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Miano-Burkhardt A, Alvarez Jerez P, Daida K, Bandres Ciga S, Billingsley KJ. The Role of Structural Variants in the Genetic Architecture of Parkinson's Disease. Int J Mol Sci 2024; 25:4801. [PMID: 38732020 PMCID: PMC11084710 DOI: 10.3390/ijms25094801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) significantly impacts millions of individuals worldwide. Although our understanding of the genetic foundations of PD has advanced, a substantial portion of the genetic variation contributing to disease risk remains unknown. Current PD genetic studies have primarily focused on one form of genetic variation, single nucleotide variants (SNVs), while other important forms of genetic variation, such as structural variants (SVs), are mostly ignored due to the complexity of detecting these variants with traditional sequencing methods. Yet, these forms of genetic variation play crucial roles in gene expression and regulation in the human brain and are causative of numerous neurological disorders, including forms of PD. This review aims to provide a comprehensive overview of our current understanding of the involvement of coding and noncoding SVs in the genetic architecture of PD.
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Affiliation(s)
- Abigail Miano-Burkhardt
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Sara Bandres Ciga
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
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Papagiannakis N, Liu H, Koros C, Simitsi AM, Stamelou M, Maniati M, Buena-Atienza E, Kartanou C, Karadima G, Makrythanasis P, Vatsellas G, Valente EM, Gasser T, Stefanis L. Parkin mRNA Expression Levels in Peripheral Blood Mononuclear Cells in Parkin-Related Parkinson's Disease. Mov Disord 2024; 39:715-722. [PMID: 38357851 DOI: 10.1002/mds.29739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
INTRODUCTION Pathogenic variants in parkin (PRKN gene) are the second most prevalent known monogenic cause of Parkinson's disease (PD). How monoallelic or biallelic pathogenic variants in the PRKN gene may affect its transcription in patient-derived biological material has not been systematically studied. METHODS PRKN mRNA expression levels were measured with real-time polymerase chain reaction (RT-PCR) in peripheral blood mononuclear cells (PBMCs). PBMCs were derived from PRKN-mutated PD patients (PRKN-PD) (n = 12), sporadic PD (sPD) (n = 21) and healthy controls (n = 21). Six of the PRKN-PD patients were heterozygous, four were compound heterozygous, and two were homozygous for PRKN variants. RESULTS A statistically significant decrease in PRKN expression levels was present, compared to healthy controls and sPD, in heterozygous (P = 0.019 and 0.031 respectively) and biallelic (P < 0.001 for both) PRKN-PD. PRKN expression levels in biallelic PD patients were uniformly very low and were reduced, albeit not significantly, compared to heterozygotes. Based on receiver operating characteristic analysis, low PRKN expression levels were a sensitive and extremely specific indicator for the presence of PRKN pathogenic variants. CONCLUSIONS Assessment of PRKN mRNA levels in PBMCs may be a useful way to screen for biallelic pathogenic variants in the PRKN gene. Suspicion for certain variants in a heterozygous state may also be raised based on low PRKN mRNA levels. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Nikolaos Papagiannakis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Hui Liu
- Department of Neurodegenerative Diseases, Hertie Center for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christos Koros
- 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athina-Maria Simitsi
- 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Stamelou
- 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Matina Maniati
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Elena Buena-Atienza
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Chrysoula Kartanou
- 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgia Karadima
- 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Periklis Makrythanasis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Department of Genetic Medicine and Development, Medical School, University of Geneva, Geneva, Switzerland
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Giannis Vatsellas
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie Center for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Leonidas Stefanis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Lo T, Kushima I, Kimura H, Aleksic B, Okada T, Kato H, Inada T, Nawa Y, Torii Y, Yamamoto M, Kimura R, Funabiki Y, Kosaka H, Numata S, Kasai K, Sasaki T, Yokoyama S, Munesue T, Hashimoto R, Yasuda Y, Fujimoto M, Usami M, Itokawa M, Arai M, Ohi K, Someya T, Watanabe Y, Egawa J, Takahashi T, Suzuki M, Yamasue H, Iwata N, Ikeda M, Ozaki N. Association between copy number variations in parkin (PRKN) and schizophrenia and autism spectrum disorder: A case-control study. Neuropsychopharmacol Rep 2024; 44:42-50. [PMID: 37915257 PMCID: PMC10932780 DOI: 10.1002/npr2.12370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 11/03/2023] Open
Abstract
AIM The present study aimed to examine the association between copy number variations (CNVs) in parkin (PRKN) and schizophrenia (SCZ) and autism spectrum disorder (ASD) in a large case-control sample. METHOD Array comparative genomic hybridization was performed on 3111 cases with SCZ, 1236 cases with ASD, and 2713 controls. We systematically prioritized likely pathogenic CNVs (LP-CNVs) in PRKN and examined their association with SCZ and ASD. RESULTS In total, 3014 SCZ cases (96.9%), 1205 ASD cases (97.5%), and 2671 controls (98.5%) passed quality control. We found that monoallelic carriers of LP-CNVs in PRKN were common (70/6890, 1.02%) and were not at higher risk of SCZ (p = 0.29) or ASD (p = 0.72). We observed that the distribution pattern of LP-CNVs in the Japanese population was consistent with those in other populations. We also identified a patient diagnosed with SCZ and early-onset Parkinson's disease carrying biallelic pathogenic CNVs in PRKN. The absence of Parkinson's symptoms in 10 other monoallelic carriers of the same pathogenic CNV further reflects the lack of effect of monoallelic pathogenic variants in PRKN in the absence of a second hit. CONCLUSION The present findings suggest that monoallelic CNVs in PRKN do not confer a significant risk for SCZ or ASD. However, further studies to investigate the association between biallelic CNVs in PRKN and SCZ and ASD are warranted.
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Grants
- JP15K19720 Japan Society for the Promotion of Science
- JP17H05090 Japan Society for the Promotion of Science
- JP18H04040 Japan Society for the Promotion of Science
- JP18K19511 Japan Society for the Promotion of Science
- JP19K17087 Japan Society for the Promotion of Science
- JP20H03608 Japan Society for the Promotion of Science
- JP20K07942 Japan Society for the Promotion of Science
- JP20K20602 Japan Society for the Promotion of Science
- JP21H00194 Japan Society for the Promotion of Science
- JP21H04815 Japan Society for the Promotion of Science
- JP21H05326 Japan Society for the Promotion of Science
- JP21K07543 Japan Society for the Promotion of Science
- JP22H00986 Japan Society for the Promotion of Science
- JP16dm0107134 Ministry of Education, Culture, Sports, Science and Technology
- JP19ak0101113 Ministry of Education, Culture, Sports, Science and Technology
- JP19dm0207075 Ministry of Education, Culture, Sports, Science and Technology
- JP19ek0109411 Ministry of Education, Culture, Sports, Science and Technology
- JP19km0405216 Ministry of Education, Culture, Sports, Science and Technology
- JP20ek0109488 Ministry of Education, Culture, Sports, Science and Technology
- JP21dk0307103 Ministry of Education, Culture, Sports, Science and Technology
- JP21tm0424220 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425007 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425008 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425012 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0425019 Ministry of Education, Culture, Sports, Science and Technology
- JP21wm0525024 Ministry of Education, Culture, Sports, Science and Technology
- JP22tm0424222 Ministry of Education, Culture, Sports, Science and Technology
- Otsuka Toshimi Scholarship Foundation
- SENSHIN Medical Research Foundation
- Uehara Memorial Foundation
- Japan Society for the Promotion of Science
- Ministry of Education, Culture, Sports, Science and Technology
- Otsuka Toshimi Scholarship Foundation
- SENSHIN Medical Research Foundation
- Uehara Memorial Foundation
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Affiliation(s)
- Tzuyao Lo
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Itaru Kushima
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
- Medical Genomics CenterNagoya University HospitalNagoyaJapan
| | - Hiroki Kimura
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Branko Aleksic
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Takashi Okada
- Department of Developmental Disorders, National Institute of Mental HealthNational Center of Neurology and PsychiatryNagoyaJapan
| | - Hidekazu Kato
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Toshiya Inada
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yoshihiro Nawa
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Youta Torii
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Maeri Yamamoto
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
| | - Ryo Kimura
- Department of Anatomy and Developmental BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Yasuko Funabiki
- Department of Cognitive, Behavioral and Health Sciences, Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Hirotaka Kosaka
- Department of Neuropsychiatry, Faculty of Medical SciencesUniversity of FukuiFukuiJapan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical ScienceTokushima UniversityTokushimaJapan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of MedicineUniversity of TokyoTokyoJapan
- International Research Center for Neurointelligence at University of Tokyo Institutes for Advanced StudyTokyoJapan
| | - Tsukasa Sasaki
- Laboratory of Health Education, Graduate School of EducationUniversity of TokyoTokyoJapan
| | - Shigeru Yokoyama
- Research Center for Child Mental DevelopmentKanazawa UniversityIshikawaJapan
| | - Toshio Munesue
- Research Center for Child Mental DevelopmentKanazawa UniversityIshikawaJapan
| | - Ryota Hashimoto
- Department of Pathology of Mental DiseasesNational Institute of Mental HealthNational Center of Neurology and PsychiatryTokyoJapan
| | - Yuka Yasuda
- Department of Pathology of Mental DiseasesNational Institute of Mental HealthNational Center of Neurology and PsychiatryTokyoJapan
| | - Michiko Fujimoto
- Department of PsychiatryOsaka University Graduate School of MedicineOsakaJapan
| | - Masahide Usami
- Department of Child and Adolescent PsychiatryKohnodai Hospital, National Center for Global Health and MedicineChibaJapan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral SciencesTokyo Metropolitan Institute of Medical ScienceTokyoJapan
- Department of PsychiatryTokyo Metropolitan Matsuzawa HospitalTokyoJapan
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral SciencesTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Kazutaka Ohi
- Department of PsychiatryGifu University Graduate School of MedicineGifuJapan
- Department of General Internal MedicineKanazawa Medical UniversityIshikawaJapan
| | - Toshiyuki Someya
- Department of PsychiatryNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Yuichiro Watanabe
- Department of PsychiatryNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Jun Egawa
- Department of PsychiatryNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Tsutomu Takahashi
- Department of NeuropsychiatryUniversity of Toyama Graduate School of Medicine and Pharmaceutical SciencesToyamaJapan
- Research Center for Idling Brain ScienceUniversity of ToyamaToyamaJapan
| | - Michio Suzuki
- Department of NeuropsychiatryUniversity of Toyama Graduate School of Medicine and Pharmaceutical SciencesToyamaJapan
- Research Center for Idling Brain ScienceUniversity of ToyamaToyamaJapan
| | - Hidenori Yamasue
- Department of PsychiatryHamamatsu University School of MedicineHamamatsuJapan
| | - Nakao Iwata
- Department of PsychiatryFujita Health University School of MedicineToyoakeJapan
| | - Masashi Ikeda
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
- Department of PsychiatryFujita Health University School of MedicineToyoakeJapan
| | - Norio Ozaki
- Department of PsychiatryNagoya University Graduate School of MedicineNagoyaJapan
- Institute for Glyco‐core ResearchNagoya UniversityNagoyaJapan
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Rački V, Bergant G, Papić E, Kovanda A, Hero M, Rožmarić G, Starčević Čizmarević N, Ristić S, Ostojić S, Kapović M, Maver A, Peterlin B, Vuletić V. GiOPARK Project: The Genetic Study of Parkinson's Disease in the Croatian Population. Genes (Basel) 2024; 15:255. [PMID: 38397244 PMCID: PMC10888376 DOI: 10.3390/genes15020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease is a neurological disorder that affects motor function, autonomic functions, and cognitive abilities. It is likely that both genetic and environmental factors, along with age, contribute to the cause. However, there is no comprehensive guideline for genetic testing for Parkinson's disease, and more research is needed to understand genetic variations in different populations. There has been no research on the genetic background of Parkinson's disease in Croatia so far. Therefore, with the GiOPARK project, we aimed to investigate the genetic variants responsible for Parkinson's disease in 153 Croatian patients with early onset, familial onset, and sporadic late-onset using whole-exome sequencing, along with multiplex ligation-dependent probe amplification and Sanger sequencing in select patients. We found causative variants in 7.84% of the patients, with GBA being the most common gene (4.58%), followed by PRKN (1.96%), ITM2B (0.65%), and MAPT (0.65%). Moreover, variants of uncertain significance were identified in 26.14% of the patients. The causative variants were found in all three subgroups, indicating that genetic factors play a role in all the analyzed Parkinson's disease subtypes. This study emphasizes the need for more inclusive research and improved guidelines to better understand the genetic basis of Parkinson's disease and facilitate more effective clinical management.
