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Chu J, Li J, Sun L, Wei J. The Role of Cellular Defense Systems of Ferroptosis in Parkinson's Disease and Alzheimer's Disease. Int J Mol Sci 2023; 24:14108. [PMID: 37762411 PMCID: PMC10531775 DOI: 10.3390/ijms241814108] [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: 08/05/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Parkinson's disease (PD) and Alzheimer's disease (AD) are the most common rapidly developing neurodegenerative diseases that lead to serious health and socio-economic consequences. Ferroptosis is a non-apoptotic form of cell death; there is growing evidence to support the notion that ferroptosis is involved in a variety of pathophysiological contexts, and there is increasing interest in the role of ferroptosis in PD and AD. Simultaneously, cells may have evolved four defense systems to counteract the toxic effects of ferroptosis occasioned by lipid peroxidation. This review, which focuses on the analysis of ferroptosis in the PD and AD context, outlines four cellular defense systems against ferroptosis and how each of them is involved in PD and AD.
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Affiliation(s)
- Jie Chu
- School of Physical Education, Henan University, Kaifeng 475004, China; (J.C.); (J.L.)
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jingwen Li
- School of Physical Education, Henan University, Kaifeng 475004, China; (J.C.); (J.L.)
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Lin Sun
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
- College of Chemistry and Molecular Sciences, Henan University, Kaifeng 475004, China
| | - Jianshe Wei
- School of Physical Education, Henan University, Kaifeng 475004, China; (J.C.); (J.L.)
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
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2
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Xue J, Ding DX, Xu GY, Wang PZ, Ge YL, Zhang JR, Cheng XY, Wang YM, Jin H, Luo SY, Zheng YH, Chen J, Wang F, Li D, Mao CJ, Li K, Liu CF. A systematic analysis of genotype-phenotype associations with PLA2G6. Parkinsonism Relat Disord 2023; 112:105477. [PMID: 37285793 DOI: 10.1016/j.parkreldis.2023.105477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND PLA2G6-associated neurodegeneration (PLAN) can be categorized into infantile neuroaxonal dystrophy (INAD), atypical neuroaxonal dystrophy (aNAD), neurodegeneration with brain iron accumulation (NBIA), and early-onset parkinsonism (EOP). OBJECTIVES To determine the genotype-phenotype association in PLAN. METHODS "PLA2G6" or "PARK14" or "phospholipase A2 group VI" or "iPLA2β" were searched across MEDLINE from June 23, 1997, to March 1, 2023. A total of 391 patients were identified, and 340 patients of them were finally included in the assessment. RESULTS The loss of function (LOF) mutation ratios were significantly different (p < 0.001), highest in INAD, followed by NBIA, aNAD, and EOP. Four ensemble scores (i.e., BayesDel, VARITY, ClinPred, and MetaRNN) were assessed to predict the deleteriousness of missense mutations and demonstrated significant differences (p < 0.001). Binary logistic regression analyses demonstrated that LOF mutations were independently associated with brain iron accumulation (p = 0.006) and ataxia (p = 0.025). CONCLUSIONS LOF or more deleterious missense mutations are more likely to promote the development of serious phenotype of PLAN, and LOF mutations are independently associated with brain iron accumulation and ataxia.
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Affiliation(s)
- Jian Xue
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Dong-Xue Ding
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | - Pu-Zhi Wang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi-Lun Ge
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jin-Ru Zhang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiao-Yu Cheng
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi-Ming Wang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Jin
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | | | | | - Jing Chen
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Fen Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Dan Li
- Department of Neurology, Suqian First People's Hospital, Suqian, China
| | - Cheng-Jie Mao
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Kai Li
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China.
| | - Chun-Feng Liu
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China; Department of Neurology, Suqian First People's Hospital, Suqian, China.
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3
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Cronin SJF, Yu W, Hale A, Licht-Mayer S, Crabtree MJ, Korecka JA, Tretiakov EO, Sealey-Cardona M, Somlyay M, Onji M, An M, Fox JD, Turnes BL, Gomez-Diaz C, da Luz Scheffer D, Cikes D, Nagy V, Weidinger A, Wolf A, Reither H, Chabloz A, Kavirayani A, Rao S, Andrews N, Latremoliere A, Costigan M, Douglas G, Freitas FC, Pifl C, Walz R, Konrat R, Mahad DJ, Koslov AV, Latini A, Isacson O, Harkany T, Hallett PJ, Bagby S, Woolf CJ, Channon KM, Je HS, Penninger JM. Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539795. [PMID: 37214873 PMCID: PMC10197517 DOI: 10.1101/2023.05.08.539795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Dopa-responsive dystonia (DRD) and Parkinson's disease (PD) are movement disorders caused by the dysfunction of nigrostriatal dopaminergic neurons. Identifying druggable pathways and biomarkers for guiding therapies is crucial due to the debilitating nature of these disorders. Recent genetic studies have identified variants of GTP cyclohydrolase-1 (GCH1), the rate-limiting enzyme in tetrahydrobiopterin (BH4) synthesis, as causative for these movement disorders. Here, we show that genetic and pharmacological inhibition of BH4 synthesis in mice and human midbrain-like organoids accurately recapitulates motor, behavioral and biochemical characteristics of these human diseases, with severity of the phenotype correlating with extent of BH4 deficiency. We also show that BH4 deficiency increases sensitivities to several PD-related stressors in mice and PD human cells, resulting in worse behavioral and physiological outcomes. Conversely, genetic and pharmacological augmentation of BH4 protects mice from genetically- and chemically induced PD-related stressors. Importantly, increasing BH4 levels also protects primary cells from PD-affected individuals and human midbrain-like organoids (hMLOs) from these stressors. Mechanistically, BH4 not only serves as an essential cofactor for dopamine synthesis, but also independently regulates tyrosine hydroxylase levels, protects against ferroptosis, scavenges mitochondrial ROS, maintains neuronal excitability and promotes mitochondrial ATP production, thereby enhancing mitochondrial fitness and cellular respiration in multiple preclinical PD animal models, human dopaminergic midbrain-like organoids and primary cells from PD-affected individuals. Our findings pinpoint the BH4 pathway as a key metabolic program at the intersection of multiple protective mechanisms for the health and function of midbrain dopaminergic neurons, identifying it as a potential therapeutic target for PD.
