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Integrated Analysis of Whole Exome Sequencing and Copy Number Evaluation in Parkinson's Disease. Sci Rep 2019; 9:3344. [PMID: 30833663 PMCID: PMC6399448 DOI: 10.1038/s41598-019-40102-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
Genetic studies of the familial forms of Parkinson’s disease (PD) have identified a number of causative genes with an established role in its pathogenesis. These genes only explain a fraction of the diagnosed cases. The emergence of Next Generation Sequencing (NGS) expanded the scope of rare variants identification in novel PD related genes. In this study we describe whole exome sequencing (WES) genetic findings of 60 PD patients with 125 variants validated in 51 of these cases. We used strict criteria for variant categorization that generated a list of variants in 20 genes. These variants included loss of function and missense changes in 18 genes that were never previously linked to PD (NOTCH4, BCOR, ITM2B, HRH4, CELSR1, SNAP91, FAM174A, BSN, SPG7, MAGI2, HEPHL1, EPRS, PUM1, CLSTN1, PLCB3, CLSTN3, DNAJB9 and NEFH) and 2 genes that were previously associated with PD (EIF4G1 and ATP13A2). These genes either play a critical role in neuronal function and/or have mouse models with disease related phenotypes. We highlight NOTCH4 as an interesting candidate in which we identified a deleterious truncating and a splice variant in 2 patients. Our combined molecular approach provides a comprehensive strategy applicable for complex genetic disorders.
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Abstract
Parkinson disease (PD) is one of the most widespread neurodegenerative disorders. In North America alone it affects 1 million people. It is a multifactorial disorder caused by genetic, various biological and environmental factors. One of the important features of PD is the dementia, which is believed to be due to the loss of dopaminergic neurons. In some cases the disease can be inherited as an autosomal dominant or recessive trait but in the majority of cases it is acquired. The biological causes of the disorder are unknown. The identification of mutations in the parkin gene in the autosomal recessive case and alpha-synuclein gene in autosomal dominant cases has opened a new avenue for studies to understand the basic biochemical mechanisms of pathogenesis. Although several types of treatments such as transplantation of cells that produce L-Dopa and direct gene delivery using adeno-associated viral vectors may correct animal models of PD, their usefulness in the human is not yet clear. A better understanding of the causes of neurodegeneration may lead to better therapies in the future.
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Sherwani SI, Khan HA. Role of 5-hydroxymethylcytosine in neurodegeneration. Gene 2015; 570:17-24. [PMID: 26115768 DOI: 10.1016/j.gene.2015.06.052] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/18/2015] [Accepted: 06/18/2015] [Indexed: 02/05/2023]
Abstract
The recent discovery of 5-hydroxymethylcytosine (5hmC), an epigenetic modifier and oxidation product of 5-methylcytosine (5mC), has broadened the scope and understanding of neural development and neurodegenerative diseases. By virtue of their functional groups, 5mC and 5hmC exert opposite effects on gene expression; the former is generally associated with gene silencing whereas the latter is mainly involved in up-regulation of gene expression affecting the cellular processes such as differentiation, development, and aging. Although DNA methylation plays an important role in normal neural development and neuroprotection, an altered pathway due to complex interaction with environmental and genetic factors may cause severe neurodegeneration. The levels of 5hmC in brain increase progressively from birth until death, while in patients with neurodegenerative disorders, the levels are found to be highly compromised. This article discusses the recent developments in the area of hydroxymethylation, with particular emphasis on the role of 5hmC in neurodegenerative diseases including Alzheimer's disease, Parkinson's diseases and Huntington's disease. We have also included recent findings on the role of 5hmC in brain tumors (gliomas). Despite compelling evidence on the involvement of 5hmC in neurodegeneration, it is yet to be established whether this epigenetic molecule is the cause or the effect of the onset and progression of neurodegenerative diseases.