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Affiliation(s)
- Valentino Rački
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Eliša Papić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Mario Hero
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gloria Rožmarić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Nada Starčević Čizmarević
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Smiljana Ristić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Miljenko Kapović
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Vladimira Vuletić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
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Landoulsi Z, Pachchek S, Bobbili DR, Pavelka L, May P, Krüger R. Genetic landscape of Parkinson's disease and related diseases in Luxembourg. Front Aging Neurosci 2023; 15:1282174. [PMID: 38173558 PMCID: PMC10761438 DOI: 10.3389/fnagi.2023.1282174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Objectives To explore the genetic architecture of PD in the Luxembourg Parkinson's Study including cohorts of healthy people and patients with Parkinson's disease (PD) and atypical parkinsonism (AP). Methods 809 healthy controls, 680 PD and 103 AP were genotyped using the Neurochip array. We screened and validated rare single nucleotide variants (SNVs) and copy number variants (CNVs) within seven PD-causing genes (LRRK2, SNCA, VPS35, PRKN, PARK7, PINK1 and ATP13A2). Polygenic risk scores (PRSs) were generated using the latest genome-wide association study for PD. We then estimated the role of common variants in PD risk by applying gene-set-specific PRSs. Results We identified 60 rare SNVs in seven PD-causing genes, nine of which were pathogenic in LRRK2, PINK1 and PRKN. Eleven rare CNVs were detected in PRKN including seven duplications and four deletions. The majority of PRKN SNVs and CNVs carriers were heterozygous and not differentially distributed between cases and controls. The PRSs were significantly associated with PD and identified specific molecular pathways related to protein metabolism and signal transduction as drivers of PD risk. Conclusion We performed a comprehensive genetic characterization of the deep-phenotyped individuals of the Luxembourgish Parkinson's Study. Heterozygous SNVs and CNVs in PRKN were not associated with higher PD risk. In particular, we reported novel digenic variants in PD related genes and rare LRRK2 SNVs in AP patients. Our findings will help future studies to unravel the genetic complexity of PD.
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Affiliation(s)
- Zied Landoulsi
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sinthuja Pachchek
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dheeraj Reddy Bobbili
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lukas Pavelka
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Patrick May
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease. Mov Disord 2023; 38:2249-2257. [PMID: 37926948 PMCID: PMC10843047 DOI: 10.1002/mds.29610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Parkin RBR E3 ubiquitin-protein ligase (PRKN) mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E, which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. OBJECTIVES To identify complex structural variants in PRKN using long-read sequencing. METHODS We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read sequencing. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of Accelerating Medicines Partnership Parkinson's disease (AMP-PD) and United Kingdom (UK)-Biobank datasets. RESULTS Multiple ligation probe amplification identified a heterozygous exon three deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7 Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN expression. CONCLUSIONS This is the first report describing a large 7 Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read sequencing for structural variant analysis in unresolved young-onset PD cases. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo Tokyo Koto Geriatric Medical Center 3-3-20 Shinsuna, Koto-ku, Tokyo 136-0075
| | - Risa Nonaka
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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7
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-read sequencing resolves a complex structural variant in PRKN Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.14.23293948. [PMID: 37790330 PMCID: PMC10543050 DOI: 10.1101/2023.08.14.23293948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background PRKN mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. Objectives To identify complex structural variants in PRKN using long-read sequencing. Methods We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of AMP-PD and UK-Biobank datasets. Results Multiple ligation probe amplification identified a heterozygous exon 3 deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4,941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN isoforms. Conclusions This is the first report describing a large 7Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read whole genome sequencing for structural variant analysis in unresolved young-onset PD cases.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Risa Nonaka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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8
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Castelo Rueda MP, Zanon A, Gilmozzi V, Lavdas AA, Raftopoulou A, Delcambre S, Del Greco M F, Klein C, Grünewald A, Pramstaller PP, Hicks AA, Pichler I. Molecular phenotypes of mitochondrial dysfunction in clinically non-manifesting heterozygous PRKN variant carriers. NPJ Parkinsons Dis 2023; 9:65. [PMID: 37072441 PMCID: PMC10113363 DOI: 10.1038/s41531-023-00499-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
Homozygous or compound heterozygous (biallelic) variants in PRKN are causal for PD with highly penetrant symptom expression, while the much more common heterozygous variants may predispose to PD with highly reduced penetrance, through altered mitochondrial function. In the presence of pathogenic heterozygous variants, it is therefore important to test for mitochondrial alteration in cells derived from variant carriers to establish potential presymptomatic molecular markers. We generated lymphoblasts (LCLs) and human induced pluripotent stem cell (hiPSC)-derived neurons from non-manifesting heterozygous PRKN variant carriers and tested them for mitochondrial functionality. In LCLs, we detected hyperactive mitochondrial respiration, and, although milder compared to a biallelic PRKN-PD patient, hiPSC-derived neurons of non-manifesting heterozygous variant carriers also displayed several phenotypes of altered mitochondrial function. Overall, we identified molecular phenotypes that might be used to monitor heterozygous PRKN variant carriers during the prodromal phase. Such markers might also be useful to identify individuals at greater risk of eventual disease development and for testing potential mitochondrial function-based neuroprotective therapies before neurodegeneration advances.
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Affiliation(s)
- Maria Paulina Castelo Rueda
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Valentina Gilmozzi
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Athina Raftopoulou
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Economics, University of Patras, Patras, Greece
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esche-sur-Alzette, Luxembourg
| | - Fabiola Del Greco M
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esche-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
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9
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Barone R, Cirnigliaro L, Saccuzzo L, Valdese S, Pettinato F, Prato A, Bernardini L, Fichera M, Rizzo R. PARK2 microdeletion in a multiplex family with autism spectrum disorder. Int J Dev Neurosci 2023; 83:121-131. [PMID: 36478299 DOI: 10.1002/jdn.10246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/13/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND PARK2 (PRKN; MIM*602544) encodes Parkin protein, an ubiquitin-protein ligase required for proteasomal degradation and operating in the synaptic compartments. Copy number variations (CNVs) involving PARK2 have been associated with autism spectrum disorder (ASD). We report on a family with ASD (multiplex family) harbouring a microdeletion at chr. 6q26 causing PARK2 disruption. METHODS CNV analyses were performed using CGH/SNP-array platforms, and the detected microdeletion was confirmed by real-time quantitative PCR. Standardized psychometric evaluation was used for neurobehavioral characterization. RESULTS We found an intragenic ~157 kb microdeletion of the chromosomal region 6q26 causing PARK2 disruption in two male sibs with ASD and syndromic phenotype. They both had dysmorphic facial features with coarse faces, deeply set eyes with long horizontal palpebral fissures, long eyelashes and thick eyebrows, fleshy lips and mild skeletal problems. We found an intrafamilial clinical heterogeneity owing to different severity of the autism symptoms between the affected sibs: the younger one had minimally verbal autism and severe intellectual disability, whereas his older brother presented high-functioning autism and preserved speech. Parental analysis and real-time PCR using a PRKN fragment mapping within the deletion demonstrated that the deletion was inherited from their father having subthreshold features of ASD consisting with broad autism phenotype. CONCLUSIONS The study corroborates the hypothesis that PARK2 aberrations may be associated with ASD and highlights correlations between CNV affecting PARK2 and ASD in a multiplex family. We show remarkable intrafamilial variability in the severity of inherited ASD associated with PARK2 microdeletion.
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Affiliation(s)
- Rita Barone
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.,Reseach Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Lara Cirnigliaro
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Lucia Saccuzzo
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Silvia Valdese
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Fabio Pettinato
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Adriana Prato
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.,Department of Cognitive Sciences, Psychology, Education and Cultural Studies, University of Messina, Messina, Italy
| | - Laura Bernardini
- Cytogenetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, FG, Italy
| | - Marco Fichera
- Reseach Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy.,Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Renata Rizzo
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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10
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Wang Y, Ling Y, Gong J, Zhao X, Zhou H, Xie B, Lou H, Zhuang X, Jin L, Fan S, Zhang G, Xu S. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Res 2022; 51:D1109-D1116. [PMID: 36243989 PMCID: PMC9825616 DOI: 10.1093/nar/gkac905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 01/30/2023] Open
Abstract
Structural variations (SVs) play important roles in human evolution and diseases, but there is a lack of data resources concerning representative samples, especially for East Asians. Taking advantage of both next-generation sequencing and third-generation sequencing data at the whole-genome level, we developed the database PGG.SV to provide a practical platform for both regionally and globally representative structural variants. In its current version, PGG.SV archives 584 277 SVs obtained from whole-genome sequencing data of 6048 samples, including 1030 long-read sequencing genomes representing 177 global populations. PGG.SV provides (i) high-quality SVs with fine-scale and precise genomic locations in both GRCh37 and GRCh38, covering underrepresented SVs in existing sequencing and microarray data; (ii) hierarchical estimation of SV prevalence in geographical populations; (iii) informative annotations of SV-related genes, potential functions and clinical effects; (iv) an analysis platform to facilitate SV-based case-control association studies and (v) various visualization tools for understanding the SV structures in the human genome. Taken together, PGG.SV provides a user-friendly online interface, easy-to-use analysis tools and a detailed presentation of results. PGG.SV is freely accessible via https://www.biosino.org/pggsv.
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Affiliation(s)
| | | | | | - Xiaohan Zhao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Hanwen Zhou
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo Xie
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haiyi Lou
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xinhao Zhuang
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | | | - Shaohua Fan
- Correspondence may also be addressed to Shaohua Fan.
| | - Guoqing Zhang
- Correspondence may also be addressed to Guoqing Zhang.
| | - Shuhua Xu
- To whom correspondence should be addressed. Tel: +86 21 31246617; Fax: +86 21 31246617;
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11
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Zhu W, Huang X, Yoon E, Bandres-Ciga S, Blauwendraat C, Billingsley KJ, Cade JH, Wu BP, Williams VH, Schindler AB, Brooks J, Gibbs JR, Hernandez DG, Ehrlich D, Singleton AB, Narendra DP. Heterozygous PRKN mutations are common but do not increase the risk of Parkinson's disease. Brain 2022; 145:2077-2091. [PMID: 35640906 PMCID: PMC9423714 DOI: 10.1093/brain/awab456] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/25/2021] [Indexed: 12/29/2022] Open
Abstract
PRKN mutations are the most common recessive cause of Parkinson's disease and are a promising target for gene and cell replacement therapies. Identification of biallelic PRKN patients at the population scale, however, remains a challenge, as roughly half are copy number variants and many single nucleotide polymorphisms are of unclear significance. Additionally, the true prevalence and disease risk associated with heterozygous PRKN mutations is unclear, as a comprehensive assessment of PRKN mutations has not been performed at a population scale. To address these challenges, we evaluated PRKN mutations in two cohorts with near complete genotyping of both single nucleotide polymorphisms and copy number variants: the NIH-PD + AMP-PD cohort, the largest Parkinson's disease case-control cohort with whole genome sequencing data from 4094 participants, and the UK Biobank, the largest cohort study with whole exome sequencing and genotyping array data from 200 606 participants. Using the NIH-PD participants, who were genotyped using whole genome sequencing, genotyping array, and multi-plex ligation-dependent probe amplification, we validated genotyping array for the detection of copy number variants. Additionally, in the NIH-PD cohort, functional assays of patient fibroblasts resolved variants of unclear significance in biallelic carriers and suggested that cryptic loss of function variants in monoallelic carriers are not a substantial confounder for association studies. In the UK Biobank, we identified 2692 PRKN copy number variants from genotyping array data from nearly half a million participants (the largest collection to date). Deletions or duplications involving exon 2 accounted for roughly half of all copy number variants and the vast majority (88%) involved exons 2, 3, or 4. In the UK Biobank, we found a pathogenic PRKN mutation in 1.8% of participants and two mutations in ∼1/7800 participants. Those with one PRKN pathogenic variant were as likely as non-carriers to have Parkinson's disease [odds ratio = 0.91 (0.58-1.38), P-value 0.76] or a parent with Parkinson's disease [odds ratio = 1.12 (0.94-1.31), P-value = 0.19]. Similarly, those in the NIH-PD + AMP + PD cohort with one PRKN pathogenic variant were as likely as non-carriers to have Parkinson's disease [odds ratio = 1.29 (0.74-2.38), P-value = 0.43]. Together our results demonstrate that heterozygous pathogenic PRKN mutations are common in the population but do not increase the risk of Parkinson's disease.
