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Tran J, Anastacio H, Bardy C. Genetic predispositions of Parkinson's disease revealed in patient-derived brain cells. NPJ Parkinsons Dis 2020; 6:8. [PMID: 32352027 DOI: 10.1038/s41531-020-0110-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
Parkinson's disease (PD) is the second most prevalent neurological disorder and has been the focus of intense investigations to understand its etiology and progression, but it still lacks a cure. Modeling diseases of the central nervous system in vitro with human induced pluripotent stem cells (hiPSC) is still in its infancy but has the potential to expedite the discovery and validation of new treatments. Here, we discuss the interplay between genetic predispositions and midbrain neuronal impairments in people living with PD. We first summarize the prevalence of causal Parkinson's genes and risk factors reported in 74 epidemiological and genomic studies. We then present a meta-analysis of 385 hiPSC-derived neuronal lines from 67 recent independent original research articles, which point towards specific impairments in neurons from Parkinson's patients, within the context of genetic predispositions. Despite the heterogeneous nature of the disease, current iPSC models reveal converging molecular pathways underlying neurodegeneration in a range of familial and sporadic forms of Parkinson's disease. Altogether, consolidating our understanding of robust cellular phenotypes across genetic cohorts of Parkinson's patients may guide future personalized drug screens in preclinical research.
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Han CL, Liu YP, Sui YP, Chen N, Du TT, Jiang Y, Guo CJ, Wang KL, Wang Q, Fan SY, Shimabukuro M, Meng FG, Yuan F, Zhang JG. Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson's disease. Aging (Albany NY) 2020; 12:718-739. [PMID: 31929116 PMCID: PMC6977703 DOI: 10.18632/aging.102652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/24/2019] [Indexed: 01/08/2023]
Abstract
Levodopa-induced dyskinesia (LID) is a common complication of chronic dopamine replacement therapy in the treatment of Parkinson's disease (PD). Long noncoding RNAs regulate gene expression and participate in many biological processes. However, the role of long noncoding RNAs in LID is not well understood. In the present study, we examined the lncRNA transcriptome profile of a rat model of PD and LID by RNA sequence and got a subset of lncRNAs, which were gradually decreased during the development of PD and LID. We further identified a previously uncharacterized long noncoding RNA, NONRATT023402.2, and its target genes glutathione S-transferase omega (Gsto)2 and prostaglandin E receptor (Ptger)3. All of them were decreased in the PD and LID rats as shown by quantitative real-time PCR, fluorescence in situ hybridization and western blotting. Pearson's correlation analysis showed that their expression was positively correlated with the dyskinesia score of LID rats. In vitro experiments by small interfering RNA confirmed that slicing NONRATT023402 inhibited Gsto2 and Ptger3 and promoted the inflammatory response. These results demonstrate that NONRATT023402.2 may have inhibitive effects on the development of PD and LID.
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Affiliation(s)
- Chun-Lei Han
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yun-Peng Liu
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Yun-Peng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Ning Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ting-Ting Du
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Ying Jiang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Chen-Jia Guo
- Department of Pathology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Kai-Liang Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Qiao Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Shi-Ying Fan
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Michitomo Shimabukuro
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Fan-Gang Meng
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fang Yuan
- Department of Pathophysiology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jian-Guo Zhang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Chi LM, Wang LP, Jiao D. Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson's Disease. Parkinsons Dis 2019; 2019:6078251. [PMID: 30867898 DOI: 10.1155/2019/6078251] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 12/06/2018] [Indexed: 12/28/2022]
Abstract
Objectives This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson's disease (PD) using a microarray. Methods We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. We selected 72 samples comprising 22 healthy control blood samples and 50 PD blood samples for further analysis. Later, we used Limma to screen DEGs and differentially expressed lncRNAs (DElncRNAs) and estimated their functions by the Gene Ontology (GO). Besides, the competing endogenous RNA (ceRNA) network, including microRNAs, lncRNAs, and mRNAs, was constructed to elucidate the regulatory mechanism. Furthermore, we performed the KEGG pathway enrichment with mRNAs in the ceRNA regulatory network and constructed a final network, including pathways, mRNAs, microRNAs, and lncRNAs. Results Overall, we obtained 394 DEGs, including 207 upregulated DEGs and 187 downregulated DEGs, and 7 DElncRNAs, including 2 upregulated DElncRNAs and 5 downregulated DElncRNAs. Insulin-like growth factor-1 receptor (IGF1R) was considerably enriched in the endocytosis pathway. In the ceRNA regulation network, IGF1R was the target of hsa-miR-133b and lncRNAs of XIST, and PART1 could also be the target of hsa-miR-133b. While the upregulated DEGs were enriched in the GO terms of the cytoskeleton, cytoskeletal part, and microtubule cytoskeleton, the downregulated DEGs were enriched in the immune response. PRKACA was markedly enriched in numerous pathways, including the MAPK and insulin signaling pathways. Conclusions IGF1R, PRKACA, and lncRNA-XIST could be potentially involved in PD, and these diverse molecular mechanisms could support the development of the similar treatment for PD.