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Affiliation(s)
- Shane J F Cronin
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Weonjin Yu
- Signature Program in Neuroscience and Behavioural Disorders, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ashley Hale
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Simon Licht-Mayer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Mark J Crabtree
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Joanna A Korecka
- Neurodegeneration Research Institute, Harvard Medical School/McLean Hospital, Belmont, MA, 02478, USA
| | - Evgenii O Tretiakov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Marco Sealey-Cardona
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Mate Somlyay
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Masahiro Onji
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Meilin An
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Jesse D Fox
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Bruna Lenfers Turnes
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Carlos Gomez-Diaz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Débora da Luz Scheffer
- LABOX, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, SC 88037-100, Brazil
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD); Department of Neurology, Medical University of Vienna (MUW), 1090 Vienna, Austria
| | - Adelheid Weidinger
- Ludwig Boltzmann Institute for Traumatology. The Research Center in Cooperation with AUVA, Donaueschingen Str. 13, 1200 Vienna, Austria
| | - Alexandra Wolf
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Harald Reither
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Antoine Chabloz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Anoop Kavirayani
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Shuan Rao
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Nick Andrews
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alban Latremoliere
- Neurosurgery Department, Neurosurgery Pain Research Institute, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Michael Costigan
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Gillian Douglas
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Christian Pifl
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Roger Walz
- Center for Applied Neurocience, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil; Neurology Division, Internal Medicine Department, University Hospital of UFSC, Florianópolis, Brazil
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Don J Mahad
- Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Andrey V Koslov
- Ludwig Boltzmann Institute for Traumatology. The Research Center in Cooperation with AUVA, Donaueschingen Str. 13, 1200 Vienna, Austria
| | - Alexandra Latini
- LABOX, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, SC 88037-100, Brazil
| | - Ole Isacson
- Neurodegeneration Research Institute, Harvard Medical School/McLean Hospital, Belmont, MA, 02478, USA
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Neuroscience, Biomedicum 7D, Karolinska Institute, Solna, Sweden
| | - Penelope J Hallett
- Neurodegeneration Research Institute, Harvard Medical School/McLean Hospital, Belmont, MA, 02478, USA
| | - Stefan Bagby
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Clifford J Woolf
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Keith M Channon
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Hyunsoo Shawn Je
- Signature Program in Neuroscience and Behavioural Disorders, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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4
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Tao N, Cheng B, Chai H, Cui X, Ma Y, Yan J, Zhao Y, Chen W. A Putative Guanosine Triphosphate Cyclohydrolase I Named CaGCH1 Is Involved in Hyphal Branching and Fruiting Development in Cyclocybe aegerita. Front Microbiol 2022; 13:870658. [PMID: 35535251 PMCID: PMC9076582 DOI: 10.3389/fmicb.2022.870658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) is the limiting enzyme of the tetrahydrobiopterin (BH4) synthesis pathway. The disruption of gch1 gene may cause conditional lethality due to folic acid auxotrophy in microorganisms, although the function of gch1 in basidiomycetes has not been deciphered so far. In the present study, gch1 expression in Cyclocybe aegerita (cagch1) was downregulated using the RNAi method, which resulted in growth retardation in both solid and liquid medium, with the hyphal tips exhibiting increased branching compared to that in the wild strain. The development of fruiting bodies in the mutant strains was significantly blocked, and there were short and bottle-shaped stipes. The transcriptional profile revealed that the genes of the MAPK pathway may be involved in the regulation of these effects caused by cagch1 knockdown, which provided an opportunity to study the role of gch1 in the development process of basidiomycetes.