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Affiliation(s)
- William Zhu
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Xiaoping Huang
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Esther Yoon
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3705, USA
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Kimberly J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Joshua H Cade
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Beverly P Wu
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Victoria H Williams
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Alice B Schindler
- National Institute of Neurological Disorders and Stroke, Neurogenetics Branch, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Janet Brooks
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - J Raphael Gibbs
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Dena G Hernandez
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Debra Ehrlich
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3705, USA
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD 20892-3705, USA
| | - Derek P Narendra
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-3705, USA
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12
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Seibler P, Rakovic A. Patient-derived cells - an irreplaceable tool for research of reduced penetrance in movement disorders. MED GENET-BERLIN 2022; 34:125-130. [PMID: 38835901 PMCID: PMC11006347 DOI: 10.1515/medgen-2022-2133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Movement disorders comprise a clinically, pathologically, and genetically heterogeneous group of diseases associated with the phenomenon of reduced penetrance. Penetrance refers to the likelihood that a clinical condition will occur when a particular genotype is present. Elucidating the cause of reduced penetrance may contribute to more personalized medicine by identifying genetic factors that may prevent individuals from developing disease. Therefore, patient material becomes an irreplaceable resource in this approach. It is needed to identify genetic modifiers of the disease in the first place and to subsequently elucidate underlying mechanisms in endogenous human cell models that provide the entire genetic background.
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Affiliation(s)
- Philip Seibler
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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13
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Devkota K, Schmidt H, Werenski M, Murphy JM, Erden M, Arsenescu V, Cowen LJ. GLIDER: Function Prediction from GLIDE-based Neigborhoods. Bioinformatics 2022; 38:3395-3406. [PMID: 35575379 PMCID: PMC9237677 DOI: 10.1093/bioinformatics/btac322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Protein function prediction, based on the patterns of connection in a Protein-Protein Interaction (or Association) network, is perhaps the most studied of the classical, fundamental inference problems for biological networks. A highly successful set of recent approaches use random walk-based low dimensional embeddings, that tend to place functionally similar proteins into coherent spatial regions. However, these approaches lose valuable local graph structure from the network when considering only the embedding. We introduce GLIDER, a method that replaces a protein-protein interaction or association network with a new graph-based similarity network. GLIDER is based on a variant of our previous GLIDE method, which was designed to predict missing links in Protein-Protein Association networks, capturing implicit local and global (i.e. embedding-based) graph properties. RESULTS GLIDER outperforms competing methods on the task of predicting GO functional labels in cross-validation on a heterogeneous collection of four Human Protein-Protein Association networks derived from the 2016 DREAM Disease Module Identification Challenge, and also on three different protein-protein association networks built from the STRING database. We show that this is due to the strong functional enrichment that is present in the local GLIDER neighborhood in multiple different types of protein-protein association networks. Furthermore, we introduce the GLIDER graph neighborhood as a way for biologists to visualize the local neighborhood of a disease gene. As an application, we look at the local GLIDER neighborhoods of a set of known Parkinson's Disease GWAS genes, rediscover many genes which have known involvement in Parkinson's disease pathways, plus suggest some new genes to study. AVAILABILITY All code is publicly available and can be accessed here: https://github.com/kap-devkota/GLIDER. SUPPLEMENTARY INFORMATION is available at Bioinformatics online.
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Affiliation(s)
- Kapil Devkota
- Department of Computer Science, Tufts University, Medford, MA, 02155, USA
| | - Henri Schmidt
- Department of Computer Science, Tufts University, Medford, MA, 02155, USA
| | - Matt Werenski
- Department of Computer Science, Tufts University, Medford, MA, 02155, USA
| | - James M Murphy
- Department of Mathematics, Tufts University, Medford, MA, 02155, USA
| | - Mert Erden
- Department of Computer Science, Tufts University, Medford, MA, 02155, USA
| | - Victor Arsenescu
- Department of Computer Science, Tufts University, Medford, MA, 02155, USA
| | - Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, MA, 02155, USA
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14
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Tönges L, Kwon EH, Klebe S. Monogenetic Forms of Parkinson’s Disease – Bridging the Gap Between Genetics and Biomarkers. Front Aging Neurosci 2022; 14:822949. [PMID: 35317530 PMCID: PMC8934414 DOI: 10.3389/fnagi.2022.822949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
The therapy of neurodegenerative diseases such as Parkinson’s disease (PD) is still limited to the treatment of symptoms and primarily aimed at compensating for dopaminergic hypofunction. Numerous disease-modifying therapies currently in the pipeline attempt to modify the underlying pathomechanisms. In recent decades, the results of molecular genetics and biomarker research have raised hopes of earlier diagnosis and new neuroprotective therapeutic approaches. As the disease-causing processes in monogenetic forms of PD are better understood than in sporadic PD, these disease subsets are likely to benefit first from disease-modifying therapies. Recent studies have suggested that disease-relevant changes found in genetically linked forms of PD (i.e., PARK-LRRK2, PARK-GBA) can also be reproduced in patients in whom no genetic cause can be found, i.e., those with sporadic PD. It can, therefore, be assumed that as soon as the first causal therapy for genetic forms of PD is approved, more patients with PD will undergo genetic testing and counseling. Regarding future neuroprotective trials in neurodegenerative diseases and objective parameters such as biomarkers with high sensitivity and specificity for the diagnosis and course of the disease are needed. These biomarkers will also serve to monitor treatment success in clinical trials. Promising examples in PD, such as alpha-synuclein species, lysosomal enzymes, markers of amyloid and tau pathology, and neurofilament light chain, are under investigation in blood and CSF. This paper provides an overview of the opportunities and current limitations of monogenetic diagnostic and biomarker research in PD and aims to build a bridge between current knowledge and association with PD genetics and biomarkers.
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Affiliation(s)
- Lars Tönges
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, Bochum, Germany
| | - Eun Hae Kwon
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Stephan Klebe
- Department of Neurology, University Hospital Essen, Essen, Germany
- *Correspondence: Stephan Klebe,
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15
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Castelo Rueda MP, Gilmozzi V, Riekschnitz DA, Di Segni M, Silipigni R, Pramstaller PP, Hicks AA, Pichler I, Zanon A. Generation and characterization of induced pluripotent stem cell (iPSC) lines of two asymptomatic individuals carrying a heterozygous exon 7 deletion in Parkin (PRKN) and two non-carriers from the same family. Stem Cell Res 2022; 60:102692. [PMID: 35121197 DOI: 10.1016/j.scr.2022.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/20/2022] [Accepted: 01/23/2022] [Indexed: 10/19/2022] Open
Abstract
Mutations in the Parkin (PRKN) gene are the most frequent known cause of autosomal recessive early-onset Parkinson's disease (PD). Heterozygous mutations might predispose to disease with a highly reduced penetrance. We generated iPSC lines from two individuals carrying a heterozygous deletion of exon 7 in the PRKN gene and two controls from the same family. PBMCs were reprogrammed using non-integrating episomal plasmids. The iPSC lines exhibit expression of pluripotency markers, the potential to differentiate into the three germ layers, and a stable karyotype. These lines will serve to study mechanisms of reduced penetrance in heterozygous PRKN mutation carriers.
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Affiliation(s)
- Maria Paulina Castelo Rueda
- Institute for Biomedicine, Eurac Research, Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Valentina Gilmozzi
- Institute for Biomedicine, Eurac Research, Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Diana A Riekschnitz
- Institute for Biomedicine, Eurac Research, Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Marina Di Segni
- Laboratory of Medical Genetics, Fondazione IRCCS Cá Granda, Ospedale Maggiore Policlinico, Milano, Italy
| | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Cá Granda, Ospedale Maggiore Policlinico, Milano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany; Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany.
| | - Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
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16
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Bradshaw AV, Campbell P, Schapira AHV, Morris HR, Taanman JW. The PINK1-Parkin mitophagy signalling pathway is not functional in peripheral blood mononuclear cells. PLoS One 2021; 16:e0259903. [PMID: 34762687 PMCID: PMC8584748 DOI: 10.1371/journal.pone.0259903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/28/2021] [Indexed: 12/25/2022] Open
Abstract
Mutations in the PINK1 and PRKN genes are the most common cause of early-onset familial Parkinson disease. These genes code for the PINK1 and Parkin proteins, respectively, which are involved in the degradation of dysfunctional mitochondria through mitophagy. An early step in PINK1 –Parkin mediated mitophagy is the ubiquitination of the mitofusin proteins MFN1 and -2. The ubiquitination of MFN1 and -2 in patient samples may therefore serve as a biomarker to determine the functional effects of PINK1 and PRKN mutations, and to screen idiopathic patients for potential mitophagy defects. We aimed to characterise the expression of the PINK1 –Parkin mitophagy machinery in peripheral blood mononuclear cells (PBMCs) and assess if these cells could serve as a platform to evaluate mitophagy via analysis of MFN1 and -2 ubiquitination. Mitophagy was induced through mitochondrial depolarisation by treatment with the protonophore CCCP and ubiquitinated MFN proteins were analysed by western blotting. In addition, PINK1 and PRKN mRNA and protein expression levels were characterised with reverse transcriptase quantitative PCR and western blotting, respectively. Whilst CCCP treatment led to MFN ubiquitination in primary fibroblasts, SH-SY5Y neuroblastoma cells and Jurkat leukaemic cells, treatment of PBMCs did not induce ubiquitination of MFN. PRKN mRNA and protein was readily detectable in PBMCs at comparable levels to those observed in Jurkat and fibroblast cells. In contrast, PINK1 protein was undetectable and PINK1 mRNA levels were remarkably low in control PBMCs. Our findings suggest that the PINK1 –Parkin mitophagy signalling pathway is not functional in PBMCs. Therefore, PBMCs are not a suitable biosample for analysis of mitophagy function in Parkinson disease patients.