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Book A, Guella I, Candido T, Brice A, Hattori N, Jeon B, Farrer MJ. A Meta-Analysis of α-Synuclein Multiplication in Familial Parkinsonism. Front Neurol 2018; 9:1021. [PMID: 30619023 PMCID: PMC6297377 DOI: 10.3389/fneur.2018.01021] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/13/2018] [Indexed: 11/18/2022] Open
Abstract
Chronic alpha-synuclein (SNCA) overexpression is a relatively homogenous and well-defined cause of parkinsonism and dementia. Parkinson's disease (PD), PD with dementia, dementia with Lewy bodies and multiple system atrophy all manifest in SNCA multiplication families. Herein we summarize genealogic, clinical and genetic data from 59 families (25 not previously published) with parkinsonism caused by SNCA multiplications. Longitudinal clinical assessments and genealogic relationships were documented for all family members. All probands were genotyped with an Illumina MEGA high-density genotyping array to identify copy number variants (CNV) and enable SNCA multiplication breakpoints to be defined. Three SNCA short tandem repeat (STR) markers were genotyped in all available samples to validate genomic dosage and inheritance. A web-application was built as a forum for future data sharing. CNV analysis identified 49 subjects with heterozygous SNCA duplication (CNV3), 2 with homozygous duplication (CNV4) and 7 with a triplication mutation (CNV4). Clinical presentations varied greatly throughout the cohort. SNCA dosage correlates with disease onset (mean age of onset CNV3: 46.9 ± 10.5 years vs. 34.5 ± 7.4 CNV4, p = 0.003). Atypical or more severe clinical courses were described in several patients and dementia was noted in 50.9% of the probands. Neither the multiplication size (average 2.05 ± 2.45 Mb) nor the number of genes included (range 1-50) was associated with motor symptom onset or dementia. Families with SNCA multiplication are rare and globally-distributed. Nevertheless, they may both inform and benefit from the development of SNCA targeted therapeutic strategies relevant to the treatment of all alpha-synucleinopathies.
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Affiliation(s)
- Adam Book
- Department of Medical Genetics, Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada
| | - Ilaria Guella
- Department of Medical Genetics, Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada
| | - Tara Candido
- Department of Medical Genetics, Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada
| | - Alexis Brice
- Sorbonne Universités, Université Pierre-et-Marie Curie (UPMC) Paris, UM 1127, Institut du Cerveau et de la Moelle Epinière (ICM) and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Beomseok Jeon
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Matthew J. Farrer
- Department of Medical Genetics, Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada
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Wallen ZD, Chen H, Hill-Burns EM, Factor SA, Zabetian CP, Payami H. Plasticity-related gene 3 ( LPPR1) and age at diagnosis of Parkinson disease. Neurol Genet 2018; 4:e271. [PMID: 30338293 PMCID: PMC6186025 DOI: 10.1212/nxg.0000000000000271] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022]
Abstract
Objective To identify modifiers of age at diagnosis of Parkinson disease (PD). Methods Genome-wide association study (GWAS) included 1,950 individuals with PD from the NeuroGenetics Research Consortium (NGRC) study. Replication was conducted in the Parkinson's, Genes and Environment study, including 209 prevalent (PAGEP) and 517 incident (PAGEI) PD cases. Cox regression was used to test association with age at diagnosis. Individuals without neurologic disease were used to rule out confounding. Gene-level analysis and functional annotation were conducted using Functional Mapping and Annotation of GWAS platform (FUMA). Results The GWAS revealed 2 linked but seemingly independent association signals that mapped to LPPR1 on chromosome 9. LPPR1 was significant in gene-based analysis (p = 1E-8). The top signal (rs17763929, hazard ratio [HR] = 1.88, p = 5E-8) replicated in PAGEP (HR = 1.87, p = 0.01) but not in PAGEI. The second signal (rs73656147) was robust with no evidence of heterogeneity (HR = 1.95, p = 3E-6 in NGRC; HR = 2.14, p = 1E-3 in PAGEP + PAGEI, and HR = 2.00, p = 9E-9 in meta-analysis of NGRC + PAGEP + PAGEI). The associations were with age at diagnosis, not confounded by age in patients or in the general population. The PD-associated regions included variants with Combined Annotation Dependent Depletion (CADD) scores = 10–19 (top 1%–10% most deleterious mutations in the genome), a missense with predicted destabilizing effect on LPPR1, an expression quantitative trait locus (eQTL) for GRIN3A (false discovery rate [FDR] = 4E-4), and variants that overlap with enhancers in LPPR1 and interact with promoters of LPPR1 and 9 other brain-expressed genes (Hi-C FDR < 1E-6). Conclusions Through association with age at diagnosis, we uncovered LPPR1 as a modifier gene for PD. LPPR1 expression promotes neuronal regeneration after injury in animal models. Present data provide a strong foundation for mechanistic studies to test LPPR1 as a driver of response to damage and a therapeutic target for enhancing neuroregeneration and slowing disease progression.
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Affiliation(s)
- Zachary D Wallen
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Honglei Chen
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Erin M Hill-Burns
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Stewart A Factor
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Cyrus P Zabetian
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Haydeh Payami
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
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Li J, Sun Y, Chen J. Identification of Critical Genes and miRNAs Associated with the Development of Parkinson's Disease. J Mol Neurosci 2018; 65:527-535. [PMID: 30083784 DOI: 10.1007/s12031-018-1129-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/18/2018] [Indexed: 01/18/2023]
Abstract
The purpose of this study was to explore the key mechanism involved in the pathogenesis of Parkinson's disease (PD) based on microarray analysis. The expression profile data of GSE7621, which contained 9 substantia nigra tissues isolated from normals and 16 substantia nigra tissues isolated from PD patients, was obtained from Gene Expression Omnibus. The differentially expressed genes (DEGs) were screened, followed by functional enrichment analysis and protein-protein interaction (PPI) network construction. After the miRNAs regulating the DEGs were predicted, the miRNA-DEG regulatory network was then constructed. Besides, the 6-hydroxydopamine rat model of PD was established and the expression of key DEGs and miRNA was detected. A total of 388 DEGs were identified, including 218 upregulated genes and 170 downregulated ones. Tyrosine hydroxylase (TH) and solute carrier family 6 member 3 (SLC6A3) were significantly related to the functional terms of catecholamine biosynthetic process and dopamine biosynthetic process. TH and SLC6A3 were hub nodes in the PPI network. EBF3 could be targeted by miR-218. Moreover, TH and SLC6A3 were found downregulated in the 6-OHDA rat model of PD, while miR-218 was markedly upregulated. Our results reveal that SLC6A3, TH, and EBF3 targeted by miR-218 could be involved in PD. These molecules might provide a new insight into the development of therapeutic strategies for PD.