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Affiliation(s)
- Nan Tao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China.,Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, China
| | - Bopu Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Hongmei Chai
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China.,Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, China
| | - Xianghua Cui
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China.,Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, China
| | - Yuanhao Ma
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China.,Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, China
| | - Jinping Yan
- Life Science and Technology College, Kunming University of Science and Technology, Kunming, China
| | - Yongchang Zhao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China.,Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, China
| | - Weimin Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China.,Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, China
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5
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Jian X, Zhao G, Chen H, Wang Y, Li J, Xie L, Li B. Revealing a novel contributing landscape of ferroptosis-related genes in Parkinson’s disease. Comput Struct Biotechnol J 2022; 20:5218-5225. [PMID: 36187920 PMCID: PMC9508518 DOI: 10.1016/j.csbj.2022.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/25/2022] Open
Abstract
Transcriptomics studies have yielded great insights into disease processes by detecting differentially expressed genes (DEGs). In this study, due to the high heritability of Parkinson’s disease (PD), we performed bioinformatics analyses on nine transcriptomic datasets regarding substantia nigra from Gene Expression Omnibus database, including seven microarray datasets and two next-generation sequencing datasets. As a result, between age-matched PD patients and normal control, we identified 630 DEGs, of which 22 hub DEGs involved in PD or ferroptosis were found to be associated with each other at the transcriptional level and protein-protein interaction network, suggesting their high correlations among these hub genes. Moreover, 16 DEGs were singled out due to their comparable AUC (>0.6) in random forest classifiers, including seven PD-related genes (MAP4K4, LRP10, UCHL1, PAM, RIT2, SNCA, GCH1) and nine ferroptosis-related genes (GCH1, DDIT4, RGS4, MAPK9, CAV1, RELA, DUSP1, ATP6V1G2, ATF4 and ISCU). Furthermore, to probe the potential of those hub genes in predicting the PD progression and survival, we constructed a Cox model featured by an eight-gene signature, including four PD-related genes (SNCA, UCHL1, LRP10, and GCH1) and four ferroptosis-related genes (DDIT4, RGS4, RELA, and CAV1), and validated it successful in an independent dataset, indicating that it would be an effective tool for clinical research to predict PD progression. In conclusion, ferroptosis-related DEGs identified in this study were closely correlated with the known PD-related genes, revealing the involvement of ferroptosis in the development of PD. This study presented the potential of several ferroptosis-related genes as novel clinical biomarkers for PD.
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6
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Jiang L, Mei JP, Zhao YW, Zhang R, Pan HX, Yang Y, Sun QY, Xu Q, Yan XX, Tan JQ, Li JC, Tang BS, Guo JF. Low-frequency and rare coding variants of NUS1 contribute to susceptibility and phenotype of Parkinson's disease. Neurobiol Aging 2021; 110:106-112. [PMID: 34635350 DOI: 10.1016/j.neurobiolaging.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 01/13/2023]
Abstract
NUS1 has been recently identified as a candidate gene for Parkinson's disease (PD). Few studies have examined the association of NUS1 variants with PD susceptibility and phenotypes. In the first cohort, whole-exome sequencing was performed to identify variants in NUS1 exon-coding and exon-intron regions in 1542 cases and 1625 controls. 13 variants were totally detected, of which 10 rare variants and 3 low-frequency variants. Burden analysis showed that rare NUS1 variants significantly enriched in PD (p=0.016). We also performed a meta-analysis based on previous and our studies to correlate NUS1 mutations with PD susceptibility. Integrating our previous cohort (3210 cases and 2807 controls) and the first cohort identified the significant association of rs539668656 with PD risk (odds ratio (OR) = 2.82, p = 0.016). The genotype-phenotype association analysis showed that patients carrying rare variants, or rs539668656 were significantly associated with earlier onset age, depression, emotional impairment and severe disease condition. Our results support the role of NUS1 rare variants and rs539668656 towards PD susceptibility and phenotype.
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Affiliation(s)
- Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun-Pu Mei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qi-Ying Sun
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie-Qiong Tan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jin-Chen Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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7
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Li B, Zhao G, Zhou Q, Xie Y, Wang Z, Fang Z, Lu B, Qin L, Zhao Y, Zhang R, Jiang L, Pan H, He Y, Wang X, Luo T, Zhang Y, Wang Y, Chen Q, Liu Z, Guo J, Tang B, Li J. Gene4PD: A Comprehensive Genetic Database of Parkinson's Disease. Front Neurosci 2021; 15:679568. [PMID: 33981200 PMCID: PMC8107430 DOI: 10.3389/fnins.2021.679568] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/07/2021] [Indexed: 01/02/2023] Open
Abstract
Parkinson’s disease (PD) is a complex neurodegenerative disorder with a strong genetic component. A growing number of variants and genes have been reported to be associated with PD; however, there is no database that integrate different type of genetic data, and support analyzing of PD-associated genes (PAGs). By systematic review and curation of multiple lines of public studies, we integrate multiple layers of genetic data (rare variants and copy-number variants identified from patients with PD, associated variants identified from genome-wide association studies, differentially expressed genes, and differential DNA methylation genes) and age at onset in PD. We integrated five layers of genetic data (8302 terms) with different levels of evidences from more than 3,000 studies and prioritized 124 PAGs with strong or suggestive evidences. These PAGs were identified to be significantly interacted with each other and formed an interconnected functional network enriched in several functional pathways involved in PD, suggesting these genes may contribute to the pathogenesis of PD. Furthermore, we identified 10 genes were associated with a juvenile-onset (age ≤ 30 years), 11 genes were associated with an early-onset (age of 30–50 years), whereas another 10 genes were associated with a late-onset (age > 50 years). Notably, the AAOs of patients with loss of function variants in five genes were significantly lower than that of patients with deleterious missense variants, while patients with VPS13C (P = 0.01) was opposite. Finally, we developed an online database named Gene4PD (http://genemed.tech/gene4pd) which integrated published genetic data in PD, the PAGs, and 63 popular genomic data sources, as well as an online pipeline for prioritize risk variants in PD. In conclusion, Gene4PD provides researchers and clinicians comprehensive genetic knowledge and analytic platform for PD, and would also improve the understanding of pathogenesis in PD.