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Affiliation(s)
- Aaron V. Bradshaw
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Philip Campbell
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Anthony H. V. Schapira
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Huw R. Morris
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jan-Willem Taanman
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
- * E-mail:
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17
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Castelo Rueda MP, Raftopoulou A, Gögele M, Borsche M, Emmert D, Fuchsberger C, Hantikainen EM, Vukovic V, Klein C, Pramstaller PP, Pichler I, Hicks AA. Frequency of Heterozygous Parkin ( PRKN) Variants and Penetrance of Parkinson's Disease Risk Markers in the Population-Based CHRIS Cohort. Front Neurol 2021; 12:706145. [PMID: 34434164 PMCID: PMC8382284 DOI: 10.3389/fneur.2021.706145] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/02/2021] [Indexed: 01/10/2023] Open
Abstract
Mutations in the Parkin (PRKN) gene are the most frequent cause of autosomal recessive early-onset Parkinson's disease (PD). Heterozygous PRKN mutation carriers might also be at increased risk for developing clinical symptoms of PD. Given the high frequency of heterozygous mutations in the general population, it is essential to have better estimates of the penetrance of these variants, and to investigate, which clinical and biochemical markers are present in carriers and thus potentially useful for identifying those individuals at greater risk of developing clinical symptoms later in life. In the present study, we ascertained the frequency of heterozygous PRKN mutation carriers in a large population sample of the Cooperative Health Research in South Tyrol (CHRIS) study, and screened for reported PD risk markers. 164 confirmed heterozygous PRKN mutation carriers were compared with 2,582 controls. A higher number of heterozygous mutation carriers reported a detectable increase in an akinesia-related phenotype, and a higher percentage of carriers had manifested diabetes. We also observed lower resting heart rate in the PRKN mutation carriers. Extending our risk analyses to a larger number of potential carriers and non-carriers using genotype imputation (n = 299 carriers and n = 7,127 non-carriers), from previously published biomarkers we also observed a higher neutrophil-to-lymphocyte ratio (NLR) and lower serum albumin and sodium levels in the heterozygous PRKN variant carriers. These results identify a set of biomarkers that might be useful either individually or as an ensemble to identify variant carriers at greater risk of health issues due to carrier status.
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Affiliation(s)
| | - Athina Raftopoulou
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Economics, University of Patras, Patras, Greece
| | - Martin Gögele
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Max Borsche
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - David Emmert
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Christian Fuchsberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Essi M. Hantikainen
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Vladimir Vukovic
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Centre for Disease Control and Prevention, Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Peter P. Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Neurology, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Andrew A. Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
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18
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Zhang L, Luo A, Pan C, Liu M, Liao S. Genetic study of a Chinese pedigree with early onset Parkinson's disease caused by novel compound heterozygous mutations in PARKIN gene. IBRAIN 2021; 7:108-112. [PMID: 37786907 PMCID: PMC10528791 DOI: 10.1002/j.2769-2795.2021.tb00072.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/17/2021] [Accepted: 06/13/2021] [Indexed: 10/04/2023]
Abstract
Objective To explore the genetic basis for a Chinese pedigree where two siblings were affected with early-onset Parkinson's disease (EOPD). Methods Clinical examinations and genomic analyses were performed on five subjects belonging to two generations of a Han Chinese family. Target regions capture and high throughput sequencing were used to screen these genes associated with Parkinson's disease (PD), tremor, spinocerebellar ataxia, and dystonia. The multiplex ligation dependent probe amplification (MLPA) method was applied to detect rearrangements and large deletion in PARKIN exons. Results Two family members were diagnosed with PD by clinical manifestations. Compound heterozygous mutations, consisting of a fragment deletion in exon 2 and 3 of the PARKIN gene, identified by MLPA in II-3, II-5. Individual exon2 deletion mutations were detected in II-1 while individual exon3 deletion mutations were detected in two thirds generations (III-5, III-6). The compound heterozygous mutations have co-segregated with the disease in the pedigree. Other mutations in some genes associated with PD, tremor, dystonia and other movement disorders were not detected. Conclusion A novel compound heterozygous deletion mutations of the PARKIN gene were identified in a Chinese pedigree and might represent a cause of familial EOPD with autosomal dominant inheritance. Early-onset Parkinson's disease (PD) with PARKIN gene mutation has genetic and clinical heterogeneity.
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Affiliation(s)
- Li Zhang
- Department of neurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Ai‐Di Luo
- Department of neurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Cheng‐Yu Pan
- Department of neurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Mei Liu
- Department of neurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
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19
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Kanaya Y, Kume K, Morino H, Ohsawa R, Kurashige T, Kamada M, Torii T, Izumi Y, Maruyama H, Kawakami H. Analysis of genetic risk factors in Japanese patients with Parkinson's disease. J Hum Genet 2021; 66:957-964. [PMID: 33742109 DOI: 10.1038/s10038-021-00910-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/09/2022]
Abstract
Parkinson's disease (PD) is caused by a combination of genetic and environmental factors. Notably, genetic risk factors vary according to ethnicity and geographical regions, and few studies have analyzed the frequency of PD causative genes in Japanese patients. Therefore, we performed genetic analyses of Japanese patients with PD. We recruited 221 participants, including 26 patients with familial PD. Genetic risk factors were evaluated by target sequencing and gene dosage analysis. We detected the genetic risk factors in 58 cases (26.2%) and classified patients into three groups to clarify the differences in genetic risk factors by age at onset (AAO). The early-onset group (AAO < 50 years) included 18 cases (44.7%), who tended to have a larger number of genetic risk factors than the later-onset groups. Regarding the AAO for each causative gene, patients with PRKN variants were significantly younger at onset than those bearing LRRK2 variants. LRRK2 variants showed similar frequency in each AAO group. Of note, we identified two novel variants. Patients with early-onset PD have more genetic risk factors than patients with late-onset PD. In Japanese patients with PD, PRKN, and LRRK2 were the major PD-related genes. Particularly, LRRK2 was a common genetic factor in all age groups because of the presence of the Asian-specific variant such as LRRK2 p.G2385R. Accumulation of genetic and clinical data can contribute to the development of treatments for PD.
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Affiliation(s)
- Yuhei Kanaya
- Department of Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.,Department of Clinical Neuroscience and Therapeutics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Kodai Kume
- Department of Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hiroyuki Morino
- Department of Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan. .,Department of Clinical Neuroscience and Therapeutics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.
| | - Ryosuke Ohsawa
- Department of Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takashi Kurashige
- Department of Neurology, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Kure, Japan
| | - Masaki Kamada
- Department of Gastroenterology & Neurology, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Tsuyoshi Torii
- Department of Neurology, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Kure, Japan
| | - Yuishin Izumi
- Department of Neurology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Hirofumi Maruyama
- Department of Clinical Neuroscience and Therapeutics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hideshi Kawakami
- Department of Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
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20
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Seike N, Yokoseki A, Takeuchi R, Saito K, Miyahara H, Miyashita A, Ikeda T, Aida I, Nakajima T, Kanazawa M, Wakabayashi M, Toyoshima Y, Takahashi H, Matsumoto R, Toda T, Onodera O, Ishikawa A, Ikeuchi T, Kakita A. Genetic Variations and Neuropathologic Features of Patients with PRKN Mutations. Mov Disord 2021; 36:1634-1643. [PMID: 33570211 DOI: 10.1002/mds.28521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Mutations in PRKN are the most common cause of autosomal recessive juvenile parkinsonism. The objective of this study was to investigate the association between genotype and pathology in patients with PRKN mutations. METHODS We performed a sequence and copy number variation analysis of PRKN, mRNA transcripts, Parkin protein expression, and neuropathology in 8 autopsied patients. RESULTS All the patients harbored biallelic PRKN mutations. Two patients were homozygous and heterozygous, respectively, for the missense mutation p.C431F. Seven patients had exon rearrangements, including 2 patients from a single family who harbored a homozygous deletion of exon 4, and 3 patients who carried a homozygous duplication of exons 6-7, a homozygous duplication of exons 10-11, and a heterozygous duplication of exons 2-4. In the other 2 patients, we found a compound heterozygous duplication of exon 2, deletion of exon 3, and a heterozygous duplication of exon 2. However, sequencing of cDNA prepared from mRNA revealed 2 different transcripts derived from triplication of exon 2 and deletion of exons 2-3 and from duplication of exons 2-4 and deletion of exons 3-4. Western blotting and immunohistochemistry revealed faint or no expression of Parkin in their brains. In the substantia nigra pars compacta, a subfield-specific pattern of neuronal loss and mild gliosis were evident. Lewy bodies were found in 3 patients. Peripheral sensory neuronopathy was a feature. CONCLUSIONS Genomic and mRNA analysis is needed to identify the PRKN mutations. Variable mutations may result in no or little production of mature Parkin and the histopathologic features may be similar. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Naohiko Seike
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan.,Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akio Yokoseki
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Ryoko Takeuchi
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kento Saito
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroaki Miyahara
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Tetsuhiko Ikeda
- Department of Neurology, NHO Niigata National Hospital, Kashiwazaki, Japan
| | - Izumi Aida
- Department of Neurology, NHO Niigata National Hospital, Kashiwazaki, Japan
| | - Takashi Nakajima
- Department of Neurology, NHO Niigata National Hospital, Kashiwazaki, Japan
| | - Masato Kanazawa
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | | | - Yasuko Toyoshima
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hitoshi Takahashi
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Riki Matsumoto
- Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Atsushi Ishikawa
- Department of Neurology, Brain Disease Center Agano Hospital, Agano, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
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21
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Sarihan EI, Pérez-Palma E, Niestroj LM, Loesch D, Inca-Martinez M, Horimoto AR, Cornejo-Olivas M, Torres L, Mazzetti P, Cosentino C, Sarapura-Castro E, Rivera-Valdivia A, Dieguez E, Raggio V, Lescano A, Tumas V, Borges V, Ferraz HB, Rieder CR, Schumacher-Schuh AF, Santos-Lobato BL, Velez-Pardo C, Jimenez-Del-Rio M, Lopera F, Moreno S, Chana-Cuevas P, Fernandez W, Arboleda G, Arboleda H, Arboleda-Bustos CE, Yearout D, Zabetian CP, Thornton TA, O’Connor TD, Lal D, Mata IF. Genome-Wide Analysis of Copy Number Variation in Latin American Parkinson's Disease Patients. Mov Disord 2021; 36:434-441. [PMID: 33150996 PMCID: PMC8059262 DOI: 10.1002/mds.28353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Parkinson's disease is the second most common neurodegenerative disorder and affects people from all ethnic backgrounds, yet little is known about the genetics of Parkinson's disease in non-European populations. In addition, the overall identification of copy number variants at a genome-wide level has been understudied in Parkinson's patients. The objective of this study was to understand the genome-wide burden of copy number variants in Latinos and its association with Parkinson's disease. METHODS We used genome-wide genotyping data from 747 Parkinson's disease patients and 632 controls from the Latin American Research Consortium on the Genetics of Parkinson's disease. RESULTS Genome-wide copy number burden analysis showed that patients were significantly enriched for copy number variants overlapping known Parkinson's disease genes compared with controls (odds ratio, 3.97; 95%CI, 1.69-10.5; P = 0.018). PRKN showed the strongest copy number burden, with 20 copy number variant carriers. These patients presented an earlier age of disease onset compared with patients with other copy number variants (median age at onset, 31 vs 57 years, respectively; P = 7.46 × 10-7 ). CONCLUSIONS We found that although overall genome-wide copy number variant burden was not significantly different, Parkinson's disease patients were significantly enriched with copy number variants affecting known Parkinson's disease genes. We also identified that of 250 patients with early-onset disease, 5.6% carried a copy number variant on PRKN in our cohort. Our study is the first to analyze genome-wide copy number variant association in Latino Parkinson's disease patients and provides insights about this complex disease in this understudied population. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Elif Irem Sarihan
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eduardo Pérez-Palma
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Douglas Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Miguel Inca-Martinez
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Andrea R.V.R. Horimoto
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luis Torres
- Movement Disorders Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- School of Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Pilar Mazzetti
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- School of Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carlos Cosentino
- Movement Disorders Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- School of Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | | | - Elena Dieguez
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Victor Raggio
- Department of Genetics, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Andres Lescano
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Vitor Tumas
- Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanderci Borges
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Henrique B. Ferraz
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos R. Rieder
- Departamento de Neurologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Artur F. Schumacher-Schuh
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre and Departamento de Farmacologia Universidade Federal do Rio Grande do Su, Porto Alegre, Brazil
| | | | - Carlos Velez-Pardo
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Marlene Jimenez-Del-Rio
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Francisco Lopera
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Sonia Moreno
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Pedro Chana-Cuevas
- CETRAM, Facultad de Ciencias Medicas, Universidad de Santiago de Chile, Santiago de Chile, Chile
| | - William Fernandez
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Humberto Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos E. Arboleda-Bustos
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Dora Yearout
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Cyrus P. Zabetian
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dennis Lal
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, Massachusetts, USA
- Epilepsy Center & Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ignacio F. Mata
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
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22
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Interaction between Parkin and α-Synuclein in PARK2-Mediated Parkinson's Disease. Cells 2021; 10:cells10020283. [PMID: 33572534 PMCID: PMC7911026 DOI: 10.3390/cells10020283] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Parkin and α-synuclein are two key proteins involved in the pathophysiology of Parkinson's disease (PD). Neurotoxic alterations of α-synuclein that lead to the formation of toxic oligomers and fibrils contribute to PD through synaptic dysfunction, mitochondrial impairment, defective endoplasmic reticulum and Golgi function, and nuclear dysfunction. In half of the cases, the recessively inherited early-onset PD is caused by loss of function mutations in the PARK2 gene that encodes the E3-ubiquitin ligase, parkin. Parkin is involved in the clearance of misfolded and aggregated proteins by the ubiquitin-proteasome system and regulates mitophagy and mitochondrial biogenesis. PARK2-related PD is generally thought not to be associated with Lewy body formation although it is a neuropathological hallmark of PD. In this review article, we provide an overview of post-mortem neuropathological examinations of PARK2 patients and present the current knowledge of a functional interaction between parkin and α-synuclein in the regulation of protein aggregates including Lewy bodies. Furthermore, we describe prevailing hypotheses about the formation of intracellular micro-aggregates (synuclein inclusions) that might be more likely than Lewy bodies to occur in PARK2-related PD. This information may inform future studies aiming to unveil primary signaling processes involved in PD and related neurodegenerative disorders.