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Affiliation(s)
- Jia Li
- Department of Neurology, China-Japan Union Hospital of Jilin University, Xiantai Road, Erdao District, Changchun, 130033, Jilin, China
| | - Yajuan Sun
- Department of Neurology, China-Japan Union Hospital of Jilin University, Xiantai Road, Erdao District, Changchun, 130033, Jilin, China
| | - Jiajun Chen
- Department of Neurology, China-Japan Union Hospital of Jilin University, Xiantai Road, Erdao District, Changchun, 130033, Jilin, China.
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He YC, Huang P, Li QQ, Sun Q, Li DH, Wang T, Shen JY, Du JJ, Cui SS, Gao C, Fu R, Chen SD. Mutation Analysis of HTRA2 Gene in Chinese Familial Essential Tremor and Familial Parkinson's Disease. Parkinsons Dis 2017; 2017:3217474. [PMID: 28243480 DOI: 10.1155/2017/3217474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/16/2016] [Accepted: 12/26/2016] [Indexed: 12/23/2022]
Abstract
Background. HTRA2 has already been nominated as PARK13 which may cause Parkinson's disease, though there are still discrepancies among these results. Recently, Gulsuner et al.'s study found that HTRA2 p.G399S is responsible for hereditary essential tremor and homozygotes of this allele develop Parkinson's disease by examining a six-generation family segregating essential tremor and essential tremor coexisting with Parkinson's disease. We performed this study to validate the condition of HTRA2 gene in Chinese familial essential tremor and familial Parkinson's disease patients, especially essential tremor. Methods. We directly sequenced all eight exons, exon-intron boundaries, and part of the introns in 101 familial essential tremor patients, 105 familial Parkinson's disease patients, and 100 healthy controls. Results. No exonic variant was identified, while one exon-intron boundary variant (rs2241028) and one intron variant (rs2241027) were detected, both with no clinical significance and uncertain function. There was no difference in allele, genotype, and haplotype between groups. Conclusions. HTRA2 exonic variant might be rare among Chinese Parkinson's disease and essential tremor patients with family history, and HTRA2 may not be the cause of familial Parkinson's disease and essential tremor in China.
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Hill-Burns EM, Ross OA, Wissemann WT, Soto-Ortolaza AI, Zareparsi S, Siuda J, Lynch T, Wszolek ZK, Silburn PA, Mellick GD, Ritz B, Scherzer CR, Zabetian CP, Factor SA, Breheny PJ, Payami H. Identification of genetic modifiers of age-at-onset for familial Parkinson's disease. Hum Mol Genet 2016; 25:3849-3862. [PMID: 27402877 PMCID: PMC5216611 DOI: 10.1093/hmg/ddw206] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/15/2016] [Accepted: 06/23/2016] [Indexed: 01/27/2023] Open
Abstract
Parkinson’s disease (PD) is the most common cause of neurodegenerative movement disorder and the second most common cause of dementia. Genes are thought to have a stronger effect on age-at-onset of PD than on risk, yet there has been a phenomenal success in identifying risk loci but not age-at-onset modifiers. We conducted a genome-wide study for age-at-onset. We analysed familial and non-familial PD separately, per prior evidence for strong genetic effect on age-at-onset in familial PD. GWAS was conducted in 431 unrelated PD individuals with at least one affected relative (familial PD) and 1544 non-familial PD from the NeuroGenetics Research Consortium (NGRC); an additional 737 familial PD and 2363 non-familial PD were used for replication. In familial PD, two signals were detected and replicated robustly: one mapped to LHFPL2 on 5q14.1 (PNGRC = 3E-8, PReplication = 2E-5, PNGRC + Replication = 1E-11), the second mapped to TPM1 on 15q22.2 (PNGRC = 8E-9, PReplication = 2E-4, PNGRC + Replication = 9E-11). The variants that were associated with accelerated onset had low frequencies (<0.02). The LHFPL2 variant was associated with earlier onset by 12.33 [95% CI: 6.2; 18.45] years in NGRC, 8.03 [2.95; 13.11] years in replication, and 9.79 [5.88; 13.70] years in the combined data. The TPM1 variant was associated with earlier onset by 15.30 [8.10; 22.49] years in NGRC, 9.29 [1.79; 16.79] years in replication, and 12.42 [7.23; 17.61] years in the combined data. Neither LHFPL2 nor TPM1 was associated with age-at-onset in non-familial PD. LHFPL2 (function unknown) is overexpressed in brain tumours. TPM1 encodes a highly conserved protein that regulates muscle contraction, and is a tumour-suppressor gene.