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Affiliation(s)
- Shariq I Sherwani
- Department of Internal Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Haseeb A Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
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PARK2 mediates interleukin 6 and monocyte chemoattractant protein 1 production by human macrophages. PLoS Negl Trop Dis 2013; 7:e2015. [PMID: 23350010 PMCID: PMC3547867 DOI: 10.1371/journal.pntd.0002015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/03/2012] [Indexed: 01/02/2023] Open
Abstract
Leprosy is a persistent infectious disease caused by Mycobacterium leprae that still affects over 200,000 new patients annually. The host genetic background is an important risk factor for leprosy susceptibility and the PARK2 gene is a replicated leprosy susceptibility candidate gene. The protein product of PARK2, Parkin, is an E3 ubiquitin ligase that is involved in the development of various forms of Parkinsonism. The human macrophage is both a natural host cell of M. leprae as well as a primary mediator of natural immune defenses, in part by secreting important pro-inflammatory cytokines and chemokines. Here, we report that down-regulation of Parkin in THP-1 macrophages, human monocyte-derived macrophages and human Schwann cells resulted in a consistent and specific decrease in interleukin-6 (IL-6) and monocyte chemoattractant protein 1 (MCP-1/CCL2) production in response to mycobacteria or LPS. Interestingly, production of IL-6 at 6 hours by THP-1 cells stimulated with live M. leprae and M. bovis BCG was dependent on pretreatment with 1,25-dihydroxyvitamin D3 (VD). Parkin knockdown in VD-treated cells blocked IL-6 induction by mycobacteria. However, IκB-α phosphorylation and levels of IκB-ξ, a nuclear protein required for IL-6 expression, were not affected by Parkin silencing. Phosphorylation of MAPK ERK1/2 and p38 was unaffected by Parkin silencing while JNK activation was promoted but did not explain the altered cytokine production. In a final set of experiments we found that genetic risk factors of leprosy located in the PARK2 promoter region were significantly correlated with M. leprae sonicate triggered CCL2 and IL6 transcript levels in whole blood assays. These results associated genetically controlled changes in the production of MCP-1/CCL2 and IL-6 with known leprosy susceptibility factors. Leprosy is an infectious disease with a strong host genetic component. The identification of host genetic lesions predisposing to disease is a powerful approach for mapping key junctions in the host pathogen interplay. Genetic variants located in the promoter region of the PARK2 gene are replicated leprosy susceptibility factors. To better understand a possible contribution of PARK2 to host effector mechanisms in leprosy patients, we developed a cellular model to test the contribution of the PARK2 encoded parkin protein to host responses to mycobacterial antigens. We observed that parkin was a mediator of IL-6 production in response to mycobacterial antigen in both THP-1 macrophages and human Schwann cells while human monocyte-derived macrophages needed to be pre-activated with VitD to show the same impact. Parkin also impacted on the constitutive production of MCP-1. The regulatory activity of parkin on cytokine production was found to be independent of the canonical TLR-NFκB signalling pathway. We also tested association of IL6 and CCL2 gene expression levels in whole blood assays with PARK2 polymorphisms. For both cytokines, we found significant associations with those PARK2 variants that were established leprosy susceptibility factors. Hence, our results show that genetic PARK2 variants that are correlated with leprosy susceptibility are also correlated with production of these cytokines following stimulation with M. leprae sonicate.
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Positional cloning of the autosomal recessive juvenile parkinsonism (AR-JP) gene and its diversity in deletion mutations. Parkinsonism Relat Disord 2012; 5:163-8. [PMID: 18591135 DOI: 10.1016/s1353-8020(99)00032-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autosomal recessive juvenile parkinsonism (AR-JP) is a distinct clinical and genetic entity characterized by highly selective neuronal cell death in the substantia nigra and the locus coeruleus with no Lewy body formation. We succeeded in positional cloning of the AR-JP gene by screening the Keio BAC library with a microsatellite marker, D6S305, which is located AR-JP locus (6q25.2-q27). The gene was named as parkin; parkin consists of 12 exons spanning about 1Mb with 1395bp coding sequence. Patients with AR-JP showed various deletions in 14 Japanese families and two different types of point mutations in two Turkish families. AR-JP appears to have world-wide distribution.
