVs from 40 more participants. Results WGCNA showed that 4 miRNAs were commonly associated with all stages of PD and 13 miRNAs were specifically associated with different stages of PD. Of the 17 obtained miRNAs, 7 were validated by ROC curve analysis and 7 were verified in 40 more participants by qRT-PCR. Six miRNAs were verified by both methods, which included 2 miRNAs that were commonly expressed in all stages of PD and 4 miRNAs that were specifically expressed in different stages of PD. Conclusions The 6 serum EV-derived miRNAs, hsa-miR-374a-5p, hsa-miR-374b-5p, hsa-miR-199a-3p, hsa-miR-28-5p, hsa-miR-22-5p and hsa-miR-151a-5p, may potentially be used as biomarkers for PD progression and for early diagnosis of PD in populations. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-021-00249-y.
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Affiliation(s)
- Shulei He
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Lu Huang
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China.,Department of Neurosurgery and Institute for Functional Brain Disorders, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Ci Shao
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Li Xia
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China.,Department of Neurosurgery and Institute for Functional Brain Disorders, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Bozhou Cui
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Fangfang Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Lin Zhu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Bolin Chen
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Qian Yang
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China.
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20
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Ravel-Godreuil C, Massiani-Beaudoin O, Mailly P, Prochiantz A, Joshi RL, Fuchs J. Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. iScience 2021; 24:102756. [PMID: 34278264 PMCID: PMC8264156 DOI: 10.1016/j.isci.2021.102756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/14/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Age is a major risk factor for neurodegenerative diseases like Parkinson's disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage, and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation, or Parkinson's disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson's disease.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Mailly
- Orion Imaging Facility, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Labex Memolife, Université PSL, Paris, France
| | - Alain Prochiantz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L. Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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21
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Yan Q, Forno E, Cardenas A, Qi C, Han YY, Acosta-Pérez E, Kim S, Zhang R, Boutaoui N, Canino G, Vonk JM, Xu CJ, Chen W, Marsland A, Oken E, Gold DR, Koppelman GH, Celedón JC. Exposure to violence, chronic stress, nasal DNA methylation, and atopic asthma in children. Pediatr Pulmonol 2021; 56:1896-1905. [PMID: 33751861 PMCID: PMC8217314 DOI: 10.1002/ppul.25372] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/01/2021] [Accepted: 03/04/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Exposure to violence (ETV) or chronic stress may influence asthma through unclear mechanisms. METHODS Epigenome-wide association study (EWAS) of ETV or chronic stress measures and DNA methylation in nasal epithelium from 487 Puerto Ricans aged 9-20 years who participated in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study [EVA-PR]). We assessed four measures of ETV and chronic stress in children (ETV scale, gun violence, and perceived stress) and their mothers (perceived stress). Each EWAS was conducted using linear regression, with CpGs as dependent variables and the stress/violence measure as a predictor, adjusting for age, sex, the top five principal components, and SVA latent factors. We then selected the top 100 CpGs (by p value) associated with each stress/violence measure in EVA-PR and conducted a meta-analysis of the selected CpGs and atopic asthma using data from EVA-PR and two additional cohorts (Project Viva and PIAMA). RESULTS Three CpGs (in SNN, PTPRN2, and LINC01164) were associated with maternal perceived stress or gun violence (p = 1.28-3.36 × 10-7 ), but not with atopic asthma, in EVA-PR. In a meta-analysis of three cohorts, which included the top CpGs associated with stress/violence measures in EVA-PR, 12 CpGs (in STARD3NL, SLC35F4, TSR3, CDC42SE2, KLHL25, PLCB1, BUD13, OR2B3, GALR1, TMEM196, TEAD4, and ANAPC13) were associated with atopic asthma at FDR-p < .05. CONCLUSIONS Pending confirmation in longitudinal studies, our findings suggest that nasal epithelial methylation markers associated with measures of ETV and chronic stress may be linked to atopic asthma in children and adolescents.
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Affiliation(s)
- Qi Yan
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, University of California, Berkeley, California, USA.,Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
| | - Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, The Netherlands.,University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Yueh-Ying Han
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Soyeon Kim
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rong Zhang
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Statistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nadia Boutaoui
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Judith M Vonk
- University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands.,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cheng-Jian Xu
- Department of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, The Netherlands.,University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anna Marsland
- Department of Psychology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
| | - Diane R Gold
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, The Netherlands.,University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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22
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Nasamran CA, Sachan ANS, Mott J, Kuras YI, Scherzer CR, Study HB, Ricciardelli E, Jepsen K, Edland SD, Fisch KM, Desplats P. Differential blood DNA methylation across Lewy body dementias. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12156. [PMID: 33665346 PMCID: PMC7896631 DOI: 10.1002/dad2.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, determination of clinical subtypes is challenging. The utility of blood DNA methylation as a biomarker for Lewy body disorders (LBD) is mostly unexplored. METHODS We performed a cross-sectional analysis of blood methylation in 42 DLB and 50 PDD cases applying linear models to compare groups and logistic least absolute shrinkage and selection operator regression to explore the discriminant power of methylation signals. RESULTS DLB blood shows differential methylation compared to PDD. Some methylation changes associate with core features of LBD. Sets of probes show high predictive value to discriminate between variants. DISCUSSION Our study is the first to explore LBD blood methylation. Despite overlapping clinical presentation, we detected differential epigenetic signatures that, if confirmed in independent cohorts, could be developed into useful biomarkers.