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Affiliation(s)
- Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Mobile Health Ministry of Education-China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yali Xie
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenghuan Fang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Bin Lu
- Department of Pathogen Biology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lixia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yan He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaomeng Wang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Tengfei Luo
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yijing Wang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
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8
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Rudakou U, Yu E, Krohn L, Ruskey JA, Asayesh F, Dauvilliers Y, Spiegelman D, Greenbaum L, Fahn S, Waters CH, Dupré N, Rouleau GA, Hassin-Baer S, Fon EA, Alcalay RN, Gan-Or Z. Targeted sequencing of Parkinson's disease loci genes highlights SYT11, FGF20 and other associations. Brain 2021; 144:462-472. [PMID: 33349842 DOI: 10.1093/brain/awaa401] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/13/2020] [Accepted: 09/09/2020] [Indexed: 01/13/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous loci associated with Parkinson's disease. The specific genes and variants that drive the associations within the vast majority of these loci are unknown. We aimed to perform a comprehensive analysis of selected genes to determine the potential role of rare and common genetic variants within these loci. We fully sequenced 32 genes from 25 loci previously associated with Parkinson's disease in 2657 patients and 3647 controls from three cohorts. Capture was done using molecular inversion probes targeting the exons, exon-intron boundaries and untranslated regions (UTRs) of the genes of interest, followed by sequencing. Quality control was performed to include only high-quality variants. We examined the role of rare variants (minor allele frequency < 0.01) using optimized sequence Kernel association tests. The association of common variants was estimated using regression models adjusted for age, sex and ethnicity as required in each cohort, followed by a meta-analysis. After Bonferroni correction, we identified a burden of rare variants in SYT11, FGF20 and GCH1 associated with Parkinson's disease. Nominal associations were identified in 21 additional genes. Previous reports suggested that the SYT11 GWAS association is driven by variants in the nearby GBA gene. However, the association of SYT11 was mainly driven by a rare 3' UTR variant (rs945006601) and was independent of GBA variants (P = 5.23 × 10-5 after exclusion of all GBA variant carriers). The association of FGF20 was driven by a rare 5' UTR variant (rs1034608171) located in the promoter region. The previously reported association of GCH1 with Parkinson's disease is driven by rare non-synonymous variants, some of which are known to cause dopamine-responsive dystonia. We also identified two LRRK2 variants, p.Arg793Met and p.Gln1353Lys, in 10 and eight controls, respectively, but not in patients. We identified common variants associated with Parkinson's disease in MAPT, TMEM175, BST1, SNCA and GPNMB, which are all in strong linkage disequilibrium with known GWAS hits in their respective loci. A common coding PM20D1 variant, p.Ile149Val, was nominally associated with reduced risk of Parkinson's disease (odds ratio 0.73, 95% confidence interval 0.60-0.89, P = 1.161 × 10-3). This variant is not in linkage disequilibrium with the top GWAS hits within this locus and may represent a novel association. These results further demonstrate the importance of fine mapping of GWAS loci, and suggest that SYT11, FGF20, and potentially PM20D1, BST1 and GPNMB should be considered for future studies as possible Parkinson's disease-related genes.
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Affiliation(s)
- Uladzislau Rudakou
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1A1, Canada.,Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1A1, Canada.,Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1A1, Canada.,Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Jennifer A Ruskey
- Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Farnaz Asayesh
- Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Yves Dauvilliers
- National Reference Center for Narcolepsy, Sleep Unit, Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Inserm U1061, Montpellier, France
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Cheryl H Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Québec City, QC, G1V 0A6, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1A1, Canada.,Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Sharon Hassin-Baer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Neurology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Movement Disorders Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Edward A Fon
- Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 1A1, Canada
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1A1, Canada.,Montreal Neurological Institute, McGill University, Montréal, QC, H3A 1A1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 1A1, Canada
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9
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Li B, Zhao G, Li K, Wang Z, Fang Z, Wang X, Luo T, Zhang Y, Wang Y, Chen Q, Huang Y, Dong L, Guo J, Tang B, Li J. Characterizing the Expression Patterns of Parkinson's Disease Associated Genes. Front Neurosci 2021; 15:629156. [PMID: 33867917 PMCID: PMC8049291 DOI: 10.3389/fnins.2021.629156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/12/2021] [Indexed: 01/13/2023] Open
Abstract
Background The expression pattern represents a quantitative phenotype that provides an in-depth view of the molecular mechanism in Parkinson’s disease (PD); however, the expression patterns of PD-associated genes (PAGs) and their relation to age at onset (AAO) remain unclear. Methods The known PD-causing genes and PD-risk genes, which were collected from latest published authoritative meta-analysis, were integrated as PAGs. The expression data from Genotype-Tissue Expression database, Allen Brian Map database, and BrainSpan database, were extracted to characterize the tissue specificity, inhibitory-excitatory neuron expression profile, and spatio-temporal expression pattern of PAGs, respectively. The AAO information of PD-causing gene was download from Gene4PD and MDSgene database. Results We prioritized 107 PAGs and found that the PAGs were more likely to be expressed in brain-related tissues than non-brain tissues and that more PAGs had higher expression levels in excitatory neurons than inhibitory neurons. In addition, we identified two spatio-temporal expression modules of PAGs in human brain: the first module showed a higher expression level in the adult period than in the prenatal period, and the second module showed the opposite features. It showed that more PAGs belong to the first module that the second module. Furthermore, we found that the median AAO of patients with mutations in PD-causing genes of the first module was lower than that of the second module. Conclusion In conclusion, this study provided comprehensive landscape of expression patterns, AAO features and their relationship for the first time, improving the understanding of pathogenesis, and precision medicine in PD.