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Abstract
Parkinson's disease (PD) is a progressive, neurodegenerative disorder associated with tremor, rigidity, bradykinesia, and postural instability. There exists a familial form of PD that is indistinguishable from the sporadic form. In addition, there exists a class of syndromes classified as parkinsonism-plus syndromes (PPS), in which parkinsonism is an essential but not the only phenotypic characteristic. The etiology of PD remains unclear. Both environmental and genetic factors contribute to the disease pathogenesis. Recent progress in the molecular genetics of parkinsonism has demonstrated that six different chromosomal regions are associated with forms of familial parkinsonism. Mutations in four candidate genes have been identified and include both point mutations and deletions. Both gain-of-function and loss-of-function mutational mechanisms have been implicated. The molecular genetic characterization has led to a new classification of PD and PPS based on the type of genetic defect. Understanding the mechanisms by which these mutations lead to disease should provide further insights into the etiology of parkinsonism.
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Affiliation(s)
- Z K Wszolek
- Department of Neurology, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
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Fernández M, Barcia E, Fernández-Carballido A, Garcia L, Slowing K, Negro S. Controlled release of rasagiline mesylate promotes neuroprotection in a rotenone-induced advanced model of Parkinson's disease. Int J Pharm 2012; 438:266-78. [PMID: 22985602 DOI: 10.1016/j.ijpharm.2012.09.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/04/2012] [Accepted: 09/08/2012] [Indexed: 12/21/2022]
Abstract
Microencapsulation of rasagiline mesylate (RM) into PLGA microspheres was performed by method A (O/W emulsion) and method B (W/O/W double emulsion). The best formulation regarding process yield, encapsulation efficiency and in vitro drug release was that prepared with method A, which exhibited constant drug release for two weeks (K(0)=62.3 μg/day/20mg microspheres). Exposure of SKN-AS cells to peroxide-induced oxidative stress (1 mM) resulted in cell apoptosis which was significantly reduced by RM (40.7-102.5 μM) as determined by cell viability, ROS production and DNA fragmentation. Daily doses of rotenone (2 mg/kg) given i.p. to rats for 45 days induced neuronal and behavioral changes similar to those occurring in PD. Once an advanced stage of PD was achieved, animals received RM in saline (1 mg/kg/day) or encapsulated within PLGA microspheres (amount of microspheres equivalent to 15 mg/kg RM given on days 15 and 30). After 45 days RM showed a robust effect on all analytical outcomes evaluated with non-statistically significant differences found between its administration in solution or within microparticles however; with this controlled release system administration of RM could be performed every two weeks thereby making this new therapeutic system an interesting approach for the treatment of PD.
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Affiliation(s)
- M Fernández
- Departamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
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Cai M, Tian J, Zhao GH, Luo W, Zhang BR. Study of Methylation Levels of Parkin Gene Promoter in Parkinson's Disease Patients. Int J Neurosci 2011; 121:497-502. [DOI: 10.3109/00207454.2011.580866] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Parkinson disease (PD) is the second most common neurodegenerative disorder. In most instances, PD is thought to result from a complex interaction between multiple genetic and environmental factors, though rare monogenic forms of the disease do exist. Mutations in 6 genes (SNCA, LRRK2, PRKN, DJ1, PINK1, and ATP13A2) have conclusively been shown to cause familial parkinsonism. In addition, common variation in 3 genes (MAPT, LRRK2, and SNCA) and loss-of-function mutations in GBA have been well-validated as susceptibility factors for PD. The function of these genes and their contribution to PD pathogenesis remain to be fully elucidated. The prevalence, incidence, clinical manifestations, and genetic components of PD are discussed in this review.
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Affiliation(s)
- Lynn M Bekris
- Geriatric Research, Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA.