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Affiliation(s)
- Erin M Hill-Burns
- Department of Neurology, University of Alabama at Birmingham, AL, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic Jacksonville, FL, USA
| | | | | | - Sepideh Zareparsi
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR, USA
| | - Joanna Siuda
- Department of Neurology, Medical University of Silesia, Katowice, Poland
| | - Timothy Lynch
- Dublin Neurological Institute at the Mater Misericordiae University Hospital, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland
| | | | - Peter A Silburn
- Eskitis Institute for Drug Discovery, Griffith University, Queensland, Australia
| | - George D Mellick
- Eskitis Institute for Drug Discovery, Griffith University, Queensland, Australia
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health and Neurology, Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Clemens R Scherzer
- The Neurogenomics Laboratory, Harvard Medical School and Brigham & Women's Hospital, Cambridge, MA, USA
| | - Cyrus P Zabetian
- VA Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, WA, USA
| | - Stewart A Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, AL, USA .,Center for Genomic Medicine, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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Farlow JL, Robak LA, Hetrick K, Bowling K, Boerwinkle E, Coban-Akdemir ZH, Gambin T, Gibbs RA, Gu S, Jain P, Jankovic J, Jhangiani S, Kaw K, Lai D, Lin H, Ling H, Liu Y, Lupski JR, Muzny D, Porter P, Pugh E, White J, Doheny K, Myers RM, Shulman JM, Foroud T. Whole-Exome Sequencing in Familial Parkinson Disease. JAMA Neurol 2016; 73:68-75. [PMID: 26595808 PMCID: PMC4946647 DOI: 10.1001/jamaneurol.2015.3266] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE Parkinson disease (PD) is a progressive neurodegenerative disease for which susceptibility is linked to genetic and environmental risk factors. OBJECTIVE To identify genetic variants contributing to disease risk in familial PD. DESIGN, SETTING, AND PARTICIPANTS A 2-stage study design that included a discovery cohort of families with PD and a replication cohort of familial probands was used. In the discovery cohort, rare exonic variants that segregated in multiple affected individuals in a family and were predicted to be conserved or damaging were retained. Genes with retained variants were prioritized if expressed in the brain and located within PD-relevant pathways. Genes in which prioritized variants were observed in at least 4 families were selected as candidate genes for replication in the replication cohort. The setting was among individuals with familial PD enrolled from academic movement disorder specialty clinics across the United States. All participants had a family history of PD. MAIN OUTCOMES AND MEASURES Identification of genes containing rare, likely deleterious, genetic variants in individuals with familial PD using a 2-stage exome sequencing study design. RESULTS The 93 individuals from 32 families in the discovery cohort (49.5% [46 of 93] female) had a mean (SD) age at onset of 61.8 (10.0) years. The 49 individuals with familial PD in the replication cohort (32.6% [16 of 49] female) had a mean (SD) age at onset of 50.1 (15.7) years. Discovery cohort recruitment dates were 1999 to 2009, and replication cohort recruitment dates were 2003 to 2014. Data analysis dates were 2011 to 2015. Three genes containing a total of 13 rare and potentially damaging variants were prioritized in the discovery cohort. Two of these genes (TNK2 and TNR) also had rare variants that were predicted to be damaging in the replication cohort. All 9 variants identified in the 2 replicated genes in 12 families across the discovery and replication cohorts were confirmed via Sanger sequencing. CONCLUSIONS AND RELEVANCE TNK2 and TNR harbored rare, likely deleterious, variants in individuals having familial PD, with similar findings in an independent cohort. To our knowledge, these genes have not been previously associated with PD, although they have been linked to critical neuronal functions. Further studies are required to confirm a potential role for these genes in the pathogenesis of PD.
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Affiliation(s)
- Janice L Farlow
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis
| | - Laurie A Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas4Department of Pediatrics, Texas Children's Hospital, Houston5Jan and Dan Duncan Neurological Resear
| | - Kurt Hetrick
- Center for Inherited Disease Research, The Johns Hopkins University, Baltimore, Maryland
| | - Kevin Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas9Human Genetics Center, University of Texas Health Science Center, Houston
| | | | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Preti Jain
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama10Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - Joseph Jankovic
- Department of Neurology, Baylor College of Medicine, Houston, Texas
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Kaveeta Kaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas5Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis
| | - Hai Lin
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis
| | - Hua Ling
- Center for Inherited Disease Research, The Johns Hopkins University, Baltimore, Maryland
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas4Department of Pediatrics, Texas Children's Hospital, Houston8Human Genome Sequencing Center, Baylor
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Paula Porter
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas5Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston
| | - Elizabeth Pugh
- Center for Inherited Disease Research, The Johns Hopkins University, Baltimore, Maryland
| | - Janson White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Kimberly Doheny
- Center for Inherited Disease Research, The Johns Hopkins University, Baltimore, Maryland
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Joshua M Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas5Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston11Department of Neurology, Baylor College of Medicine, Houston, Texas13Department
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis
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Escott-Price V, Nalls MA, Morris HR, Lubbe S, Brice A, Gasser T, Heutink P, Wood NW, Hardy J, Singleton AB, Williams NM. Polygenic risk of Parkinson disease is correlated with disease age at onset. Ann Neurol 2015; 77:582-91. [PMID: 25773351 PMCID: PMC4737223 DOI: 10.1002/ana.24335] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/28/2014] [Accepted: 12/07/2014] [Indexed: 02/01/2023]
Abstract
Objective We have investigated the polygenic architecture of Parkinson disease (PD) and have also explored the potential relationship between an individual's polygenic risk score and their disease age at onset. Methods This study used genotypic data from 4,294 cases and 10,340 controls obtained from the meta‐analysis of PD genome‐wide association studies. Polygenic score analysis was performed as previously described by the International Schizophrenia Consortium, testing whether the polygenic score alleles identified in 1 association study were significantly enriched in the cases relative to the controls of 3 independent studies. Linear regression was used to investigate the relationship between an individual's polygenic score for PD risk alleles and disease age at onset. Results Our polygenic score analysis has identified significant evidence for a polygenic component enriched in the cases of each of 3 independent PD genome‐wide association cohorts (minimum p = 3.76 × 10−6). Further analysis identified compelling evidence that the average polygenic score in patients with an early disease age at onset was significantly higher than in those with a late age at onset (p = 0.00014). Interpretation This provides strong support for a large polygenic contribution to the overall heritable risk of PD and also suggests that early onset forms of the illness are not exclusively caused by highly penetrant Mendelian mutations, but can also be contributed to by an accumulation of common polygenic alleles with relatively low effect sizes. Ann Neurol 2015;77:582–591
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Affiliation(s)
- Valentina Escott-Price
- Institute of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, Cardiff University School of Medicine, Cardiff, United Kingdom
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Petersen MS, Bech S, Nosova E, Aasly J, Farrer MJ. Familial aggregation of Parkinson's disease in the Faroe Islands. Mov Disord 2015; 30:538-44. [DOI: 10.1002/mds.26132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/03/2014] [Accepted: 11/30/2014] [Indexed: 01/09/2023] Open
Affiliation(s)
- Maria Skaalum Petersen
- Department of Occupational Medicine and Public Health; the Faroese Hospital System; Tórshavn Faroe Islands
| | - Sara Bech
- Department of Occupational Medicine and Public Health; the Faroese Hospital System; Tórshavn Faroe Islands
| | - Ekaterina Nosova
- Centre for Applied Neurogenetics; Djavad Mowafhagian Centre for Brain Health, Department of Medical Genetics, University of British Columbia; Vancouver BC Canada
| | - Jan Aasly
- St. Olav's Hospital, Department of Neuroscience; Norwegian University of Science and Technology; Trondheim Norway
| | - Matthew J. Farrer
- Centre for Applied Neurogenetics; Djavad Mowafhagian Centre for Brain Health, Department of Medical Genetics, University of British Columbia; Vancouver BC Canada
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12
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Gustavsson EK, Trinh J, Guella I, Vilariño-Güell C, Appel-Cresswell S, Stoessl AJ, Tsui JK, McKeown M, Rajput A, Rajput AH, Aasly JO, Farrer MJ. DNAJC13 genetic variants in parkinsonism. Mov Disord 2014; 30:273-8. [PMID: 25393719 DOI: 10.1002/mds.26064] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/15/2014] [Accepted: 09/30/2014] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND A novel mutation (p.N855S) in DNAJC13 has been linked to familial, late-onset Lewy body parkinsonism in a Dutch-German-Russian Mennonite multi-incident kindred. METHODS DNAJC13 was sequenced in 201 patients with parkinsonism and 194 controls from Canada. Rare (minor allele frequency < 0.01) missense variants identified in patients were genotyped in two Parkinson's disease case-controls cohorts. RESULTS Eighteen rare missense mutations were identified; four were observed in controls, three were observed in both patients and controls, and eleven were identified only in patients. Subsequent genotyping showed p.E1740Q and p.L2170W to be more frequent in patients, and p.R1516H being more frequent in controls. Additionally, p.P336A, p.V722L, p.N855S, p.R1266Q were seen in one patient each, and p.T1895M was found in two patients. CONCLUSION Although the contribution of rare genetic variation in DNAJC13 to parkinsonisms remains to be further elucidated, this study suggests that, in addition to p.N855S, other rare variants might affect disease susceptibility.
