1
|
Andrews SV, Kukkle PL, Menon R, Geetha TS, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Joshi D, Murugan S, Biswas A, Pal PK, Oliver M, Nair S, Kayalvizhi A, Samson PL, Deshmukh M, Bassi A, Sandeep C, Mandloi N, Davis OB, Roberts MA, Leto DE, Henry AG, Di Paolo G, Muthane U, Das SK, Peterson AS, Sandmann T, Gupta R, Ramprasad VL. The Genetic Drivers of Juvenile, Young, and Early-Onset Parkinson's Disease in India. Mov Disord 2024; 39:339-349. [PMID: 38014556 DOI: 10.1002/mds.29676] [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: 07/13/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Recent studies have advanced our understanding of the genetic drivers of Parkinson's disease (PD). Rare variants in more than 20 genes are considered causal for PD, and the latest PD genome-wide association study (GWAS) identified 90 independent risk loci. However, there remains a gap in our understanding of PD genetics outside of the European populations in which the vast majority of these studies were focused. OBJECTIVE The aim was to identify genetic risk factors for PD in a South Asian population. METHODS A total of 674 PD subjects predominantly with age of onset (AoO) ≤50 years (encompassing juvenile, young, or early-onset PD) were recruited from 10 specialty movement disorder centers across India over a 2-year period; 1376 control subjects were selected from the reference population GenomeAsia, Phase 2. We performed various case-only and case-control genetic analyses for PD diagnosis and AoO. RESULTS A genome-wide significant signal for PD diagnosis was identified in the SNCA region, strongly colocalizing with SNCA region signal from European PD GWAS. PD cases with pathogenic mutations in PD genes exhibited, on average, lower PD polygenic risk scores than PD cases lacking any PD gene mutations. Gene burden studies of rare, predicted deleterious variants identified BSN, encoding the presynaptic protein Bassoon that has been previously associated with neurodegenerative disease. CONCLUSIONS This study constitutes the largest genetic investigation of PD in a South Asian population to date. Future work should seek to expand sample numbers in this population to enable improved statistical power to detect PD genes in this understudied group. © 2023 Denali Therapeutics and The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Shan V Andrews
- Denali Therapeutics, South San Francisco, California, USA
| | - Prashanth L Kukkle
- Manipal Hospital, Bangalore, India
- Parkinson's Disease and Movement Disorders Clinic, Bangalore, India
| | | | | | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | - Rukmini Mridula Kandadai
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
- Citi Neuro Centre, Hyderabad, India
| | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
- Citi Neuro Centre, Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Soaham Desai
- Department of Neurology, Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Anand, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
- All India Institute of Medical Sciences, Bibinagar (Hyderabad Metropolitan Region), Bibinagar, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | | | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod K Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | | | | | | | | | | | | | | | | | - Oliver B Davis
- Denali Therapeutics, South San Francisco, California, USA
| | | | - Dara E Leto
- Denali Therapeutics, South San Francisco, California, USA
| | | | | | - Uday Muthane
- Parkinson and Ageing Research Foundation, Bangalore, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | | | | | | |
Collapse
|
2
|
Lin Z, Zhang J, Chen Q, Zhang X, Zhang D, Lin J, Lin D. Transcriptome analysis of the adenoma-carcinoma sequences identifies novel biomarkers associated with development of canine colorectal cancer. Front Vet Sci 2023; 10:1192525. [PMID: 38098990 PMCID: PMC10720982 DOI: 10.3389/fvets.2023.1192525] [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: 03/23/2023] [Accepted: 10/11/2023] [Indexed: 12/17/2023] Open
Abstract
The concept of adenoma-to-cancer transformation in human colorectal cancer (CRC) is widely accepted. However, the relationship between transcriptome features and adenoma to carcinoma transformation in canines is not clear. We collected transcriptome data from 8 normal colon tissues, 4 adenoma tissues, and 15 cancer tissues. Differential analysis was unable to determine the dynamic changes of genes but revealed that PFKFB3 may play a key role in this process. Enrichment analysis explained metabolic dysregulation, immunosuppression, and typical cancer pathways in canine colorectal tumors. MFuzz generated specific dynamic expression patterns of five differentially expressed genes (DEGs). Weighted correlation network analysis showed that DEGs in cluster 3 were associated with malignant tissues, revealing the key role of inflammatory and immune pathways in canine CRC, and the S100A protein family was also found to be involved in the malignant transformation of canine colorectal tumors. By comparing strategies between humans and dogs, we found five novel markers that may be drivers of CRC. Among them, GTBP4 showed excellent diagnostic and prognostic ability. This study was the first systematic exploration of transformation in canine CRC, complemented the molecular characteristics of the development and progression of canine CRC, and provided new potential biomarkers and comparative oncologic evidence for biomarker studies in human colorectal cancer.
Collapse
Affiliation(s)
- Zixiang Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiatong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qi Chen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohu Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Di Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiahao Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Degui Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| |
Collapse
|
3
|
Sipilä JOT, Kytövuori L, Rauramaa T, Rauhamaa H, Kaasinen V, Majamaa K. A severe neurodegenerative disease with Lewy bodies and a mutation in the glucocerebrosidase gene. NPJ Parkinsons Dis 2023; 9:53. [PMID: 37019925 PMCID: PMC10076383 DOI: 10.1038/s41531-023-00501-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/23/2023] [Indexed: 04/07/2023] Open
Abstract
Several heterozygous variants of the glucocerebrosidase gene (GBA1) have been reported to increase the risk of Parkinson's disease (PD) and dementia with Lewy bodies (DLB). GBA1-associated PD has been reported to be more severe than idiopathic PD, and more deleterious variants are associated with more severe clinical phenotypes. We report a family with a heterozygous p.Pro454Leu variant in GBA1. The variant was associated with a severe and rapidly progressive neurodegenerative disease with Lewy bodies that were clinically and pathologically diverse. Pathogenicity prediction algorithms and evolutionary analyses suggested that p.Pro454Leu is deleterious.