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11
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Mendelian forms of Parkinson's disease. Biochim Biophys Acta Mol Basis Dis 2009; 1792:587-96. [DOI: 10.1016/j.bbadis.2008.12.007] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 12/23/2008] [Accepted: 12/24/2008] [Indexed: 12/13/2022]
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Benamer HT, de Silva R, Siddiqui KA, Grosset DG. Parkinson's disease in Arabs: A systematic review. Mov Disord 2008; 23:1205-10. [DOI: 10.1002/mds.22041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Gherbassi D, Bhatt L, Thuret S, Simon HH. Merging mouse transcriptome analyses with Parkinson's disease linkage studies. DNA Res 2007; 14:79-89. [PMID: 17522092 PMCID: PMC2779897 DOI: 10.1093/dnares/dsm007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The hallmark of Parkinson's disease (PD OMIM #168600) is the degeneration of the nigral dopaminergic system affecting approximately 1% of the human population older than 65. In pursuit of genetic factors contributing to PD, linkage and association studies identified several susceptibility genes. The majority of these genes are expressed by the dopamine-producing neurons in the substantia nigra. We, therefore, propose expression by these neurons as a selection criterion, to narrow down, in a rational manner, the number of candidate genes in orphan PD loci, where no mutation has been associated thus far. We determined the corresponding human chromosome locations of 1435 murine cDNA fragments obtained from murine expression analyses of nigral dopaminergic neurons and combined these data with human linkage studies. These fragments represent 19 genes within orphan OMIM PD loci. We used the same approach for independent association studies and determined the genes in neighborhood to the peaks with the highest LOD score value. Our approach did not make any assumptions about disease mechanisms, but it, nevertheless, revealed α-synuclein, NR4A2 (Nurr1), and the tau genes, which had previously been associated to PD. Furthermore, our transcriptome analysis identified several classes of candidate genes for PD mutations and may also provide insight into the molecular pathways active in nigral dopaminergic neurons.
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Affiliation(s)
| | | | | | - Horst H. Simon
- To whom correspondence should be addressed. Tel. +49-6221-548342. Fax. +49-6221-545605. E-mail:
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Pramstaller PP, Schlossmacher MG, Jacques TS, Scaravilli F, Eskelson C, Pepivani I, Hedrich K, Adel S, Gonzales-McNeal M, Hilker R, Kramer PL, Klein C. Lewy body Parkinson's disease in a large pedigree with 77Parkin mutation carriers. Ann Neurol 2005; 58:411-22. [PMID: 16130111 DOI: 10.1002/ana.20587] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report the clinical, genetic, and neuropathological findings of a seven generation-spanning pedigree with 196 individuals, 25 of whom had levodopa-responsive parkinsonism. Genetic analyses indicated Parkin mutations in 77 subjects. Among the 25 patients, 5 carried compound heterozygous mutations and met criteria for definite Parkinson's disease (PD) according to UK PD Society Brain Bank guidelines; 8 subjects carried only a heterozygous Parkin mutation. The mutational status of five deceased patients was unknown, and seven PD patients had no Parkin mutation. Survival analyses showed a significant difference in the age-at-onset distribution between patients with compound heterozygous mutations and the groups of heterozygous carriers and subjects without detectable Parkin mutations. Autopsy of a 73-year-old patient, who carried two mutant Parkin alleles (delExon7 + del1072T), showed PD-type cell loss, reactive gliosis, and alpha-synuclein-positive Lewy bodies in the substantia nigra and locus ceruleus. Surviving neurons were reactive with antibodies to the N terminus of Parkin but not the In-Between-RING ("IBR") domain, which had been deleted by both mutations. This large Parkin pedigree represents a unique opportunity to prospectively study the role of heterozygous Parkin mutations as a PD risk factor, to identify additional contributors to the expression of late-onset PD in heterozygous carriers, and to reexamine the role of Parkin in inclusion formation.
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Abstract
Mutations in the Parkin gene are associated with Parkinson s disease (PD). The gene product has been shown to be an E3 protein-ubiquitin ligase, catalyzing the addition of ubiquitin to target proteins prior to their destruction via the proteasome. This activity is thus key in regulating the turnover of substrate proteins. A predictive hypothesis for how this results in PD is that the misregulation of proteasomal degradation of Parkin s substrates is deleterious to neurons. Several different laboratories have identified alternate candidate proteins. In this review, the likelihood of each of the proposed substrates for parkin being robust will be evaluated. The distribution and abundance of the proteins will be examined for clues as to which are the pathologically important substrates for parkin. The possibility that loss of regulation of turnover of one or more of these substrates contributes to the selective neurodegeneration seen in PD is also discussed.