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Affiliation(s)
- Emil K Gustavsson
- Djavad Mowafaghian Centre for Brain Health, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway; Department of Neurology, St. Olav's Hospital, Trondheim, Norway
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13
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Petersen MS, Guella I, Bech S, Gustavsson E, Farrer MJ. Parkinson's disease, genetic variability and the Faroe Islands. Parkinsonism Relat Disord 2014; 21:75-8. [PMID: 25466404 DOI: 10.1016/j.parkreldis.2014.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 10/10/2014] [Accepted: 10/29/2014] [Indexed: 10/24/2022]
Abstract
INTRODUCTION The Faroe Islands is a geographically isolated population in the North Atlantic with a high prevalence of Parkinson disease (PD). The disease etiology is still unknown, although dietary pollutants are considered a risk factor. The genetic risk underlying disease susceptibility has yet to be elucidated. METHODS Sequence analysis was performed in genes previously linked with PD in 91 patients and 96 healthy control subjects. RESULTS Fourteen missense mutations, of which one was novel, were identified in six genes. One patient (1%) did carry the known pathogenic mutation LRRK2 p.G2019S mutation, 19 patients (22%) did carry mutations of unknown significance while 70 patients (78.0%) did not have any identifiable genetic risk. A total of 14 controls (14.6%) carried mutations of unknown significance. CONCLUSION This study suggests that rare variants in genes previously linked to PD are not major contributors to PD in the Faroe Islands. Further exome sequencing and comparative analyses within and among well-described pedigrees with multi-incident PD are now warranted.
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Affiliation(s)
- Maria Skaalum Petersen
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Sigmundargøta 5, Postbox 14, FO-110 Tórshavn, Faroe Islands.
| | - Ilaria Guella
- Djavad Mowafaghian Centre for Brain Health, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| | - Sara Bech
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Sigmundargøta 5, Postbox 14, FO-110 Tórshavn, Faroe Islands.
| | - Emil Gustavsson
- Djavad Mowafaghian Centre for Brain Health, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| | - Matthew J Farrer
- Djavad Mowafaghian Centre for Brain Health, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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Fujioka S, Ogaki K, Tacik PM, Uitti RJ, Ross OA, Wszolek ZK. Update on novel familial forms of Parkinson's disease and multiple system atrophy. Parkinsonism Relat Disord 2014; 20 Suppl 1:S29-34. [PMID: 24262183 DOI: 10.1016/S1353-8020(13)70010-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Parkinson's disease (PD) and multiple system atrophy (MSA) are progressive neurodegenerative disorders classified as synucleinopathies, which are defined by the presence of α-synuclein protein pathology. Genetic studies have identified a total of 18 PARK loci that are associated with PD. The SNCA gene encodes the α-synuclein protein. The first pathogenic α-synuclein p.A53T substitution was discovered in 1997; this was followed by the identification of p.A30P and p.E46K pathogenic substitutions in 1998 and 2004, respectively. In the last year, two possible α-synuclein pathogenic substitutions, p.A18T and p.A29S, and two probable pathogenic substitutions, p.H50Q and p.G51D have been nominated. Next-generation sequencing approaches in familial PD have identified mutations in the VPS35 gene. A VPS35 p.D620N substitution remains the only confirmed pathogenic substitution. A second synucleinopathy, MSA, originally was considered a sporadic condition with little or no familial aggregation. However, recessive COQ2 mutations recently were nominated to be the genetic cause in a subset of familial and sporadic MSA cases. Further studies on the clinicogenetics and pathology of parkinsonian disorders will facilitate clarification of the molecular characteristics and pathomechanisms underlying these disorders.
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15
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Kim JS, Cho JW, Shin H, Lee WY, Ki CS, Cho AR, Kim HT. A Korean Parkinson's disease family with the LRRK2 p.Tyr1699Cys mutation showing clinical heterogeneity. Mov Disord 2011; 27:320-4. [PMID: 22162019 DOI: 10.1002/mds.24033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/09/2011] [Accepted: 10/20/2011] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Although leucine-rich repeat kinase 2 (LRRK2) is the gene most commonly linked to autosomal dominant inherited Parkinson's disease (PD), there have been few reports in Asia, probably because of population-specific differences in allele frequencies. METHODS We identified a large Korean PD family with the p.Tyr1699Cys mutation in LRRK2 and analyzed genealogical, clinical, and genetic data from the family. RESULTS Although the clinical findings of these patients were indistinguishable from those of patients with sporadic PD, the patients with the p.Tyr1699Cys mutation demonstrated clinical heterogeneity including differences in age at onset, rate of disease progression, clinical phenotype, and prognosis. CONCLUSIONS This is the first report describing an Asian PD family with the p.Tyr1699Cys mutation in LRRK2. The affected members of this family showed clinical heterogeneity.