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Affiliation(s)
- Bin Li
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Mobile Health Ministry of Education-China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Guihu Zhao
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Kuokuo Li
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Zheng Wang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenghuan Fang
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Xiaomeng Wang
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Tengfei Luo
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Yi Zhang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yijing Wang
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qian Chen
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanfeng Huang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lijie Dong
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Beisha Tang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Jinchen Li
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
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10
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Varghaei P, Yoon G, Estiar MA, Veyron S, Leveille E, Dupré N, Trempe JF, Rouleau GA, Gan-Or Z. GCH1 mutations in hereditary spastic paraplegia. Clin Genet 2021; 100:51-58. [PMID: 33713342 DOI: 10.1111/cge.13955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 01/09/2023]
Abstract
GCH1 mutations have been associated with dopa-responsive dystonia (DRD), Parkinson's disease (PD) and tetrahydrobiopterin (BH4 )-deficient hyperphenylalaninemia B. Recently, GCH1 mutations have been reported in five patients with hereditary spastic paraplegia (HSP). Here, we analyzed a total of 400 HSP patients (291 families) from different centers across Canada by whole exome sequencing (WES). Three patients with heterozygous GCH1 variants were identified: monozygotic twins with a p.(Ser77_Leu82del) variant, and a patient with a p.(Val205Glu) variant. The former variant is predicted to be likely pathogenic and the latter is pathogenic. The three patients presented with childhood-onset lower limb spasticity, hyperreflexia and abnormal plantar responses. One of the patients had diurnal fluctuations, and none had parkinsonism or dystonia. Phenotypic differences between the monozygotic twins were observed, who responded well to levodopa treatment. Pathway enrichment analysis suggested that GCH1 shares processes and pathways with other HSP-associated genes, and structural analysis of the variants indicated a disruptive effect. In conclusion, GCH1 mutations may cause HSP; therefore, we suggest a levodopa trial in HSP patients and including GCH1 in the screening panels of HSP genes. Clinical differences between monozygotic twins suggest that environmental factors, epigenetics, and stochasticity could play a role in the clinical presentation.
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Affiliation(s)
- Parizad Varghaei
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Grace Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada
| | - Mehrdad A Estiar
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Simon Veyron
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montréal, Canada
| | - Etienne Leveille
- Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Nicolas Dupré
- Axe Neurosciences, CHU de Québec-Université Laval, Quebec City, Québec, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montréal, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Ziv Gan-Or
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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11
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Jiang L, Pan HX, Zhao YW, Zeng Q, Liu ZH, Sun QY, Xu Q, Tan JQ, Yan XX, Li JC, Tang BS, Guo JF. Contribution of coding/non-coding variants in NUS1 to late-onset sporadic Parkinson's disease. Parkinsonism Relat Disord 2021; 84:29-34. [PMID: 33548880 DOI: 10.1016/j.parkreldis.2021.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022]
Abstract
INTRODUCTION A recent study reported that rare variants in NUS1 were associated with Parkinson's disease (PD). We aimed to assess the relative contribution of rare and common coding/non-coding variants of NUS1 to late-onset PD patients (LOPD). METHODS Whole genome sequencing data were analyzed for target NUS1 regions, derived from a cohort of 1962 cases and 1279 controls. The genetic association analyses were performed using logistic regression analysis and Sequence Kernel association test. Expression quantitative trait loci (eQTL) analysis was conducted to further explore the association of variants with NUS1 expression based on the data from GTEx database. RESULTS We identified 18 rare coding variants. p.Y131C was first identified in LOPD. However, no significant burden of rare NUS1 coding variants in LOPD was found. The rare variant sets of two regulatory elements (GH06J117605 and GH06J117674) were significantly enriched in LOPD even after Bonferroni correction (adjusted P = 0.013; adjusted P = 0.010). Considering the joint effect of rare and common variants, all variant sets within GH06J117605 and GH06J117674 showed association with LOPD but were no longer significant after Bonferroni correction. None of the common variants within coding/non-coding regions were significant after Bonferroni correction. The eQTL results suggested these variants in GH06J117605 and GH06J117674 could potentially have eQTL effects on the brain tissues. CONCLUSIONS These findings provide novel insight into the role of NUS1 regulatory regions in the development of LOPD and indicate that the variants in regulatory elements of NUS1 may be associated with LOPD by influencing the gene expression level.
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Affiliation(s)
- Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Zhen-Hua Liu
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Qi-Ying Sun
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Jie-Qiong Tan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410008, Changsha, Hunan, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Jin-Chen Li
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410008, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410008, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410008, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China.