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Affiliation(s)
- Mark R Cookson
- Laboratory of Neurogenetics National Institute on Agins, NIH, Bethesda, MD 20892, USA.
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Abstract
Two intellectually disabled adults with Angelman Syndrome are reported who developed intermittent episodes of a severe resting tremor, cogwheel rigidity and bradykinesia in their late teens. The Parkinsonism was not due to medications and there was a dramatic improvement with levodopa therapy. The association between Angelman Syndrome and Parkinsonism has not previously been described.
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Affiliation(s)
- M Harbord
- Department of Paediatrics and Child Health, Flinders Medical Centre, Bedford Park, SA, Australia
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West A, Farrer M, Petrucelli L, Cookson M, Lockhart P, Hardy J. Identification and characterization of the human parkin gene promoter. J Neurochem 2001; 78:1146-52. [PMID: 11553688 DOI: 10.1046/j.1471-4159.2001.00512.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Compound mutations and homozygous loss of function of the parkin gene causes juvenile and early onset, autosomal recessive parkinsonism. Pathologically, the disease is associated with loss of dopaminergic neurons in the substantia nigra pars compacta and locus ceruleus, usually without Lewy body pathology. Hemizygous families have been described that may harbor mutations outside of the open reading frame. The parkin gene promoter has yet to be characterized, and therein, mutations in hemizygous families may plausibly be identified. To identify the promoter of the parkin gene, the transcription start site was defined by a combination of primer extension and 5' RACE. Five kilobases of DNA 5' to the parkin start codon were directly sequenced from a BAC containing parkin exon 1 and evaluated for promoter motifs. The parkin promoter lacks TATA or CAAT boxes and appears to share homology to the alpha-synuclein promoter. Deletion constructs demonstrated core promoter activity and tissue specific enhancing regions in HEK-293T and SH-SY5Y cells.
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Affiliation(s)
- A West
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224, USA
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Klein C, Pramstaller PP, Kis B, Page CC, Kann M, Leung J, Woodward H, Castellan CC, Scherer M, Vieregge P, Breakefield XO, Kramer PL, Ozelius LJ. Parkin deletions in a family with adult-onset, tremor-dominant parkinsonism: Expanding the phenotype. Ann Neurol 2001. [DOI: 10.1002/1531-8249(200007)48:1<65::aid-ana10>3.0.co;2-l] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Saito M, Maruyama M, Ikeuchi K, Kondo H, Ishikawa A, Yuasa T, Tsuji S. Autosomal recessive juvenile parkinsonism. Brain Dev 2000; 22 Suppl 1:S115-7. [PMID: 10984671 DOI: 10.1016/s0387-7604(00)00137-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Autosomal recessive juvenile parkinsonism (AR-JP) is a hereditary neurodegenerative disorder characterized by levodopa-responsive parkinsonism with onset before age 40 years and a slowly progressive course. Families with this condition have been described predominantly in Japanese population, occasionally under different names including an autosomal recessive early-onset parkinsonism with diurnal fluctuation (AR-EPDF) or a familial form of juvenile parkinsonism. Recently, the causative gene for AR-JP was mapped on chromosome 6q25.2-q27, and subsequently a novel gene 'parkin' was identified by means of positional cloning. In this manuscript, we review the clinical, pathological and genetical aspects of AR-JP. It would not only promise to provide important insights into the molecular mechanisms of selective degeneration of dopaminergic neurons in AR-JP, but also bring insights into the mechanisms of degeneration of these neurons in Parkinson's disease.