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Affiliation(s)
- Ji Sun Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Vilariño-Güell C, Wider C, Ross OA, Dachsel JC, Kachergus JM, Lincoln SJ, Soto-Ortolaza AI, Cobb SA, Wilhoite GJ, Bacon JA, Behrouz B, Melrose HL, Hentati E, Puschmann A, Evans DM, Conibear E, Wasserman WW, Aasly JO, Burkhard PR, Djaldetti R, Ghika J, Hentati F, Krygowska-Wajs A, Lynch T, Melamed E, Rajput A, Rajput AH, Solida A, Wu RM, Uitti RJ, Wszolek ZK, Vingerhoets F, Farrer MJ. VPS35 mutations in Parkinson disease. Am J Hum Genet 2011; 89:162-7. [PMID: 21763482 DOI: 10.1016/j.ajhg.2011.06.001] [Citation(s) in RCA: 625] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/28/2011] [Accepted: 06/01/2011] [Indexed: 01/23/2023] Open
Abstract
The identification of genetic causes for Mendelian disorders has been based on the collection of multi-incident families, linkage analysis, and sequencing of genes in candidate intervals. This study describes the application of next-generation sequencing technologies to a Swiss kindred presenting with autosomal-dominant, late-onset Parkinson disease (PD). The family has tremor-predominant dopa-responsive parkinsonism with a mean onset of 50.6 ± 7.3 years. Exome analysis suggests that an aspartic-acid-to-asparagine mutation within vacuolar protein sorting 35 (VPS35 c.1858G>A; p.Asp620Asn) is the genetic determinant of disease. VPS35 is a central component of the retromer cargo-recognition complex, is critical for endosome-trans-golgi trafficking and membrane-protein recycling, and is evolutionarily highly conserved. VPS35 c.1858G>A was found in all affected members of the Swiss kindred and in three more families and one patient with sporadic PD, but it was not observed in 3,309 controls. Further sequencing of familial affected probands revealed only one other missense variant, VPS35 c.946C>T; (p.Pro316Ser), in a pedigree with one unaffected and two affected carriers, and thus the pathogenicity of this mutation remains uncertain. Retromer-mediated sorting and transport is best characterized for acid hydrolase receptors. However, the complex has many types of cargo and is involved in a diverse array of biologic pathways from developmental Wnt signaling to lysosome biogenesis. Our study implicates disruption of VPS35 and retromer-mediated trans-membrane protein sorting, rescue, and recycling in the neurodegenerative process leading to PD.
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Butler MW, Burt A, Edwards TL, Zuchner S, Scott WK, Martin ER, Vance JM, Wang L. Vitamin D receptor gene as a candidate gene for Parkinson disease. Ann Hum Genet 2011; 75:201-10. [PMID: 21309754 DOI: 10.1111/j.1469-1809.2010.00631.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vitamin D and vitamin D receptor (VDR) have been postulated as environmental and genetic factors in neurodegeneration disorders including multiple sclerosis (MS), Alzheimer disease (AD), and recently Parkinson disease (PD). Given the sparse data on PD, we conducted a two-stage study to evaluate the genetic effects of VDR in PD. In the discovery stage, 30 tagSNPs in VDR were tested for association with risk as a discrete trait and age-at-onset (AAO) as a quantitative trait in 770 Caucasian PD families. In the validation stage, 18 VDR SNPs were tested in an independent Caucasian cohort (267 cases and 267 controls) constructed from a genome-wide association study (GWAS). In the discovery dataset, SNPs in the 5' end of VDR were associated with both risk and AAO with more significant evidence of association with AAO (P= 0.0008-0.02). These 5' SNPs were also associated with AD in another study. In the validation dataset, SNPs in the 3' end of VDR were associated with AAO (P= 0.003) but not risk. The 3' end SNP has been associated with both MS and AD in previous studies. Our findings suggest VDR as a potential susceptibility gene and support an essential role of vitamin D in PD.
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Affiliation(s)
- Megan W Butler
- Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Durham, NC, USA
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18
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Abstract
PURPOSE OF REVIEW Elucidating the genetic background of Parkinson disease and essential tremor is crucial to understand the pathogenesis and improve diagnostic and therapeutic strategies. RECENT FINDINGS A number of approaches have been applied including familial and association studies, and studies of gene expression profiles to identify genes involved in susceptibility to Parkinson disease. These studies have nominated a number of candidate Parkinson disease genes and novel loci including Omi/HtrA2, GIGYF2, FGF20, PDXK, EIF4G1 and PARK16. A recent notable finding has been the confirmation for the role of heterozygous mutations in glucocerebrosidase (GBA) as risk factors for Parkinson disease. Finally, association studies have nominated genetic variation in the leucine-rich repeat and Ig containing 1 gene (LINGO1) as a risk for both Parkinson disease and essential tremor, providing the first genetic evidence of a link between the two conditions. SUMMARY Although undoubtedly genes remain to be identified, considerable progress has been achieved in the understanding of the genetic basis of Parkinson disease. This same effort is now required for essential tremor. The use of next-generation high-throughput sequencing and genotyping technologies will help pave the way for future insight leading to advances in diagnosis, prevention and cure.
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Affiliation(s)
- Christian Wider
- Division of Neurology, Department of Clinical Neuroscience, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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19
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Abstract
We questioned whether the evidence for the genetic component in Parkinson's disease (PD) in Caucasians could be explained by the causative and susceptibility genes that have already been identified. We estimated heritability of risk and age at onset of PD in a well-characterized sample of 504 nuclear families (2828 individuals). After excluding families with known pathogenic mutations and accounting for the major susceptibility genes, the heritability of risk of developing PD was 0.41 (P=0.01). These data suggest that approximately 40% of the variation in susceptibility to PD is due to as-yet unidentified genes, the remainder is likely environmental.