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12
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Zhao Y, Qin L, Pan H, Liu Z, Jiang L, He Y, Zeng Q, Zhou X, Zhou X, Zhou Y, Fang Z, Wang Z, Xiang Y, Yang H, Wang Y, Zhang K, Zhang R, He R, Zhou X, Zhou Z, Yang N, Liang D, Chen J, Zhang X, Zhou Y, Liu H, Deng P, Xu K, Xu K, Zhou C, Zhong J, Xu Q, Sun Q, Li B, Zhao G, Wang T, Chen L, Shang H, Liu W, Chan P, Xue Z, Wang Q, Guo L, Wang X, Xu C, Zhang Z, Chen T, Lei L, Zhang H, Wang C, Tan J, Yan X, Shen L, Jiang H, Zhang Z, Hu Z, Xia K, Yue Z, Li J, Guo J, Tang B. The role of genetics in Parkinson's disease: a large cohort study in Chinese mainland population. Brain 2020; 143:2220-2234. [PMID: 32613234 DOI: 10.1093/brain/awaa167] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/19/2020] [Accepted: 04/06/2020] [Indexed: 02/05/2023] Open
Abstract
This study aimed to determine the mutational spectrum of familial Parkinson's disease and sporadic early-onset Parkinson's disease (sEOPD) in a mainland Chinese population and the clinical features of mutation carriers. We performed multiplex ligation-dependent probe amplification assays and whole-exome sequencing for 1676 unrelated patients with Parkinson's disease in a mainland Chinese population, including 192 probands from families with autosomal-recessive Parkinson's disease, 242 probands from families with autosomal-dominant Parkinson's disease, and 1242 sEOPD patients (age at onset ≤ 50). According to standards and guidelines from the American College of Medical Genetics and Genomics, pathogenic/likely pathogenic variants in 23 known Parkinson's disease-associated genes occurred more frequently in the autosomal-recessive Parkinson's disease cohort (65 of 192, 33.85%) than in the autosomal-dominant Parkinson's disease cohort (10 of 242, 4.13%) and the sEOPD cohort (57 of 1242, 4.59%), which leads to an overall molecular diagnostic yield of 7.88% (132 of 1676). We found that PRKN was the most frequently mutated gene (n = 83, 4.95%) and present the first evidence of an SNCA duplication and LRRK2 p.N1437D variant in mainland China. In addition, several novel pathogenic/likely pathogenic variants including LRRK2 (p.V1447M and p.Y1645S), ATP13A2 (p.R735X and p.A819D), FBXO7 (p.G67E), LRP10 (c.322dupC/p.G109Rfs*51) and TMEM230 (c.429delT/p.P144Qfs*2) were identified in our cohort. Furthermore, the age at onset of the 132 probands with genetic diagnoses (median, 31.5 years) was about 14.5 years earlier than that of patients without molecular diagnoses (i.e. non-carriers, median 46.0 years). Specifically, the age at onset of Parkinson's disease patients with pathogenic/likely pathogenic variants in ATP13A2, PLA2G6, PRKN, or PINK1 was significantly lower than that of non-carriers, while the age at onset of carriers with other gene pathogenic/likely pathogenic variants was similar to that of non-carriers. The clinical spectrum of Parkinson's disease-associated gene carriers in this mainland Chinese population was similar to that of other populations. We also detected 61 probands with GBA possibly pathogenic variants (3.64%) and 59 probands with GBA p.L444P (3.52%). These results shed insight into the genetic spectrum and clinical manifestations of Parkinson's disease in mainland China and expand the existing repertoire of pathogenic or likely pathogenic variants involved in known Parkinson's disease-associated genes. Our data highlight the importance of genetic testing in Parkinson's disease patients with age at onset < 40 years, especially in those from families with a recessive inheritance pattern, who may benefit from early diagnosis and treatment.
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Affiliation(s)
- Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lixia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yan He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xun Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaoxia Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yangjie Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenghuan Fang
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yaqin Xiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Honglan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kailin Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Runcheng He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaoting Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhou Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Nannan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Dongxiao Liang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Juan Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xuxiang Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yao Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hongli Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Penghui Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ke Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Chaojun Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Junfei Zhong
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qiying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tao Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Ling Chen
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Huifang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Weiguo Liu
- Department of Neurology, Affiliated Brain Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Piu Chan
- Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China.,Parkinson's Disease Center, Beijing Institute for Brain Disorders, Beijing 100101, China
| | - Zheng Xue
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Qing Wang
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong 510282, China
| | - Li Guo
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, China
| | - Xuejing Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450047, China
| | - Changshui Xu
- Department of Neurology, Henan provincial people's hospital, Zhengzhou, Henan 450003, China
| | - Zhentao Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Tao Chen
- Department of Neurology, Hainan General Hospital, Haikou, Hainan 570311, China
| | - Lifang Lei
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Hainan Zhang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Chunyu Wang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jieqiong Tan
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Xinxiang Yan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuohua Zhang
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Zhengmao Hu
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jinchen Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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13
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Pan HX, Zhao YW, Mei JP, Fang ZH, Wang Y, Zhou X, Zhou YJ, Zhang R, Zhang KL, Jiang L, Zeng Q, He Y, Wang Z, Liu ZH, Xu Q, Sun QY, Yang Y, Hu YC, Chen YS, Du J, Lei LF, Zhang HN, Wang CY, Yan XX, Shen L, Jiang H, Tan JQ, Li JC, Tang BS, Guo JF. GCH1 variants contribute to the risk and earlier age-at-onset of Parkinson's disease: a two-cohort case-control study. Transl Neurodegener 2020; 9:31. [PMID: 32746945 PMCID: PMC7401216 DOI: 10.1186/s40035-020-00212-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/21/2020] [Indexed: 12/26/2022] Open