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Affiliation(s)
- M Saito
- Department of Neurology, National West Niigata Central Hospital, 950-2085, Niigata, Japan
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Abstract
We studied the clinical features, laboratory investigation, management and natural history of a cohort of patients with Juvenile Parkinsonism (JP), seen at a tertiary referral centre. JP was defined as Parkinsonism with onset at age 20 years or less. Six patients (five male, one female) entered the study. The mean age at onset of Parkinsonism was 12.5 years (range 7-19) and the mean follow-up time was 49.3 months (range 40-57). Bradykinesia, rigidity, and postural instability were observed in all patients and five subjects had tremor. Dystonia was present in four subjects. Other clinical features were dementia (five subjects), supranuclear ophthalmoparesis (five subjects), seizures (three subjects), multifocal myoclonus (one subject), decreased deep reflexes (one subject), pyramidal signs (one subject). Family history of Parkinson's disease (PD) was positive in one subject. Work-up for Wilson's disease was negative in all patients. Neuroimaging studies showed cortical atrophy in two subjects and mild brainstem atrophy in two others. Sea-blue histiocytes were found in one subject. L-dopa improved the Parkinsonism in all subjects but four rapidly developed fluctuations and dyskinesias, requiring, in one, stereotaxic surgery. After a mean disease duration of 6.5 years, five subjects require assistance for performance of all daily activities. JP is a heterogeneous clinical entity. In the majority of patients, no underlying cause is identified. The unusual clinical features suggest most subjects have a CNS degenerative disease distinct from PD. There is, however, evidence suggesting that PD may rarely cause JP. Gangliosidosis is another cause of L-dopa-responsive JP. Regardless of the cause, in the present study JP displays an aggressive and rapidly progressive course in most patients.
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Affiliation(s)
- F Cardoso
- Movement Disorders Clinic, Department of Neurology, The Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Abstract
In an effort to accelerate likelihood computations on pedigrees, Lange and Goradia defined a genotype-elimination algorithm that aims to identify those genotypes that need not be considered during the likelihood computation. For pedigrees without loops, they showed that their algorithm was optimal, in the sense that it identified all genotypes that lead to a Mendelian inconsistency. Their algorithm, however, is not optimal for pedigrees with loops, which continue to pose daunting computational challenges. We present here a simple extension of the Lange-Goradia algorithm that we prove is optimal on pedigrees with loops, and we give examples of how our new algorithm can be used to detect genotyping errors. We also introduce a more efficient and faster algorithm for carrying out the fundamental step in the Lange-Goradia algorithm-namely, genotype elimination within a nuclear family. Finally, we improve a common algorithm for computing the likelihood of a pedigree with multiple loops. This algorithm breaks each loop by duplicating a person in that loop and then carrying out a separate likelihood calculation for each vector of possible genotypes of the loop breakers. This algorithm, however, does unnecessary computations when the loop-breaker vector is inconsistent. In this paper we present a new recursive loop breaker-elimination algorithm that solves this problem and illustrate its effectiveness on a pedigree with six loops.
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Affiliation(s)
- J R O'Connell
- University of Pittsburgh, Department of Human Genetics, Pittsburgh, PA 15261, USA.
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Abstract
Since the first description of Parkinson's disease in 1817 there have been numerous attempts to clarify the relative contribution of hereditary and environmental factors in its aetiology. Epidemiological and case-control studies as well as the existence of families with monogenic Parkinson's disease point clearly to a genetic contribution. Insights into the genetic basis of Parkinson's disease will lead to a greater understanding of the condition at a molecular level which will in turn allow the development of new rational therapeutic option.
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Affiliation(s)
- S D Spacey
- Department of Clinical Neurology, Institute of Neurology, London, UK
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Abstract
INTRODUCTION What is the role of genetic factors in the pathophysiology of idiopathic Parkinson's disease, one of the most frequent neurodegenerative disorders? In the past two years, identification of two genes and localization of a third one have supported the hypothesis that genetics factors are involved in idiopathic Parkinson's disease. We present arguments that support such hypothesis, and describe recent advances in genetic studies of idiopathic Parkinson's disease. CURRENT KNOWLEDGE AND KEY POINTS The first gene identified on chromosome 4 encodes alpha-synuclein. It causes a rare form of autosomal dominant Parkinson's disease. A locus on the short arm of chromosome 2 was recently identified in families with autosomal dominant Parkinson's disease. More recently, the gene encoding Parkin (located on chromosome 6) has been described. It already appears to be an important locus for juvenile parkinsonism with autosomal recessive transmission. CONCLUSION We now have to understand how mutations in these genes lead to selective degeneration of dopaminergic neurons, and to determine whether or not they participate in the genetic susceptibility of idiopathic Parkinson's disease.