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Affiliation(s)
- Taye H Hamza
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY 12201-2002, USA
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20
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Latourelle JC, Pankratz N, Dumitriu A, Wilk JB, Goldwurm S, Pezzoli G, Mariani CB, DeStefano AL, Halter C, Gusella JF, Nichols WC, Myers RH, Foroud T. Genomewide association study for onset age in Parkinson disease. BMC Med Genet 2009; 10:98. [PMID: 19772629 PMCID: PMC2758866 DOI: 10.1186/1471-2350-10-98] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 09/22/2009] [Indexed: 12/04/2022]
Abstract
Background Age at onset in Parkinson disease (PD) is a highly heritable quantitative trait for which a significant genetic influence is supported by multiple segregation analyses. Because genes associated with onset age may represent invaluable therapeutic targets to delay the disease, we sought to identify such genetic modifiers using a genomewide association study in familial PD. There have been previous genomewide association studies (GWAS) to identify genes influencing PD susceptibility, but this is the first to identify genes contributing to the variation in onset age. Methods Initial analyses were performed using genotypes generated with the Illumina HumanCNV370Duo array in a sample of 857 unrelated, familial PD cases. Subsequently, a meta-analysis of imputed SNPs was performed combining the familial PD data with that from a previous GWAS of 440 idiopathic PD cases. The SNPs from the meta-analysis with the lowest p-values and consistency in the direction of effect for onset age were then genotyped in a replication sample of 747 idiopathic PD cases from the Parkinson Institute Biobank of Milan, Italy. Results Meta-analysis across the three studies detected consistent association (p < 1 × 10-5) with five SNPs, none of which reached genomewide significance. On chromosome 11, the SNP with the lowest p-value (rs10767971; p = 5.4 × 10-7) lies between the genes QSER1 and PRRG4. Near the PARK3 linkage region on chromosome 2p13, association was observed with a SNP (rs7577851; p = 8.7 × 10-6) which lies in an intron of the AAK1 gene. This gene is closely related to GAK, identified as a possible PD susceptibility gene in the GWAS of the familial PD cases. Conclusion Taken together, these results suggest an influence of genes involved in endocytosis and lysosomal sorting in PD pathogenesis.
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Elbaz A, Clavel J, Rathouz PJ, Moisan F, Galanaud JP, Delemotte B, Alpérovitch A, Tzourio C. Professional exposure to pesticides and Parkinson disease. Ann Neurol 2009; 66:494-504. [DOI: 10.1002/ana.21717] [Citation(s) in RCA: 191] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Abstract
PURPOSE OF REVIEW Parkinson's disease is the second most common age-related neurodegenerative disorder and is characterized clinically by classical parkinsonism and pathologically by selective loss of dopaminergic neurons in the substantia nigra and Lewy bodies. Although for most classical parkinsonism the etiology is unknown, a clear genetic component has been determined in a minority. Mutations in five causative genes combined [alpha-Synuclein (SNCA), Parkin, PTEN-induced kinase 1 (PINK1), DJ-1, Leucine-rich repeat kinase 2 (LRRK2)] account for 2-3% of all cases with classical parkinsonism, often clinically indistinguishable from idiopathic Parkinson's disease. RECENT FINDINGS The functional role of PINK1 and LRRK2 as kinases has been clearly established. Further, mutations in the ATP13A2 gene have been linked to Kufor-Rakeb syndrome (PARK9), a form of atypical parkinsonism. ATP13A2 encodes a lysosomal ATPase and shows elevated expression levels in the brains of sporadic patients, suggesting a potential role in the more common idiopathic Parkinson's disease. Finally, first promising pilot studies have been performed to identify differentially expressed genes and proteins as biomarkers for parkinsonism. SUMMARY The identification of single genes and their functional characterization has enhanced our understanding of the pathogenesis of parkinsonism, has led to improvement of diagnostic tools for genetic parkinsonism, and allows for the purposeful consideration of novel therapeutic targets.
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Affiliation(s)
- Christine Klein
- Departments of Neurology and Human Genetics, Lübeck University, Lübeck, Germany.
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Lesnick TG, Papapetropoulos S, Mash DC, Ffrench-Mullen J, Shehadeh L, de Andrade M, Henley JR, Rocca WA, Ahlskog JE, Maraganore DM. A genomic pathway approach to a complex disease: axon guidance and Parkinson disease. PLoS Genet 2007; 3:e98. [PMID: 17571925 PMCID: PMC1904362 DOI: 10.1371/journal.pgen.0030098] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 05/02/2007] [Indexed: 11/18/2022] Open
Abstract
While major inroads have been made in identifying the genetic causes of rare Mendelian disorders, little progress has been made in the discovery of common gene variations that predispose to complex diseases. The single gene variants that have been shown to associate reproducibly with complex diseases typically have small effect sizes or attributable risks. However, the joint actions of common gene variants within pathways may play a major role in predisposing to complex diseases (the paradigm of complex genetics). The goal of this study was to determine whether polymorphism in a candidate pathway (axon guidance) predisposed to a complex disease (Parkinson disease [PD]). We mined a whole-genome association dataset and identified single nucleotide polymorphisms (SNPs) that were within axon-guidance pathway genes. We then constructed models of axon-guidance pathway SNPs that predicted three outcomes: PD susceptibility (odds ratio = 90.8, p = 4.64 × 10−38), survival free of PD (hazards ratio = 19.0, p = 5.43 × 10−48), and PD age at onset (R2 = 0.68, p = 1.68 × 10−51). By contrast, models constructed from thousands of random selections of genomic SNPs predicted the three PD outcomes poorly. Mining of a second whole-genome association dataset and mining of an expression profiling dataset also supported a role for many axon-guidance pathway genes in PD. These findings could have important implications regarding the pathogenesis of PD. This genomic pathway approach may also offer insights into other complex diseases such as Alzheimer disease, diabetes mellitus, nicotine and alcohol dependence, and several cancers. Complex diseases are common disorders that are believed to have many causes. Examples include Alzheimer disease, diabetes mellitus, nicotine and alcohol dependence, and several cancers. This study represents a paradigm shift from single gene to pathway studies of complex diseases. We present the example of Parkinson disease (PD) and a complex array of chemical signals that wires the brain during fetal development (the axon guidance pathway). We mined a dataset that studied hundreds of thousands of DNA variations (single nucleotide polymorphisms [SNPs]) in persons with and without PD and identified SNPs that were assigned to axon-guidance pathway genes. We then identified sets of SNPs that were highly predictive of PD susceptibility, survival free of PD, and age at onset of PD. The effect sizes and the statistical significance observed for the pathway were far greater than for any single gene. We validated our findings for the pathway using a second SNP dataset for PD and also a dataset for PD that studied RNA variations. There is prior evidence that the axon guidance pathway might play a role in other brain disorders (e.g., Alzheimer disease, Tourette syndrome, dyslexia, epilepsy, and schizophrenia). A genomic pathway approach may lead to important breakthroughs for many complex diseases.