Abstract
Background Common and rare variants of guanosine triphosphate cyclohydrolase 1 (GCH1) gene may play important roles in Parkinson’s disease (PD). However, there is a lack of comprehensive analysis of GCH1 genotypes, especially in non-coding regions. The aim of this study was to explore the genetic characteristics of GCH1, including rare and common variants in coding and non-coding regions, in a large population of PD patients in Chinese mainland, as well as the phenotypic characteristics of GCH1 variant carriers. Methods In the first cohort of this case-control study, we performed whole-exome sequencing in 1555 patients with early-onset or familial PD and 2234 healthy controls; then in the second cohort, whole-genome sequencing was performed in sporadic late-onset PD samples (1962 patients), as well as 1279 controls. Variants at target GCH1 regions were extracted, and then genetic and detailed phenotypic data were analyzed using regression models and the sequence kernel association test. We also performed a meta-analysis to correlate deleterious GCH1 variants with age at onset (AAO) in PD patients. Results For coding variants, we identified a significant burden of GCH1 deleterious variants in early-onset or familial PD cases compared to controls (1.2% vs 0.1%, P < 0.0001). In the analysis of possible regulatory variants in GCH1 non-coding regions, rs12323905 (P = 0.001, odds ratio = 1.19, 95%CI 1.07–1.32) was significantly associated with PD, and variant sets in untranslated regions and intron regions, GCH1 brain-specific expression quantitative trait loci, and two possible promoter/enhancer (GH14J054857 and GH14J054880) were suggestively associated with PD. Genotype-phenotype correlation analysis revealed that the carriers of GCH1 deleterious variants manifested younger AAO (P < 0.0001), and had milder motor symptoms, milder fatigue symptoms and more autonomic nervous dysfunctions. Meta-analysis of six studies demonstrated 6.4-year earlier onset in GCH1 deleterious variant carriers (P = 0.0009). Conclusions The results highlight the importance of deleterious variants and non-coding variants of GCH1 in PD in Chinese mainland and suggest that GCH1 mutation can influence the PD phenotype, which may help design experimental studies to elucidate the mechanisms of GCH1 in the pathogenesis of PD.
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Affiliation(s)
- Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Jun-Pu Mei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zheng-Huan Fang
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Xun Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yang-Jie Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Kai-Lin Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yan He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zheng Wang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhen-Hua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qi-Ying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yang Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ya-Cen Hu
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ya-Se Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Juan Du
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Li-Fang Lei
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Hai-Nan Zhang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Chun-Yu Wang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
| | - Jie-Qiong Tan
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China
| | - Jin-Chen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China. .,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China.
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China. .,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China.
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14
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Genetic analysis of N6-methyladenosine modification genes in Parkinson's disease. Neurobiol Aging 2020; 93:143.e9-143.e13. [PMID: 32371107 DOI: 10.1016/j.neurobiolaging.2020.03.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/23/2020] [Accepted: 03/29/2020] [Indexed: 02/06/2023]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease with a relatively unclear etiology. Previous studies have shown that N6-methyladenosine (m6A) is a vital RNA modification enriched in brain tissue, and that the genes involved in m6A modification are implicated in various neurologic diseases. Here, we conducted a comprehensive genetic analysis using targeted sequencing with molecular inversion probes (MIPs) to identify m6A-modification genes (including METTL3, METTL14, WTAP, FTO, ALKBH5, YTHDF1, YTHDF2, YTHDF3, HNRNPC, and ELAVL1) in a total of 1647 sporadic PD patients and 1372 controls of Han Chinese origin. PD patients were divided into early-onset PD (EOPD) and late-onset PD (LOPD) based on whether the onset of motor symptoms occurred before or after 50 years of age. Rare variants were subjected to gene-based burden tests and common variants were subjected to single-variant association analyses. As a result, we identified 214 rare variants in all 10 m6A-modification genes and 16 common variants in 7 genes. Gene-wise association analyses of rare variants in each m6A-modification gene did not achieved a p value of less than 0.05 in either total cohorts or 2 age groups. In fact, p values greater than 0.05 were found when conducting single-variant association analyses on common variants of these genes between PD and control patients. Our comprehensive analyses of m6A-modification genes suggest that there is no significant association between these 10 m6A-modification genes and the risk of sporadic PD.
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15
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Zolotareva O, Kleine M. A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2018-0069/jib-2018-0069.xml. [PMID: 31494632 PMCID: PMC7074139 DOI: 10.1515/jib-2018-0069] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/12/2019] [Indexed: 12/16/2022] Open
Abstract
Modern high-throughput experiments provide us with numerous potential associations between genes and diseases. Experimental validation of all the discovered associations, let alone all the possible interactions between them, is time-consuming and expensive. To facilitate the discovery of causative genes, various approaches for prioritization of genes according to their relevance for a given disease have been developed. In this article, we explain the gene prioritization problem and provide an overview of computational tools for gene prioritization. Among about a hundred of published gene prioritization tools, we select and briefly describe 14 most up-to-date and user-friendly. Also, we discuss the advantages and disadvantages of existing tools, challenges of their validation, and the directions for future research.