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23
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Lubbe SJ, Bustos BI, Hu J, Krainc D, Joseph T, Hehir J, Tan M, Zhang W, Escott-Price V, Williams NM, Blauwendraat C, Singleton AB, Morris HR. Assessing the relationship between monoallelic PRKN mutations and Parkinson's risk. Hum Mol Genet 2021; 30:78-86. [PMID: 33448283 PMCID: PMC8033143 DOI: 10.1093/hmg/ddaa273] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/10/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Biallelic Parkin (PRKN) mutations cause autosomal recessive Parkinson’s disease (PD); however, the role of monoallelic PRKN mutations as a risk factor for PD remains unclear. We investigated the role of single heterozygous PRKN mutations in three large independent case-control cohorts totalling 10 858 PD cases and 8328 controls. Overall, after exclusion of biallelic carriers, single PRKN mutations were more common in PD than controls conferring a >1.5-fold increase in the risk of PD [P-value (P) = 0.035], with meta-analysis (19 574 PD cases and 468 488 controls) confirming increased risk [Odds ratio (OR) = 1.65, P = 3.69E-07]. Carriers were shown to have significantly younger ages at the onset compared with non-carriers (NeuroX: 56.4 vs. 61.4 years; exome: 38.5 vs. 43.1 years). Stratifying by mutation type, we provide preliminary evidence for a more pathogenic risk profile for single PRKN copy number variant (CNV) carriers compared with single nucleotide variant carriers. Studies that did not assess biallelic PRKN mutations or consist of predominantly early-onset cases may be biasing these estimates, and removal of these resulted in a loss of association (OR = 1.23, P = 0.614; n = 4). Importantly, when we looked for additional CNVs in 30% of PD cases with apparent monoallellic PRKN mutations, we found that 44% had biallelic mutations, suggesting that previous estimates may be influenced by cryptic biallelic mutation status. While this study supports the association of single PRKN mutations with PD, it highlights confounding effects; therefore, caution is needed when interpreting current risk estimates. Together, we demonstrate that comprehensive assessment of biallelic mutation status is essential when elucidating PD risk associated with monoallelic PRKN mutations.
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Affiliation(s)
- Steven J Lubbe
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jing Hu
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Dimitri Krainc
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Theresita Joseph
- Department of Clinical and Movement Neurosciences, and UCL Movement Disorders Centre, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jason Hehir
- National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Manuela Tan
- Department of Clinical and Movement Neurosciences, and UCL Movement Disorders Centre, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Weijia Zhang
- Department of Clinical and Movement Neurosciences, and UCL Movement Disorders Centre, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Valentina Escott-Price
- Institute of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, CF24 4HQ, UK.,Dementia Research Institute at Cardiff, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Nigel M Williams
- Institute of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, CF24 4HQ, UK
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, and UCL Movement Disorders Centre, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
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24
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Borsche M, König IR, Delcambre S, Petrucci S, Balck A, Brüggemann N, Zimprich A, Wasner K, Pereira SL, Avenali M, Deuschle C, Badanjak K, Ghelfi J, Gasser T, Kasten M, Rosenstiel P, Lohmann K, Brockmann K, Valente EM, Youle RJ, Grünewald A, Klein C. Mitochondrial damage-associated inflammation highlights biomarkers in PRKN/PINK1 parkinsonism. Brain 2020; 143:3041-3051. [PMID: 33029617 PMCID: PMC7586086 DOI: 10.1093/brain/awaa246] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/14/2020] [Accepted: 06/17/2020] [Indexed: 12/14/2022] Open
Abstract
There is increasing evidence for a role of inflammation in Parkinson's disease. Recent research in murine models suggests that parkin and PINK1 deficiency leads to impaired mitophagy, which causes the release of mitochondrial DNA (mtDNA), thereby triggering inflammation. Specifically, the CGAS (cyclic GMP-AMP synthase)-STING (stimulator of interferon genes) pathway mitigates activation of the innate immune system, quantifiable as increased interleukin-6 (IL6) levels. However, the role of IL6 and circulating cell-free mtDNA in unaffected and affected individuals harbouring mutations in PRKN/PINK1 and idiopathic Parkinson's disease patients remain elusive. We investigated IL6, C-reactive protein, and circulating cell-free mtDNA in serum of 245 participants in two cohorts from tertiary movement disorder centres. We performed a hypothesis-driven rank-based statistical approach adjusting for multiple testing. We detected (i) elevated IL6 levels in patients with biallelic PRKN/PINK1 mutations compared to healthy control subjects in a German cohort, supporting the concept of a role for inflammation in PRKN/PINK1-linked Parkinson's disease. In addition, the comparison of patients with biallelic and heterozygous mutations in PRKN/PINK1 suggests a gene dosage effect. The differences in IL6 levels were validated in a second independent Italian cohort; (ii) a correlation between IL6 levels and disease duration in carriers of PRKN/PINK1 mutations, while no such association was observed for idiopathic Parkinson's disease patients. These results highlight the potential of IL6 as progression marker in Parkinson's disease due to PRKN/PINK1 mutations; (iii) increased circulating cell-free mtDNA serum levels in both patients with biallelic or with heterozygous PRKN/PINK1 mutations compared to idiopathic Parkinson's disease, which is in line with previous findings in murine models. By contrast, circulating cell-free mtDNA concentrations in unaffected heterozygous carriers of PRKN/PINK1 mutations were comparable to control levels; and (iv) that circulating cell-free mtDNA levels have good predictive potential to discriminate between idiopathic Parkinson's disease and Parkinson's disease linked to heterozygous PRKN/PINK1 mutations, providing functional evidence for a role of heterozygous mutations in PRKN or PINK1 as Parkinson's disease risk factor. Taken together, our study further implicates inflammation due to impaired mitophagy and subsequent mtDNA release in the pathogenesis of PRKN/PINK1-linked Parkinson's disease. In individuals carrying mutations in PRKN/PINK1, IL6 and circulating cell-free mtDNA levels may serve as markers of Parkinson's disease state and progression, respectively. Finally, our study suggests that targeting the immune system with anti-inflammatory medication holds the potential to influence the disease course of Parkinson's disease, at least in this subset of patients.
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Affiliation(s)
- Max Borsche
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Inke R König
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Simona Petrucci
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Division of Medical Genetics, IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Alexander Balck
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | | | - Kobi Wasner
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sandro L Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Christian Deuschle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Katja Badanjak
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jenny Ghelfi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Meike Kasten
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Psychiatry, University of Lübeck, Lübeck, Germany
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Kathrin Brockmann
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Enza Maria Valente
- IRCCS Mondino Foundation, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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25
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Yu E, Rudakou U, Krohn L, Mufti K, Ruskey JA, Asayesh F, Estiar MA, Spiegelman D, Surface M, Fahn S, Waters CH, Greenbaum L, Espay AJ, Dauvilliers Y, Dupré N, Rouleau GA, Hassin-Baer S, Fon EA, Alcalay RN, Gan-Or Z. Analysis of Heterozygous PRKN Variants and Copy-Number Variations in Parkinson's Disease. Mov Disord 2020; 36:178-187. [PMID: 32970363 DOI: 10.1002/mds.28299] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/19/2020] [Accepted: 08/30/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Biallelic PRKN mutation carriers with Parkinson's disease (PD) typically have an earlier disease onset, slow disease progression, and, often, different neuropathology compared to sporadic PD patients. However, the role of heterozygous PRKN variants in the risk of PD is controversial. OBJECTIVES Our aim was to examine the association between heterozygous PRKN variants, including single-nucleotide variants and copy-number variations (CNVs), and PD. METHODS We fully sequenced PRKN in 2809 PD patients and 3629 healthy controls, including 1965 late-onset (63.97 ± 7.79 years, 63% men) and 553 early-onset PD patients (43.33 ± 6.59 years, 68% men). PRKN was sequenced using targeted next-generation sequencing with molecular inversion probes. CNVs were identified using a combination of multiplex ligation-dependent probe amplification and ExomeDepth. To examine whether rare heterozygous single-nucleotide variants and CNVs in PRKN are associated with PD risk and onset, we used optimized sequence kernel association tests and regression models. RESULTS We did not find any associations between all types of PRKN variants and risk of PD. Pathogenic and likely-pathogenic heterozygous single-nucleotide variants and CNVs were less common among PD patients (1.52%) than among controls (1.8%, false discovery rate-corrected P = 0.55). No associations with age at onset and in stratified analyses were found. CONCLUSIONS Heterozygous single-nucleotide variants and CNVs in PRKN are not associated with PD. Molecular inversion probes allow for rapid and cost-effective detection of all types of PRKN variants, which may be useful for pretrial screening and for clinical and basic science studies targeting specifically PRKN patients. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Eric Yu
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Uladzislau Rudakou
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Kheireddin Mufti
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Jennifer A Ruskey
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Farnaz Asayesh
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Mehrdad A Estiar
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Matthew Surface
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Cheryl H Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Alberto J Espay
- UC Gardner Neuroscience Institute and Gardner Family Center for Parkinson's Disease and Movement Disorders, Cincinnati, Ohio, USA
| | - Yves Dauvilliers
- Department of Neurology, National Reference Center for Narcolepsy, Sleep Unit, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Laval, Quebec, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Laval, Quebec, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Sharon Hassin-Baer
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Neurology, Movement Disorders Institute, Sheba Medical Center, Ramat-Gan, Israel
| | - Edward A Fon
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
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26
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Greuel A, Trezzi JP, Glaab E, Ruppert MC, Maier F, Jäger C, Hodak Z, Lohmann K, Ma Y, Eidelberg D, Timmermann L, Hiller K, Tittgemeyer M, Drzezga A, Diederich N, Eggers C. GBA Variants in Parkinson's Disease: Clinical, Metabolomic, and Multimodal Neuroimaging Phenotypes. Mov Disord 2020; 35:2201-2210. [PMID: 32853481 DOI: 10.1002/mds.28225] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/23/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Alterations in the GBA gene (NM_000157.3) are the most important genetic risk factor for Parkinson's disease (PD). Biallelic GBA mutations cause the lysosomal storage disorder Gaucher's disease. The GBA variants p.E365K and p.T408M are associated with PD but not with Gaucher's disease. The pathophysiological role of these variants needs to be further explored. OBJECTIVE This study analyzed clinical, neuropsychological, metabolic, and neuroimaging phenotypes of patients with PD carrying the GBA variants p.E365K and p.T408M. METHODS GBA was sequenced in 56 patients with mid-stage PD. Carriers of GBA variants were compared with noncarriers regarding clinical history and symptoms, neuropsychological features, metabolomics, and multimodal neuroimaging. Blood plasma gas chromatography coupled to mass spectrometry, 6-[18 F]fluoro-L-Dopa positron emission tomography (PET), [18 F]fluorodeoxyglucose PET, and resting-state functional magnetic resonance imaging were performed. RESULTS Sequence analysis detected 13 heterozygous GBA variant carriers (7 with p.E365K, 6 with p.T408M). One patient carried a GBA mutation (p.N409S) and was excluded. Clinical history and symptoms were not significantly different between groups. Global cognitive performance was lower in variant carriers. Metabolomic group differences were suggestive of more severe PD-related alterations in carriers versus noncarriers. Both PET scans showed signs of a more advanced disease; [18 F]fluorodeoxyglucose PET and functional magnetic resonance imaging showed similarities with Lewy body dementia and PD dementia in carriers. CONCLUSIONS This is the first study to comprehensively assess (neuro-)biological phenotypes of GBA variants in PD. Metabolomics and neuroimaging detected more significant group differences than clinical and behavioral evaluation. These alterations could be promising to monitor effects of disease-modifying treatments targeting glucocerebrosidase metabolism. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Andrea Greuel