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Affiliation(s)
- D Brassat
- Fédération de neurologie, hôpital de la Pitié-Salpêtrière, Paris, France
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Affiliation(s)
- F S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
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Fujishige K, Kotera J, Michibata H, Yuasa K, Takebayashi S, Okumura K, Omori K. Cloning and characterization of a novel human phosphodiesterase that hydrolyzes both cAMP and cGMP (PDE10A). J Biol Chem 1999; 274:18438-45. [PMID: 10373451 DOI: 10.1074/jbc.274.26.18438] [Citation(s) in RCA: 332] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
cDNA encoding a novel phosphodiesterase (PDE) was isolated from a human fetal lung cDNA library and designated PDE10A. The deduced amino acid sequence contains 779 amino acids, including a putative cGMP binding sequence in the amino-terminal portion of the molecule and a catalytic domain that is 16-47% identical in amino acid sequence to those of other PDE families. Recombinant PDE10A transfected and expressed in COS-7 cells hydrolyzed cAMP and cGMP with Km values of 0.26 and 7.2 microM, respectively, and Vmax with cGMP was almost twice that with cAMP. Of the PDE inhibitors tested, dipyridamole was most effective, with IC50 values of 1.2 and 0.45 microM for inhibition of cAMP and cGMP hydrolysis, respectively. cGMP inhibited hydrolysis of cAMP, and cAMP inhibited cGMP hydrolysis with IC50 values of 14 and 0.39 microM, respectively. Thus, PDE10A exhibited properties of a cAMP PDE and a cAMP-inhibited cGMP PDE. PDE10A transcripts were particularly abundant in the putamen and caudate nucleus regions of brain and in thyroid and testis, and in much lower amounts in other tissues. The PDE10A gene was located on chromosome 6q26 by fluorescent in situ hybridization analysis. PDE10A represents a new member of the PDE superfamily, exhibiting unique kinetic properties and inhibitor sensitivity.
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Affiliation(s)
- K Fujishige
- Discovery Research Laboratory, Tanabe Seiyaku Co. Ltd., 2-50, Kawagishi-2-chome, Toda, Saitama 335-8505, Japan
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Abbas N, Lücking CB, Ricard S, Dürr A, Bonifati V, De Michele G, Bouley S, Vaughan JR, Gasser T, Marconi R, Broussolle E, Brefel-Courbon C, Harhangi BS, Oostra BA, Fabrizio E, Böhme GA, Pradier L, Wood NW, Filla A, Meco G, Denefle P, Agid Y, Brice A. A wide variety of mutations in the parkin gene are responsible for autosomal recessive parkinsonism in Europe. French Parkinson's Disease Genetics Study Group and the European Consortium on Genetic Susceptibility in Parkinson's Disease. Hum Mol Genet 1999; 8:567-74. [PMID: 10072423 DOI: 10.1093/hmg/8.4.567] [Citation(s) in RCA: 364] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Autosomal recessive juvenile parkinsonism (AR-JP, PARK2; OMIM 602544), one of the monogenic forms of Parkinson's disease (PD), was initially described in Japan. It is characterized by early onset (before age 40), marked response to levodopa treatment and levodopa-induced dyskinesias. The gene responsible for AR-JP was recently identified and designated parkin. We have analysed the 12 coding exons of the parkin gene in 35 mostly European families with early onset autosomal recessive parkinsonism. In one family, a homozygous deletion of exon 4 could be demonstrated. By direct sequencing of the exons in the index patients of the remaining 34 families, eight previously undescribed point mutations (homozygous or heterozygous) were detected in eight families that included 20 patients. The mutations segregated with the disease in the families and were not detected on 110-166 control chromosomes. Four mutations caused truncation of the parkin protein. Three were frameshifts (202-203delAG, 255delA and 321-322insGT) and one a nonsense mutation (Trp453Stop). The other four were missense mutations (Lys161Asn, Arg256Cys, Arg275Trp and Thr415Asn) that probably affect amino acids that are important for the function of the parkin protein, since they result in the same phenotype as truncating mutations or homozygous exon deletions. Mean age at onset was 38 +/- 12 years, but onset up to age 58 was observed. Mutations in the parkin gene are therefore not invariably associated with early onset parkinsonism. In many patients, the phenotype is indistinguishable from that of idiopathic PD. This study has shown that a wide variety of different mutations in the parkin gene are a common cause of autosomal recessive parkinsonism in Europe and that different types of point mutations seem to be more frequently responsible for the disease phenotype than are deletions.