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Affiliation(s)
- Chanond A. Nasamran
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anubhav Nikunj Singh Sachan
- Division of Biostatistics, Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jennifer Mott
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Yuliya I. Kuras
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | - Clemens R. Scherzer
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | | | - Eugenia Ricciardelli
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kristen Jepsen
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steven D. Edland
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kathleen M. Fisch
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Paula Desplats
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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23
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Yan Q, Forno E, Cardenas A, Qi C, Han YY, Acosta-Pérez E, Kim S, Zhang R, Boutaoui N, Canino G, Vonk JM, Xu CJ, Chen W, Oken E, Gold DR, Koppelman GH, Celedón JC. Exposure to violence, chronic stress, nasal DNA methylation, and atopic asthma in children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020. [PMID: 33173928 DOI: 10.1101/2020.11.03.20225250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Exposure to violence (ETV) or stress may cause asthma through unclear mechanisms. Methods Epigenome-wide association study (EWAS) of DNA methylation in nasal epithelium and four ETV or chronic stress measures in 487 Puerto Ricans aged 9-20 years who participated in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study [EVA-PR]). We assessed measures of ETV or chronic stress in children (ETV scale, gun violence, and perceived stress) and their mothers (perceived stress). Each EWAS was conducted using linear regression, with CpGs as dependent variables and the stress/violence measure as a predictor, adjusting for age, sex, the top five principal components, and SVA latent factors. We then selected the top 100 CpGs (by P-value) associated with each stress/violence measure in EVA-PR and conducted a meta-analysis of the selected CpGs and atopic asthma using data from EVA-PR and two additional cohorts (Project Viva and PIAMA). Results In the EWAS of stress/violence in EVA-PR, gun violence was associated with methylation of cg18961589 in LINC01164 (β=0.03, P =1.28×10 -7 ), and maternal stress was associated with methylation of cg03402351 in SNN (β=0.04, P =1.69×10 -7 ) and cg19064846 in PTPRN2 (β=0.03, P =3.36×10 -7 ). In a meta-analysis of three cohorts, which included the top CpGs associated with stress/violence in EVA-PR, CpGs in STARD3NL, SLC35F4, TSR3, CDC42SE2, KLHL25, PLCB1, BUD13, OR2B3, GALR1, TMEM196, TEAD4 and ANAPC13 were associated with atopic asthma at FDR- P < 0.05. Conclusions ETV and chronic stress may increase the risk of atopic asthma through DNA methylation in airway epithelium, though this needs confirmation in future longitudinal studies.
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Marchetti B. Nrf2/Wnt resilience orchestrates rejuvenation of glia-neuron dialogue in Parkinson's disease. Redox Biol 2020; 36:101664. [PMID: 32863224 PMCID: PMC7395594 DOI: 10.1016/j.redox.2020.101664] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress and inflammation have long been recognized to contribute to Parkinson's disease (PD), a common movement disorder characterized by the selective loss of midbrain dopaminergic neurons (mDAn) of the substantia nigra pars compacta (SNpc). The causes and mechanisms still remain elusive, but a complex interplay between several genes and a number of interconnected environmental factors, are chiefly involved in mDAn demise, as they intersect the key cellular functions affected in PD, such as the inflammatory response, mitochondrial, lysosomal, proteosomal and autophagic functions. Nuclear factor erythroid 2 -like 2 (NFE2L2/Nrf2), the master regulator of cellular defense against oxidative stress and inflammation, and Wingless (Wnt)/β-catenin signaling cascade, a vital pathway for mDAn neurogenesis and neuroprotection, emerge as critical intertwinned actors in mDAn physiopathology, as a decline of an Nrf2/Wnt/β-catenin prosurvival axis with age underlying PD mutations and a variety of noxious environmental exposures drive PD neurodegeneration. Unexpectedly, astrocytes, the so-called "star-shaped" cells, harbouring an arsenal of "beneficial" and "harmful" molecules represent the turning point in the physiopathological and therapeutical scenario of PD. Fascinatingly, "astrocyte's fil rouge" brings back to Nrf2/Wnt resilience, as boosting the Nrf2/Wnt resilience program rejuvenates astrocytes, in turn (i) mitigating nigrostriatal degeneration of aged mice, (ii) reactivating neural stem progenitor cell proliferation and neuron differentiation in the brain and (iii) promoting a beneficial immunomodulation via bidirectional communication with mDAns. Then, through resilience of Nrf2/Wnt/β-catenin anti-ageing, prosurvival and proregenerative molecular programs, it seems possible to boost the inherent endogenous self-repair mechanisms. Here, the cellular and molecular aspects as well as the therapeutical options for rejuvenating glia-neuron dialogue will be discussed together with major glial-derived mechanisms and therapies that will be fundamental to the identification of novel diagnostic tools and treatments for neurodegenerative diseases (NDs), to fight ageing and nigrostriatal DAergic degeneration and promote functional recovery.