- Department of Neurology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Jean-Pierre Trezzi
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, Dudelange, Luxembourg.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marina C Ruppert
- Department of Neurology, University Hospital Giessen and Marburg, Marburg, Germany.,Center for Mind, Brain and Behavior, Universities of Marburg and Giessen, Marburg, Germany
| | - Franziska Maier
- Department of Psychiatry and Psychotherapy, Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Zdenka Hodak
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Yilong Ma
- Center for Neurosciences, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - David Eidelberg
- Center for Neurosciences, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Lars Timmermann
- Department of Neurology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Karsten Hiller
- Institute for Biochemistry, Biotechnology and Bioinformatics, University of Braunschweig, Braunschweig, Germany
| | - Marc Tittgemeyer
- Max Planck Institute for Metabolism Research, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress and Aging-Associated Disease, Cologne, Germany
| | - Alexander Drzezga
- Department of Nuclear Medicine, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany.,Cognitive Neuroscience, Institute of Neuroscience and Medicine, Research Center Jülich, Jülich, Germany
| | - Nico Diederich
- Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg
| | - Carsten Eggers
- Department of Neurology, University Hospital Giessen and Marburg, Marburg, Germany.,Center for Mind, Brain and Behavior, Universities of Marburg and Giessen, Marburg, Germany
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27
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Genetic predispositions of Parkinson's disease revealed in patient-derived brain cells. NPJ PARKINSONS DISEASE 2020; 6:8. [PMID: 32352027 PMCID: PMC7181694 DOI: 10.1038/s41531-020-0110-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [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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28
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Hartman JH, Gonzalez-Hunt C, Hall SM, Ryde IT, Caldwell KA, Caldwell GA, Meyer JN. Genetic Defects in Mitochondrial Dynamics in Caenorhabditis elegans Impact Ultraviolet C Radiation- and 6-hydroxydopamine-Induced Neurodegeneration. Int J Mol Sci 2019; 20:ijms20133202. [PMID: 31261893 PMCID: PMC6651461 DOI: 10.3390/ijms20133202] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/30/2022] Open
Abstract
Background: Parkinson’s disease (PD) is one of the most common neurodegenerative disorders involving devastating loss of dopaminergic neurons in the substantia nigra. Early steps in PD pathogenesis include mitochondrial dysfunction, and mutations in mitochondrial genes have been linked to familial forms of the disease. However, low penetrance of mutations indicates a likely important role for environmental factors in PD risk through gene by environment interactions. Herein, we study how genetic deficiencies in mitochondrial dynamics processes including fission, fusion, and mitophagy interact with environmental exposures to impact neurodegeneration. Methods: We utilized the powerful model organism Caenorhabditis elegans to study ultraviolet C radiation (UVC)- and 6-hydroxydopamine-induced degeneration of fluorescently-tagged dopaminergic neurons in the background of fusion deficiency (MFN1/2 homolog, fzo-1), fission deficiency (DMN1L homolog, drp-1), and mitochondria-specific autophagy (mitophagy) deficiency (PINK1 and PRKN homologs, pink-1 and pdr-1). Results: Overall, we found that deficiency in either mitochondrial fusion or fission sensitizes nematodes to UVC exposure (used to model common environmental pollutants) but protects from 6-hydroxydopamine-induced neurodegeneration. By contrast, mitophagy deficiency makes animals more sensitive to these stressors with an interesting exception—pink-1 deficiency conferred remarkable protection from 6-hydroxydopamine. We found that this protection could not be explained by compensatory antioxidant gene expression in pink-1 mutants or by differences in mitochondrial morphology. Conclusions: Together, our results support a strong role for gene by environment interactions in driving dopaminergic neurodegeneration and suggest that genetic deficiency in mitochondrial processes can have complex effects on neurodegeneration.
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Affiliation(s)
- Jessica H Hartman
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | | | - Samantha M Hall
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Ian T Ryde
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA.
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29
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The role of monogenic genes in idiopathic Parkinson's disease. Neurobiol Dis 2018; 124:230-239. [PMID: 30448284 DOI: 10.1016/j.nbd.2018.11.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/01/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Abstract
In the past two decades, mutations in multiple genes have been linked to autosomal dominant or recessive forms of monogenic Parkinson's disease (PD). Collectively, these monogenic (often familial) cases account for less than 5% of all PD, the majority being apparently sporadic cases. More recently, large-scale genome-wide association studies have identified over 40 loci that increase risk of PD. Importantly, there is overlap between monogenic and sporadic PD genes, particularly for the loci that contain the genes SNCA and LRRK2, which are mutated in monogenic dominant PD. There have also been reports of idiopathic PD cases with heterozygous variants in autosomal recessive genes suggesting that these mutations may increase risk of PD. These observations suggest that monogenic and idiopathic PD may have shared pathogenic mechanisms. Here, we focus mainly on the role of monogenic PD genes that represent pleomorphic risk loci for idiopathic PD. We also discuss the functional mechanisms that may play a role in increasing risk of disease in both monogenic and idiopathic forms.
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30
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Jabbari K, Bobbili DR, Lal D, Reinthaler EM, Schubert J, Wolking S, Sinha V, Motameny S, Thiele H, Kawalia A, Altmüller J, Toliat MR, Kraaij R, van Rooij J, Uitterlinden AG, Ikram MA, Zara F, Lehesjoki AE, Krause R, Zimprich F, Sander T, Neubauer BA, May P, Lerche H, Nürnberg P. Rare gene deletions in genetic generalized and Rolandic epilepsies. PLoS One 2018; 13:e0202022. [PMID: 30148849 PMCID: PMC6110470 DOI: 10.1371/journal.pone.0202022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Genetic Generalized Epilepsy (GGE) and benign epilepsy with centro-temporal spikes or Rolandic Epilepsy (RE) are common forms of genetic epilepsies. Rare copy number variants have been recognized as important risk factors in brain disorders. We performed a systematic survey of rare deletions affecting protein-coding genes derived from exome data of patients with common forms of genetic epilepsies. We analysed exomes from 390 European patients (196 GGE and 194 RE) and 572 population controls to identify low-frequency genic deletions. We found that 75 (32 GGE and 43 RE) patients out of 390, i.e. ~19%, carried rare genic deletions. In particular, large deletions (>400 kb) represent a higher burden in both GGE and RE syndromes as compared to controls. The detected low-frequency deletions (1) share genes with brain-expressed exons that are under negative selection, (2) overlap with known autism and epilepsy-associated candidate genes, (3) are enriched for CNV intolerant genes recorded by the Exome Aggregation Consortium (ExAC) and (4) coincide with likely disruptive de novo mutations from the NPdenovo database. Employing several knowledge databases, we discuss the most prominent epilepsy candidate genes and their protein-protein networks for GGE and RE.
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Affiliation(s)
- Kamel Jabbari
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Biocenter, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Dheeraj R. Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Stefan Wolking
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Vishal Sinha
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Susanne Motameny
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Amit Kawalia
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | | | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - M. Arfan Ikram
- Departments of Epidemiology, Neurology, and Radiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Neuroscience Center and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, Medical Faculty University Giessen, Giessen, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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Ferese R, Scala S, Biagioni F, Giardina E, Zampatti S, Modugno N, Colonnese C, Storto M, Fornai F, Novelli G, Ruggieri S, Gambardella S. Heterozygous PLA2G6 Mutation Leads to Iron Accumulation Within Basal Ganglia and Parkinson's Disease. Front Neurol 2018; 9:536. [PMID: 30042723 PMCID: PMC6048271 DOI: 10.3389/fneur.2018.00536] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/18/2018] [Indexed: 12/11/2022] Open
Abstract
Mutations of PLA2G6 gene are responsible for PARK14, an autosomal recessive L-DOPA responsive dystonia/parkinsonism with early/adult onset. This phenotype possesses an high clinical variability, which consists in the occurrence of cerebral and cerebellar atrophy, iron accumulation in the basal ganglia, and cognitive decline. This report describes a PD patient carrying an heterozygous PLA2G6 mutation, which was identified also in his PD affected sister. This patient is characterized by a L-DOPA responsive typical parkinsonian syndrome without the occurrence of dystonia, a slight cognitive decline, presence of iron accumulation both in neo and paleostriatum while cerebellar atrophy was absent. Clinical and imaging features are compatible with the PARK14 phenotype. Although PARK14 has been previously reported to be inherited as a recessive disorder, clinical and genetic analysis of this proband and his family rise the hypothesis that even heterozygous PLA2G6 mutations may cause PARK14. It remains to be analyzed whether these heterozygous variants may act as dominant mutations, or they merely increase the risk to develop PD by acting within a context of synergistic genetic and/or environmental backgrounds.
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Affiliation(s)
| | | | | | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Stefania Zampatti
- IRCCS Neuromed, Pozzilli, Italy.,Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | | | - Claudio Colonnese
- IRCCS Neuromed, Pozzilli, Italy.,DAI Neurology and Psichiatry, Department of Neuroradiology, Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | - Francesco Fornai
- IRCCS Neuromed, Pozzilli, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Giuseppe Novelli
- IRCCS Neuromed, Pozzilli, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
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Diez-Fairen M, Benitez BA, Ortega-Cubero S, Lorenzo-Betancor O, Cruchaga C, Lorenzo E, Samaranch L, Carcel M, Obeso JA, Rodriguez-Oroz MC, Aguilar M, Coria F, Pastor MA, Pastor P. Pooled-DNA target sequencing of Parkinson genes reveals novel phenotypic associations in Spanish population. Neurobiol Aging 2018; 70:325.e1-325.e5. [PMID: 29887346 DOI: 10.1016/j.neurobiolaging.2018.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 04/20/2018] [Accepted: 05/06/2018] [Indexed: 10/16/2022]
Abstract
Eighteen loci and several susceptibility genes have been related to Parkinson's disease (PD). However, most studies focus on single genes in small PD series. Our aim was to establish the genetic background of a large Spanish PD sample. Pooled-DNA target sequencing of 7 major PD genes (SNCA, PARK2, PINK1, DJ-1, LRRK2, GBA, and MAPT) was performed in 562 PD cases. Forty-four variants were found among 114 individuals (20.28%, p<0.05). Among these variants, 30 were found in Mendelian genes (68.18%) and 14 in PD susceptibility genes (31.82%). Seven novel variants were identified. Interestingly, most variants were found in PARK2 and PINK1 genes, whereas SNCA and DJ-1 variants were rare. Validated variants were also genotyped in Spanish healthy controls (n = 597). Carriers of heterozygous PARK2 variants presented earlier disease onset and showed dementia more frequently. PD subjects carrying 2 variants at different genes (1.42%) had an earlier age of onset and a predominantly akinetic-rigid PD phenotype (55.6%, p < 0.05), suggesting that the accumulation of genetic risk variants could modify PD phenotype.