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Affiliation(s)
- N Abbas
- INSERM U289, Hôpital de la Salpêtrière, 47 Boulevard de l'Hôpital, 75651 Paris Cedex 13, France
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Abstract
Here we review familial Parkinson's disease from clinical, as well as molecular genetic aspects. To date, two genes responsible for familial Parkinson's disease have been identified: one is the alpha-synuclein gene located in the long arm of chromosome 4, and the other is the parkin gene located in the long arm of chromosome 6. The mode of inheritance of the former is autosomal dominant and clinical features consist of levodopa-responsive parkinsonism; the age of onset is younger than that of the sporadic cases (in their 40s), and the progression is faster (average disease duration approximately nine years). The latter form is transmitted as an autosomal recessive, and clinical features consist of early onset (in their 20s), levodopa-responsive parkinsonism, and a slow progression of the disease. In addition, the tau gene has been shown to be the disease gene for familial frontotemporal dementia and parkinsonism linked to chromosome 17. There are many other clinical phenotypes of familial Parkinson's disease among which three forms have been mapped to certain chromosome loci: one is in the short arm of chromosome 2, the two other forms are in the different loci of the short arm of chromosome 4. All of them are transmitted as autosomal dominant traits manifesting levodopa responsive parkinsonism. There still exists however, other clinical phenotypes of chromosome loci which are not known. Molecular cloning of these familial Parkinson's disease genes and the elucidation of the functions of the proteins encoded will certainly contribute greatly to the investigation of the etiology and pathogenesis of more common sporadic form of Parkinson's disease.
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Affiliation(s)
- Y Mizuno
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
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Abstract
The cause of Parkinson's disease (PD) is unknown. The major risk factors identified to date are family history, age, and elements of rural living. Nearly one-third of all PD cases are familial, a small subset of which appears autosomal dominant; however, the majority exhibit no clear inheritance pattern. Autosomal dominant PD is genetically heterogeneous: two PD genes have been mapped to chromosomes 2 and 4 and there may be additional as yet unidentified genes. The common forms of PD-both familial and sporadic cases-appear to involve a complex interplay of genetic susceptibility and environmental exposure. The observations that rural residence and pesticide exposure increase the risk of developing PD, and that a synthetic drug, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, can cause parkinsonism, suggest that at least a subset of PD may be caused by a toxin. Furthermore, modest but significant associations have been reported between PD susceptibility and genes that regulate metabolism of drugs and neurotoxins. There is also evidence for mitochondrial dysfunction in PD, a finding that was recently traced to anomalies in mitochondrial DNA. At the present time, the genetics of PD appear to be complex, involving multiple nuclear genes and possibly mitochondrial genes as well.
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Affiliation(s)
- H Payami
- Department of Molecular and Medical Genetics, Oregon Health Sciences University, Portland 97201-3098, USA
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Lücking CB, Abbas N, Dürr A, Bonifati V, Bonnet AM, de Broucker T, De Michele G, Wood NW, Agid Y, Brice A. Homozygous deletions in parkin gene in European and North African families with autosomal recessive juvenile parkinsonism. The European Consortium on Genetic Susceptibility in Parkinson's Disease and the French Parkinson's Disease Genetics Study Group. Lancet 1998; 352:1355-6. [PMID: 9802278 DOI: 10.1016/s0140-6736(05)60746-5] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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