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Affiliation(s)
- Olga Zolotareva
- Bielefeld University, Faculty of Technology and Center for Biotechnology, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Universitätsstraße 25, Bielefeld, Germany
| | - Maren Kleine
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Universitätsstraße 25, Bielefeld, Germany
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16
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Shu L, Qin L, Min S, Pan H, Zhong J, Guo J, Sun Q, Yan X, Chen C, Tang B, Xu Q. Genetic analysis of DNA methylation and hydroxymethylation genes in Parkinson's disease. Neurobiol Aging 2019; 84:242.e13-242.e16. [PMID: 30948140 DOI: 10.1016/j.neurobiolaging.2019.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/04/2019] [Accepted: 02/27/2019] [Indexed: 01/15/2023]
Abstract
DNA methylation is an important regulatory mechanism of Parkinson's disease (PD). To investigate the relationship between DNA methylation and hydroxymethylation genes and PD, we performed gene-targeted sequencing using molecular inversion probes in a Chinese PD population. We sequenced 12 genes related to DNA methylation and hydroxymethylation in 1657 patients and 1394 control subjects. We conducted genewise association analyses of rare variants detected in the present study and identified the TET1 gene as important in PD (p = 0.0037738, 0.013, 0.019521 (b.collapse test, variable threshold test, and skat-o test, respectively; sex + age as covariates). However, no positive results were observed when conducting association analyses on common variants in these genes. We performed a comprehensive analysis of associations between variants of DNA methylation and hydroxymethylation genes and PD, resulting in determination that TET1 might play a role in PD.
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Affiliation(s)
- Li Shu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lixia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shishi Min
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Junfei Zhong
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Parkinson's Disease Center of Beijing Institute for Brain Disorders, Beijing, China; Collaborative Innovation Center for Brain Science, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Shanghai, China
| | - Qiying Sun
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Chao Chen
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Parkinson's Disease Center of Beijing Institute for Brain Disorders, Beijing, China; Collaborative Innovation Center for Brain Science, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Shanghai, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China.
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17
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Trinh J, Lohmann K, Baumann H, Balck A, Borsche M, Brüggemann N, Dure L, Dean M, Volkmann J, Tunc S, Prasuhn J, Pawlack H, Imhoff S, Lill CM, Kasten M, Bauer P, Rolfs A, Klein C. Utility and implications of exome sequencing in early‐onset Parkinson's disease. Mov Disord 2018; 34:133-137. [DOI: 10.1002/mds.27559] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Joanne Trinh
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Katja Lohmann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Hauke Baumann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Alexander Balck
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Max Borsche
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Leon Dure
- Department of Neurology University of Alabama at Birmingham Birmingham Alabama USA
| | - Marissa Dean
- Department of Neurology University of Alabama at Birmingham Birmingham Alabama USA
| | - Jens Volkmann
- Departement of Neurology Universitatsklinikum Würzburg Würzburg Germany
| | - Sinem Tunc
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Jannik Prasuhn
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Heike Pawlack
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Sophie Imhoff
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | | | - Meike Kasten
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Psychiatry University of Lübeck Lübeck Germany
| | - Peter Bauer
- Centogene AG, Institute for Rare Diseases Rostock Germany
| | - Arndt Rolfs
- Centogene AG, Institute for Rare Diseases Rostock Germany
- Albrecht Kossel Institute for Neuroregeneration University Hospital Rostock Rostock Germany
| | - Christine Klein
- Institute of Neurogenetics University of Lübeck Lübeck Germany
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18
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Rudakou U, Ouled Amar Bencheikh B, Ruskey JA, Krohn L, Laurent SB, Spiegelman D, Liong C, Fahn S, Waters C, Monchi O, Fon EA, Dauvilliers Y, Alcalay RN, Dupré N, Gan-Or Z. Common and rare GCH1 variants are associated with Parkinson's disease. Neurobiol Aging 2018; 73:231.e1-231.e6. [PMID: 30314816 DOI: 10.1016/j.neurobiolaging.2018.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 01/19/2023]
Abstract
GCH1 encodes the enzyme guanosine triphospahte (GTP) cyclohydrolase 1, essential for dopamine synthesis in nigrostriatal cells, and rare mutations in GCH1 may lead to Dopa-responsive dystonia (DRD). While GCH1 is implicated in genomewide association studies in Parkinson's disease (PD), only a few studies examined the role of rare GCH1 variants in PD, with conflicting results. In the present study, GCH1 and its 5' and 3' untranslated regions were sequenced in 1113 patients with PD and 1111 controls. To examine the association of rare GCH1 variants with PD, burden analysis was performed. Three rare GCH1 variants, which were previously reported to be pathogenic in DRD, were found in five patients with PD and not in controls (sequence Kernel association test, p = 0.024). A common haplotype, tagged by rs841, was associated with a reduced risk for PD (OR = 0.71, 95% CI = 0.61-0.83, p = 1.24 × 10-4), and with increased GCH1 expression in brain regions relevant for PD (www.gtexportal.org). Our results support a role for rare, DRD-related variants, and common GCH1 variants in the pathogenesis of PD.
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Affiliation(s)
- Uladzislau Rudakou
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Bouchra Ouled Amar Bencheikh
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Centre de Recherche, Centre Hospitalier de l'Universite de Montreal, Montreal, Quebec, Canada
| | - Jennifer A Ruskey
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Sandra B Laurent
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Christopher Liong
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Cheryl Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Oury Monchi
- Department of Clinical Neurosciences and Department of Radiology, University of Calgary, Calgary, Alberta, Canada; Cumming School of Medicine, Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Edward A Fon
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Yves Dauvilliers
- National Reference Center for Narcolepsy, Sleep Unit, Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Inserm U1061, Montpellier, France
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Québec City, Quebec, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Québec City, Quebec, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada.
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