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Affiliation(s)
- Monica Diez-Fairen
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain; Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain
| | - Bruno A Benitez
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO, USA
| | - Sara Ortega-Cubero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain; Division of Neurosciences, Neurogenetics Laboratory, Center for Applied Medical Research, University of Navarra (CIMA), Pamplona, Spain; Department of Neurology and Neurosurgery, Hospital Universitario de Burgos, Burgos, Spain
| | - Oswaldo Lorenzo-Betancor
- Department of Neurology, Veterans Affairs Puget Sound Health Care System, University of Washington School of Medicine, Seattle, WA, USA
| | - Carlos Cruchaga
- Department of Neurology, University of Washington School of Medicine, St. Louis, MO, USA; Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St. Louis, MO, USA
| | - Elena Lorenzo
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain; Division of Neurosciences, Neurogenetics Laboratory, Center for Applied Medical Research, University of Navarra (CIMA), Pamplona, Spain
| | - Lluis Samaranch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Maria Carcel
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain; Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Jose A Obeso
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain; Centre for Integrative Neurosciences AC (CINAC), Hospital HM Puerta del Sur, Fundación Hospitales de Madrid, Madrid, Spain; CEU San Pablo University, Campus de Moncloa, Madrid, Spain
| | - Maria Cruz Rodriguez-Oroz
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain; Department of Neurology, University Hospital Donostia, Neuroscience Unit BioDonostia Research Institute, San Sebastian, Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Miquel Aguilar
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain; Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Francisco Coria
- Clinic for Nervous Disorders, Service of Neurology, Son Espases University Hospital, Palma de Mallorca, Spain
| | - Maria A Pastor
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain; Department of Neurology, Clínica Universidad de Navarra, University of Navarra School of Medicine, Pamplona, Spain; Neuroimaging Laboratory, Division of Neurosciences, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Pau Pastor
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain; Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain.
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33
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Shi Y, Kawakami H, Zang W, Li G, Zhang J, Xu C. Novel compound heterozygous mutations in the PARK2 gene identified in a Chinese pedigree with early-onset Parkinson's disease. Brain Behav 2018; 8:e00901. [PMID: 29568695 PMCID: PMC5853629 DOI: 10.1002/brb3.901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 01/23/2023] Open
Abstract
OBJECTS To capture point mutations and short insertions/deletions in 49 previously reported genes associated with Parkinson's disease (PD) in a Chinese pedigree with early-onset Parkinson's disease (EOPD)-affected individuals. METHODS Clinical examinations and genomic analysis were performed on 21 subjects belonging to three generations of a Chinese family. Target region capture and high-throughput sequencing were used for screening 49 genes, which were previously reported to be associated with PD. The direct Sanger sequencing method in all subjects further verified the abnormal DNA fragments in the PARK2 gene. RESULTS Four family members, including a mother (I-1) and her three children (II-2, II-3, and II-7), were diagnosed with PD by clinical manifestations and/or PET/CT imaging analyses. Novel compound heterozygous mutations, consisting of a fragment deletion in exon 1 to 2 (EX 1-2 del) and a splicing point mutation c.619-1 (G > C) in the 6th intron of the PARK2 gene, were identified in II-2, II-3, and II-7. Individual EX 1-2 del or c.619-1 (G > C) mutations were detected in I-1 and the third generation (III-2, 3, 5, 10, and 11).Other mutations were not detected in the 49 known PD-associated genes. CONCLUSION Novel compound heterozygous mutations were identified in a Chinese pedigree and might represent a cause of familial EOPD with autosomal dominant inheritance.
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Affiliation(s)
- Yingying Shi
- Department of Neurology Henan Provincial People's Hospital Zhengzhou China
| | - Hideshi Kawakami
- Department of Epidemiology Research Institute for Radiation Biology and Medicine Hiroshima University Hiroshima Japan
| | - Weizhou Zang
- Department of Neurology Henan Provincial People's Hospital Zhengzhou China
| | - Gang Li
- Department of Neurology Henan Provincial People's Hospital Zhengzhou China
| | - Jiewen Zhang
- Department of Neurology Henan Provincial People's Hospital Zhengzhou China
| | - Changshui Xu
- Department of Neurology Henan Provincial People's Hospital Zhengzhou China
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34
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Schneider SA, Alcalay RN. Neuropathology of genetic synucleinopathies with parkinsonism: Review of the literature. Mov Disord 2017; 32:1504-1523. [PMID: 29124790 PMCID: PMC5726430 DOI: 10.1002/mds.27193] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/18/2017] [Accepted: 09/13/2017] [Indexed: 12/27/2022] Open
Abstract
Clinical-pathological studies remain the gold-standard for the diagnosis of Parkinson's disease (PD). However, mounting data from genetic PD autopsies challenge the diagnosis of PD based on Lewy body pathology. Most of the confirmed genetic risks for PD show heterogenous neuropathology, even within kindreds, which may or may not include Lewy body pathology. We review the literature of genetic PD autopsies from cases with molecularly confirmed PD or parkinsonism and summarize main findings on SNCA (n = 25), Parkin (n = 20, 17 bi-allelic and 3 heterozygotes), PINK1 (n = 5, 1 bi-allelic and 4 heterozygotes), DJ-1 (n = 1), LRRK2 (n = 55), GBA (n = 10 Gaucher disease patients with parkinsonism), DNAJC13, GCH1, ATP13A2, PLA2G6 (n = 8 patients, 2 with PD), MPAN (n = 2), FBXO7, RAB39B, and ATXN2 (SCA2), as well as on 22q deletion syndrome (n = 3). Findings from autopsies of heterozygous mutation carriers of genes that are traditionally considered recessively inherited are also discussed. Lewy bodies may be present in syndromes clinically distinctive from PD (eg, MPAN-related neurodegeneration) and absent in patients with clinical PD syndrome (eg, LRRK2-PD or Parkin-PD). Therefore, the authors can conclude that the presence of Lewy bodies are not specific to the diagnosis of PD and that PD can be diagnosed even in the absence of Lewy body pathology. Interventions that reduce alpha-synuclein load may be more justified in SNCA-PD or GBA-PD than in other genetic forms of PD. The number of reported genetic PD autopsies remains small, and there are limited genotype-clinical-pathological-phenotype studies. Therefore, larger series of autopsies from genetic PD patients are required. © 2017 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Susanne A Schneider
- Department of Neurology, Ludwig-Maximilians-University of München, Munich, Germany
| | - Roy N. Alcalay
- Department of Neurology, Columbia University Medical Center, New York, New York
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35
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Lubbe SJ, Escott-Price V, Gibbs JR, Nalls MA, Bras J, Price TR, Nicolas A, Jansen IE, Mok KY, Pittman AM, Tomkins JE, Lewis PA, Noyce AJ, Lesage S, Sharma M, Schiff ER, Levine AP, Brice A, Gasser T, Hardy J, Heutink P, Wood NW, Singleton AB, Williams NM, Morris HR. Additional rare variant analysis in Parkinson's disease cases with and without known pathogenic mutations: evidence for oligogenic inheritance. Hum Mol Genet 2017; 25:5483-5489. [PMID: 27798102 PMCID: PMC5418836 DOI: 10.1093/hmg/ddw348] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022] Open
Abstract
Oligogenic inheritance implies a role for several genetic factors in disease etiology. We studied oligogenic inheritance in Parkinson’s (PD) by assessing the potential burden of additional rare variants in established Mendelian genes and/or GBA, in individuals with and without a primary pathogenic genetic cause in two large independent cohorts totaling 7,900 PD cases and 6,166 controls. An excess (≥30%) of cases with a recognised primary genetic cause had ≥1 additional rare variants in Mendelian PD genes, as compared with no known mutation PD cases (17%) and unaffected controls (16%), supporting our hypothesis. Carriers of additional Mendelian gene variants have younger ages at onset (AAO). The effect of additional Mendelian variants in LRRK2 G2019S mutation carriers, of which ATP13A2 variation is particularly common, may account for some of the variation in penetrance. About 10% of No Known Mutation-PD cases harbour a rare GBA variant compared to known pathogenic mutation PD cases (8%) and controls (5%), with carriers having earlier AAOs. Together, the data suggest that the oligogenic inheritance of rare Mendelian variants may be important in patient with a primary pathogenic cause, whereas GBA increases risk across all forms of PD. This study highlights the potential genetic complexity of Mendelian PD. The identification of potential modifying variants provides new insights into disease mechanisms by potentially separating relevant from benign variants and by the interaction between genes in specific pathways. In the future this may be relevant to genetic testing and counselling of patients with PD and their families.
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Affiliation(s)
- Steven J Lubbe
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, UK
| | - Valentina Escott-Price
- Department of Psychological Medicine and Neurology, Institute of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Jose Bras
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - T Ryan Price
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Iris E Jansen
- Department of Clinical Genetics, VU University Medical Center (VUmc), Amsterdam, The Netherlands.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Kin Y Mok
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China
| | - Alan M Pittman
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - James E Tomkins
- School of Pharmacy, University of Reading, Whiteknights, Reading, UK.,Centre for Integrated Neuroscience and Neurodynamics, University of Reading, Whiteknights, Reading, UK
| | - Patrick A Lewis
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,School of Pharmacy, University of Reading, Whiteknights, Reading, UK.,Centre for Integrated Neuroscience and Neurodynamics, University of Reading, Whiteknights, Reading, UK
| | - Alastair J Noyce
- Reta Lila Weston Institute, University College London Institute of Neurology, Queen Square, London, UK
| | - Suzanne Lesage
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Manu Sharma
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Elena R Schiff
- Division of Medicine, University College London, London, UK and 15UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, London, UK
| | - Adam P Levine
- Division of Medicine, University College London, London, UK and 15UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, London, UK
| | - Alexis Brice
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Thomas Gasser
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.,Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - John Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,Reta Lila Weston Institute, University College London Institute of Neurology, Queen Square, London, UK
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.,Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Nicholas W Wood
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, UK.,Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,Department of Clinical Genetics, VU University Medical Center (VUmc), Amsterdam, The Netherlands
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Nigel M Williams
- Department of Psychological Medicine and Neurology, Institute of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - Huw R Morris
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, UK
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36
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Koros C, Simitsi A, Stefanis L. Genetics of Parkinson's Disease: Genotype-Phenotype Correlations. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2017; 132:197-231. [PMID: 28554408 DOI: 10.1016/bs.irn.2017.01.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the first discovery of a specific genetic defect in the SNCA gene, encoding for α-synuclein, as a causative factor for Parkinson's disease 20 years ago, a multitude of other genes have been linked to this disease in rare cases with Mendelian inheritance. Furthermore, the genetic contribution to the much more common sporadic disease has been demonstrated through case control association studies and, more recently, genome-wide association studies. Interestingly, some of the genes with Mendelian inheritance, such as SNCA, are also relevant to the sporadic disease, suggesting common pathogenetic mechanisms. In this review, we place an emphasis on Mendelian forms, and in particular genetic defects which present predominantly with Parkinsonism. We provide details into the particular phenotypes associated with each genetic defect, with a particular emphasis on nonmotor symptoms. For genetic defects for whom a sufficient number of patients has been assessed, there are evident genotype-phenotype correlations. However, it should be noted that patients with the same causative mutation may present with distinctly divergent phenotypes. This phenotypic variability may be due to genetic, epigenetic or environmental factors. From a clinical and genetic point of view, it will be especially interesting in the future to identify genetic factors that modify disease penetrance, the age of onset or other specific phenotypic features.
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Affiliation(s)
- Christos Koros
- National and Kapodistrian University of Athens Medical School, "Attikon" Hospital, Athens, Greece
| | - Athina Simitsi
- National and Kapodistrian University of Athens Medical School, "Attikon" Hospital, Athens, Greece
| | - Leonidas Stefanis
- National and Kapodistrian University of Athens Medical School, "Attikon" Hospital, Athens, Greece.