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Affiliation(s)
- Timothy G Lesnick
- Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Spiridon Papapetropoulos
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | | | - Lina Shehadeh
- Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Mariza de Andrade
- Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - John R Henley
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Walter A Rocca
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - J. Eric Ahlskog
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Demetrius M Maraganore
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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Perez-Pastene C, Cobb SA, Díaz-Grez F, Hulihan MM, Miranda M, Venegas P, Godoy OT, Kachergus JM, Ross OA, Layson L, Farrer MJ, Segura-Aguilar J. Lrrk2 mutations in South America: A study of Chilean Parkinson's disease. Neurosci Lett 2007; 422:193-7. [PMID: 17614198 PMCID: PMC1986707 DOI: 10.1016/j.neulet.2007.06.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 06/08/2007] [Accepted: 06/11/2007] [Indexed: 11/27/2022]
Abstract
Pathogenic substitutions in the leucine-rich repeat kinase 2 protein (Lrrk2), R1441G and G2019S, are a prevalent cause of autosomal dominant and sporadic Parkinson's disease in the Northern Spanish population. In this study we examined the frequency of these two substitutions in 166 Parkinson's disease patients and 153 controls from Chile, a population with Spanish/European-Amerindian admixture. Lrrk2 R1441G was not observed, however Lrrk2 G2019S was detected in one familial and four sporadic Parkinson's disease patients. These findings suggest Lrrk2 G2019S may play an important role in Parkinson's disease on the South American Continent and further studies are now warranted.
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Affiliation(s)
- Carolina Perez-Pastene
- Molecular and Clinical Pharmacology, ICBM, Faculty of Medicine, University of Chile, Casilla 70000, Santiago-7, Chile
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Rocca WA, Bower JH, Ahlskog JE, Elbaz A, Grossardt BR, McDonnell SK, Schaid DJ, Maraganore DM. Increased risk of essential tremor in first-degree relatives of patients with Parkinson's disease. Mov Disord 2007; 22:1607-14. [PMID: 17546668 DOI: 10.1002/mds.21584] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We conducted a historical cohort study of 981 first-degree relatives of 162 patients with Parkinson's disease (PD) and of 838 first-degree relatives of 147 controls representative of the population of Olmsted County, Minnesota. In addition, we studied 2,684 first-degree relatives of 411 patients with PD referred to the Mayo Clinic. Relatives were interviewed and screened for tremor either directly or through a proxy, and those who screened positive were examined or copies of their medical records were obtained to confirm the diagnosis of essential tremor (ET). We also obtained ET information from a medical records-linkage system (family study method). In the population-based sample, the risk of ET was significantly increased for relatives of patients with onset of PD<or=66 years (first tertile; hazard ratio [HR]=2.24; 95% confidence interval [95% CI]=1.26-3.98; P=0.006). In the referral-based sample, the risk of ET among relatives increased with younger onset of PD in patients (linear trend; P=0.001), and was higher in relatives of PD patients with the tremor-predominant or mixed form when compared with relatives of patients with the akinetic-rigid form, and in men compared with women. These findings suggest that PD and ET may share familial susceptibility factors.
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Affiliation(s)
- Walter A Rocca
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
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Sundquist K, Li X, Hemminki K. Familial risks of hospitalization for Parkinson’s disease in first-degree relatives: a nationwide follow-up study from Sweden. Neurogenetics 2006; 7:231-7. [PMID: 16944085 DOI: 10.1007/s10048-006-0055-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Accepted: 06/29/2006] [Indexed: 10/24/2022]
Abstract
The aim of this study was to estimate familial risks of Parkinson's disease (PD) in first-degree relatives of probands with PD compared with first-degree relatives of control probands. Standardized incidence ratios (SIRs) of PD were estimated in the total Swedish population for the period January 1, 1987 to December 31, 2001. SIRs were calculated by age, sex, occupation, geographic region, family size, and type of related proband on the basis of first hospital diagnoses of PD during the study period. Results showed that during the study period, there were 65 cases of first-degree relatives who were hospitalized for PD out of the total 13,276 events (first hospital diagnoses of PD) between 1987 and 2001. Age-specific analyses of familial PD revealed that there was no apparent difference in SIRs by age category. Overall, significant SIRs for PD in first-degree relatives were 3.1 (95% CI 2.1-4.3) for men and 4.0 (95% CI 2.8-5.7) for women. When the related PD proband was a sibling, the SIR was significantly higher (8.7) than when the related proband was a parent (SIR=2.9, p=0.01) or a child (SIR=3.6, p=0.04). For spouses, no increased risks were found. In conclusion, the findings of the present study suggest that genetic factors are important in early- (age < or =50 years) and later (age >50 years) onset PD, and that shared environmental factors during childhood or recessive effects may partly be important for familial aggregation of the disease.
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Affiliation(s)
- Kristina Sundquist
- Department of Family and Community Medicine, Karolinska Institute, Alfred Nobels allé 12, S-141 83, Huddinge, Sweden.
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