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Affiliation(s)
- Bianca Marchetti
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Pharmacology Section, Medical School, University of Catania, Via S. Sofia 65, 95125, Catania, Italy; Oasi Research Institute-IRCCS, Neuropharmacology Section, Via Conte Ruggero 73, 94018, Troina, EN, Italy.
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25
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Ohnmacht J, May P, Sinkkonen L, Krüger R. Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. J Neural Transm (Vienna) 2020; 127:729-748. [PMID: 32248367 PMCID: PMC7242266 DOI: 10.1007/s00702-020-02184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder caused by a complex interplay of genetic and environmental factors. For the stratification of PD patients and the development of advanced clinical trials, including causative treatments, a better understanding of the underlying genetic architecture of PD is required. Despite substantial efforts, genome-wide association studies have not been able to explain most of the observed heritability. The majority of PD-associated genetic variants are located in non-coding regions of the genome. A systematic assessment of their functional role is hampered by our incomplete understanding of genotype–phenotype correlations, for example through differential regulation of gene expression. Here, the recent progress and remaining challenges for the elucidation of the role of non-coding genetic variants is reviewed with a focus on PD as a complex disease with multifactorial origins. The function of gene regulatory elements and the impact of non-coding variants on them, and the means to map these elements on a genome-wide level, will be delineated. Moreover, examples of how the integration of functional genomic annotations can serve to identify disease-associated pathways and to prioritize disease- and cell type-specific regulatory variants will be given. Finally, strategies for functional validation and considerations for suitable model systems are outlined. Together this emphasizes the contribution of rare and common genetic variants to the complex pathogenesis of PD and points to remaining challenges for the dissection of genetic complexity that may allow for better stratification, improved diagnostics and more targeted treatments for PD in the future.
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Affiliation(s)
- Jochen Ohnmacht
- LCSB, University of Luxembourg, Belvaux, Luxembourg.,Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- LCSB, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- LCSB, University of Luxembourg, Belvaux, Luxembourg. .,Luxembourg Institute of Health (LIH), Transversal Translational Medicine, Strassen, Luxembourg. .,Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
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26
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Yang X, Xu S, Qian Y, He X, Chen S, Xiao Q. Hypermethylation of the Gene Coding for PGC-1α in Peripheral Blood Leukocytes of Patients With Parkinson's Disease. Front Neurosci 2020; 14:97. [PMID: 32174806 PMCID: PMC7054441 DOI: 10.3389/fnins.2020.00097] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Decreased expression of peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) is implicated in the pathophysiology of Parkinson’s disease (PD). However, our understanding of the mechanism regulating the PGC-1α expression is still limited. We sought to determine whether the epigenetic modification of PPARGC1A (the gene encoding PGC-1α) could account for its diminished expression. We performed a study of PPARGC1A risk-SNP genotypes, methylation level, and the expression in blood from 171 subjects. The mean DNA methylation level of PPARGC1A intron 1 in patients with PD was higher than that in the controls (7.18 ± 1.74 vs. 6.36 ± 1.28, P = 0.007). A detailed comparison of the DNA methylation level at each CpG site showed that CpG_1, CpG_13.14, CpG_17.18, and CpG_20 were significantly hypermethylated in patients with PD. There was a significant negative correlation between PPARGC1A methylation and expression level (R = −0.404, P < 0.001). We found no correlations between the PPARGC1A methylation level and the clinical features, while the CpG_13.14 site methylation level was positively correlated with H&Y stage (R = 0.246, P = 0.020) and was increased in people carrying the rs2970848 AA genotype compared with that in carriers of the AG/GG genotype (7.27 ± 1.86 vs. 6.65 ± 1.92, P = 0.032). Our results support a link between PPARGC1A methylation, gene expression, and variability, which indicated that a novel epigenetic regulatory mechanism controlling PPARGC1A expression influences PD pathogenesis.
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Affiliation(s)
- Xiaodong Yang
- Department of Neurology, Ruijin Hospital Affiliated with the School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoqing Xu
- Department of Neurology, Ruijin Hospital Affiliated with the School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiwei Qian
- Department of Neurology, Ruijin Hospital Affiliated with the School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqin He
- Department of Neurology, Ruijin Hospital Affiliated with the School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shengdi Chen
- Department of Neurology, Ruijin Hospital Affiliated with the School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Xiao
- Department of Neurology, Ruijin Hospital Affiliated with the School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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