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37
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Truban D, Hou X, Caulfield TR, Fiesel FC, Springer W. PINK1, Parkin, and Mitochondrial Quality Control: What can we Learn about Parkinson's Disease Pathobiology? JOURNAL OF PARKINSON'S DISEASE 2017; 7:13-29. [PMID: 27911343 PMCID: PMC5302033 DOI: 10.3233/jpd-160989] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/10/2016] [Indexed: 12/12/2022]
Abstract
The first clinical description of Parkinson's disease (PD) will embrace its two century anniversary in 2017. For the past 30 years, mitochondrial dysfunction has been hypothesized to play a central role in the pathobiology of this devastating neurodegenerative disease. The identifications of mutations in genes encoding PINK1 (PTEN-induced kinase 1) and Parkin (E3 ubiquitin ligase) in familial PD and their functional association with mitochondrial quality control provided further support to this hypothesis. Recent research focused mainly on their key involvement in the clearance of damaged mitochondria, a process known as mitophagy. It has become evident that there are many other aspects of this complex regulated, multifaceted pathway that provides neuroprotection. As such, numerous additional factors that impact PINK1/Parkin have already been identified including genes involved in other forms of PD. A great pathogenic overlap amongst different forms of familial, environmental and even sporadic disease is emerging that potentially converges at the level of mitochondrial quality control. Tremendous efforts now seek to further detail the roles and exploit PINK1 and Parkin, their upstream regulators and downstream signaling pathways for future translation. This review summarizes the latest findings on PINK1/Parkin-directed mitochondrial quality control, its integration and cross-talk with other disease factors and pathways as well as the implications for idiopathic PD. In addition, we highlight novel avenues for the development of biomarkers and disease-modifying therapies that are based on a detailed understanding of the PINK1/Parkin pathway.
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Affiliation(s)
- Dominika Truban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Xu Hou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
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Copy number variability in Parkinson's disease: assembling the puzzle through a systems biology approach. Hum Genet 2016; 136:13-37. [PMID: 27896429 PMCID: PMC5214768 DOI: 10.1007/s00439-016-1749-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Abstract
Parkinson’s disease (PD), the second most common progressive neurodegenerative disorder of aging, was long believed to be a non-genetic sporadic origin syndrome. The proof that several genetic loci are responsible for rare Mendelian forms has represented a revolutionary breakthrough, enabling to reveal molecular mechanisms underlying this debilitating still incurable condition. While single nucleotide polymorphisms (SNPs) and small indels constitute the most commonly investigated DNA variations accounting for only a limited number of PD cases, larger genomic molecular rearrangements have emerged as significant PD-causing mutations, including submicroscopic Copy Number Variations (CNVs). CNVs constitute a prevalent source of genomic variations and substantially participate in each individual’s genomic makeup and phenotypic outcome. However, the majority of genetic studies have focused their attention on single candidate-gene mutations or on common variants reaching a significant statistical level of acceptance. This gene-centric approach is insufficient to uncover the genetic background of polygenic multifactorial disorders like PD, and potentially masks rare individual CNVs that all together might contribute to disease development or progression. In this review, we will discuss literature and bioinformatic data describing the involvement of CNVs on PD pathobiology. We will analyze the most frequent copy number changes in familiar PD genes and provide a “systems biology” overview of rare individual rearrangements that could functionally act on commonly deregulated molecular pathways. Assessing the global genome-wide burden of CNVs in PD patients may reveal new disease-related molecular mechanisms, and open the window to a new possible genetic scenario in the unsolved PD puzzle.
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Shulskaya MV, Shadrina MI, Fedotova EY, Abramycheva NY, Limborska SA, Illarioshkin SN, Slominsky PA. Second mutation in PARK2 is absent in patients with sporadic Parkinson's disease and heterozygous exonic deletions/duplications in parkin gene. Int J Neurosci 2016; 127:781-784. [DOI: 10.1080/00207454.2016.1255612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marina V. Shulskaya
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria I. Shadrina
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Yu. Fedotova
- Department of Neurogenetics, Federal State Scientific Institution ‘Scientific Center of Neurology’, Moscow, Russia
| | - Nataliya Yu. Abramycheva
- Department of Neurogenetics, Federal State Scientific Institution ‘Scientific Center of Neurology’, Moscow, Russia
| | - Svetlana A. Limborska
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey N. Illarioshkin
- Department of Neurogenetics, Federal State Scientific Institution ‘Scientific Center of Neurology’, Moscow, Russia
| | - Petr A. Slominsky
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Bandrés-Ciga S, Price TR, Barrero FJ, Escamilla-Sevilla F, Pelegrina J, Arepalli S, Hernández D, Gutiérrez B, Cervilla J, Rivera M, Rivera A, Ding JH, Vives F, Nalls M, Singleton A, Durán R. Genome-wide assessment of Parkinson's disease in a Southern Spanish population. Neurobiol Aging 2016; 45:213.e3-213.e9. [PMID: 27393345 PMCID: PMC4976046 DOI: 10.1016/j.neurobiolaging.2016.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022]
Abstract
Here, we set out to study the genetic architecture of Parkinson's disease (PD) through a Genome-Wide Association Study in a Southern Spanish population. About 240 PD cases and 192 controls were genotyped on the NeuroX array. We estimated genetic variation associated with PD risk and age at onset (AAO). Risk profile analyses for PD and AAO were performed using a weighted genetic risk score. Total heritability was estimated by genome-wide complex trait analysis. Rare variants were screened with single-variant and burden tests. We also screened for variation in known PD genes. Finally, we explored runs of homozygosity and structural genomic variations. We replicate PD association (uncorrected p-value < 0.05) at the following loci: ACMSD/TMEM163, MAPT, STK39, MIR4697, and SREBF/RAI1. Subjects in the highest genetic risk score quintile showed significantly increased risk of PD versus the lowest quintile (odds ratio = 3.6, p-value < 4e(-7)), but no significant difference in AAO. We found evidence of runs of homozygosity in 2 PD-associated regions: one intersecting the HLA-DQB1 gene in 6 patients and 1 control; and another intersecting the GBA-SYT11 gene in PD case. The GBA N370S and the LRRK2 G2019S variants were found in 8 and 7 cases, respectively, replicating previous work. A structural variant was found in 1 case in the PARK2 gene locus. This current work represents a comprehensive assessment at a genome-wide level characterizing a novel population in PD genetics.
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Affiliation(s)
- Sara Bandrés-Ciga
- Department of Physiology and Institute of Neurosciences Federico Olóriz, Centro de Investigaciones Biomedicas (CIBM), University of Granada, Granada, Spain
| | | | | | - Francisco Escamilla-Sevilla
- Movement Disorders Unit, Department of Neurology, Instituto de Investigación Biosanitaria (IBS), University Hospital Virgen de las Nieves, Granada, Spain
| | - Javier Pelegrina
- Movement Disorders Unit, University Hospital San Cecilio, Granada, Spain
| | | | - Dena Hernández
- Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, USA
| | - Blanca Gutiérrez
- Department of Psychiatry and Institute of Neurosciences Federico Olóriz, Centro de Investigaciones Biomedicas (CIBM), University of Granada, Granada, Spain; CIBER en Salud Mental (CIBERSAM), University of Granada, Granada, Spain
| | - Jorge Cervilla
- Department of Psychiatry and Institute of Neurosciences Federico Olóriz, Centro de Investigaciones Biomedicas (CIBM), University of Granada, Granada, Spain; CIBER en Salud Mental (CIBERSAM), University of Granada, Granada, Spain
| | - Margarita Rivera
- Department of Psychiatry and Institute of Neurosciences Federico Olóriz, Centro de Investigaciones Biomedicas (CIBM), University of Granada, Granada, Spain; CIBER en Salud Mental (CIBERSAM), University of Granada, Granada, Spain
| | - Alberto Rivera
- Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, USA
| | - Jing-Hui Ding
- Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, USA
| | - Francisco Vives
- Department of Physiology and Institute of Neurosciences Federico Olóriz, Centro de Investigaciones Biomedicas (CIBM), University of Granada, Granada, Spain
| | - Michael Nalls
- Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, USA
| | | | - Raquel Durán
- Department of Physiology and Institute of Neurosciences Federico Olóriz, Centro de Investigaciones Biomedicas (CIBM), University of Granada, Granada, Spain.
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Yin CL, Chen HI, Li LH, Chien YL, Liao HM, Chou MC, Chou WJ, Tsai WC, Chiu YN, Wu YY, Lo CZ, Wu JY, Chen YT, Gau SSF. Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder. Mol Autism 2016; 7:23. [PMID: 27042285 PMCID: PMC4818409 DOI: 10.1186/s13229-016-0087-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/22/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder with complex genetic underpinning in its etiology. Copy number variations (CNVs) as one of the genetic factors associated with ASD have been addressed in recent genome-wide association studies (GWAS). However, the significance of CNV has not been well investigated in non-Caucasian ASD population. METHODS To identify the pathogenic CNVs responsible for ASD in Han Chinese, we performed a segment-based GWAS of CNV in 335 ASD cases and 1093 healthy controls using Affymetrix single nucleotide polymorphism (SNP) array by focusing on case-specific CNVs. PARK2 was one of the important genes with several case-specific regions overlapped on it. The findings were validated in the initial screen sample set and replicated in another sample set by real-time quantitative PCR (qPCR). RESULTS A total of six CNVs at 6q26 that spanned different exons of PARK2 were identified. The PARK2 expression level was down-regulated at exon-dependent manner in cases with either deletion or duplication. The result revealed that the gene function might be disrupted by exonic deletion and duplication. We also observed that the ASD case with exonic duplication demonstrated a more severe interference of PARK2 expression and the clinical feature than the ones with deletion at the exons 2-4 of the PARK2 gene. CONCLUSIONS Our finding provides evidence to support that CNVs affecting PARK2 function might contribute to genetic etiology of a proportion of cases with ASD. The intriguing results of this work warrant further study on characterizing the functional impact of various exonic CNVs on the PARK2 gene. TRIAL REGISTRATION ClinicalTrials.gov NCT00494754.
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Affiliation(s)
- Chia-Lin Yin
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan.,Graduate Institute of Brain Sciences, National Yang-Ming University, Taipei, 11221 Taiwan
| | - Hsin-I Chen
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yi-Ling Chien
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Hsiao-Mei Liao
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan.,Section on Molecular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, 20892 USA
| | - Miao Chun Chou
- Department of Child Psychiatry, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Chang Gung University College of Medicine, Kaohsiung, 83301 Taiwan
| | - Wen-Jiun Chou
- Department of Child Psychiatry, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Chang Gung University College of Medicine, Kaohsiung, 83301 Taiwan
| | - Wen-Che Tsai
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Yen-Nan Chiu
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Yu-Yu Wu
- Department of Child Psychiatry, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, 33302 Taiwan
| | - Chen-Zen Lo
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Susan Shur-Fen Gau
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
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Two rare deletions upstream of the NRXN1 gene (2p16.3) affecting the non-coding mRNA AK127244 segregate with diverse psychopathological phenotypes in a family. Eur J Med Genet 2015; 58:650-3. [PMID: 26563496 DOI: 10.1016/j.ejmg.2015.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/14/2015] [Accepted: 11/05/2015] [Indexed: 11/20/2022]
Abstract
CNVs spanning the 2p16.3 (NRXN1) and the 15q11.2 gene rich region have been associated with severe neuropsychiatric disorders including schizophrenia. Recently, studies have also revealed that CNVs in non-coding regions play an essential role in genomic variability in addition to disease susceptibility. In this study, we describe a family affected by a wide range of psychiatric disorders including early onset schizophrenia, schizophreniform disorder, and affective disorders. Microarray analysis identified two rare deletions immediately upstream of the NRXN1 gene affecting the non-coding mRNA AK127244 in addition to the pathogenic 15q11.2 deletion in distinct family members. The two deletions upstream of the NRXN1 gene were found to segregate with psychiatric disorders in the family and further similar deletions have been observed in patients diagnosed with autism spectrum disorder. Thus, we suggest that non-coding regions upstream of the NRXN1 gene affecting AK127244 might (as NRXN1) contain susceptibility regions for a wide spectrum of neuropsychiatric disorders.
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