Collapse
Affiliation(s)
- Jussi O T Sipilä
- Clinical Neurosciences, University of Turku, Turku, Finland.
- Department of Neurology, Siun Sote North Karelia Central Hospital, Joensuu, Finland.
| | - Laura Kytövuori
- Research Unit of Clinical Medicine and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Neurocenter, Neurology, Oulu University Hospital, Oulu, Finland
| | - Tuomas Rauramaa
- Unit of Pathology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Hugo Rauhamaa
- Research Unit of Clinical Medicine and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Neurocenter, Neurology, Oulu University Hospital, Oulu, Finland
| | - Valtteri Kaasinen
- Clinical Neurosciences, University of Turku, Turku, Finland
- Neurocenter, Turku University Hospital, Turku, Finland
| | - Kari Majamaa
- Research Unit of Clinical Medicine and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Neurocenter, Neurology, Oulu University Hospital, Oulu, Finland
| |
Collapse
|
4
|
Ylikotila P, Sipilä J, Alapirtti T, Ahmasalo R, Koshimizu E, Miyatake S, Hurme-Niiranen A, Siitonen A, Doi H, Tanaka F, Matsumoto N, Majamaa K, Kytövuori L. Association of biallelic RFC1 expansion with early-onset Parkinson's disease. Eur J Neurol 2023; 30:1256-1261. [PMID: 36705320 DOI: 10.1111/ene.15717] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND AND PURPOSE The biallelic repeat expansion (AAGGG)exp in the replication factor C subunit 1 gene (RFC1) is a frequent cause of cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) as well as late-onset ataxia. The clinical spectrum of RFC1 disease has expanded since the first identification of biallelic (AAGGG)exp and includes now various nonclassical phenotypes. Biallelic (AAGGG)exp in RFC1 in patients with clinically confirmed Parkinson's disease (PD) has recently been found. METHODS A nationwide cohort of 273 Finnish patients with early-onset PD was examined for the biallelic intronic expansion in RFC1. The expansion (AAGGG)exp was first screened using extra long polymerase chain reactions (Extra Large-PCRs) and flanking multiplex PCR. The presence of biallelic (AAGGG)exp was then confirmed by repeat-primed PCR and, finally, the repeat length was determined by long-read sequencing. RESULTS Three patients were found with the biallelic (AAGGG)exp in RFC1 giving a frequency of 1.10% (0.23%-3.18%; 95% confidence interval). The three patients fulfilled the diagnostic criteria of PD, none of them had ataxia or neuropathy, and only one patient had a mild vestibular dysfunction. The age at onset of PD symptoms was 40-48 years and their disease course had been unremarkable apart from the early onset. CONCLUSIONS Our results suggest that (AAGGG)exp in RFC1 is a rare cause of early-onset PD. Other populations should be examined in order to determine whether our findings are specific to the Finnish population.
Collapse
Affiliation(s)
- Pauli Ylikotila
- Clinical Neurosciences, University of Turku, Turku, Finland.,Neurocenter Turku University Hospital, Turku, Finland
| | - Jussi Sipilä
- Clinical Neurosciences, University of Turku, Turku, Finland.,Department of Neurology, Siun Sote North Karelia Central Hospital, Joensuu, Finland
| | - Tiina Alapirtti
- Department of Neurology, Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Riitta Ahmasalo
- Department of Neurology, Lapland Central Hospital, Rovaniemi, Finland
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Anri Hurme-Niiranen
- Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Neurocenter, Neurology, Oulu University Hospital, Oulu, Finland
| | - Ari Siitonen
- Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Neurocenter, Neurology, Oulu University Hospital, Oulu, Finland
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kari Majamaa
- Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Neurocenter, Neurology, Oulu University Hospital, Oulu, Finland
| | - Laura Kytövuori
- Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Neurocenter, Neurology, Oulu University Hospital, Oulu, Finland
| |
Collapse
|
5
|
Associations of genes of DNA repair systems with Parkinson’s disease. ACTA BIOMEDICA SCIENTIFICA 2022. [DOI: 10.29413/abs.2022-7.6.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background. Approximately 5–10 % of cases of Parkinson’s disease (PD) are monogenic, in other cases the pathology has a multifactorial etiology. One of recognized pathogenetic pathways of PD is mitochondrial dysfunction, in particular the accumulation of damage in mitochondrial DNA. Hence, the genes of DNA repair proteins are promising candidate genes for multifactorial forms of PD.The aim. To study the involvement of genes of DNA repair proteins in the development of Parkinson’s disease.Materials and methods. The associative analysis was carried out while comparing a group of patients with PD (n = 133) with a Tomsk population sample (n = 344). SNaPshot analysis was used to study 8 SNPs in genes of DNA repair proteins (rs560191 (TP53BP1); rs1805800 and rs709816 (NBN); rs473297 (MRE11A); rs1189037 and rs1801516 (ATM); rs1799977 (MLH1); rs1805321 (PMS2)).Results. Common alleles and homozygous rs1801516 genotypes in the ATM gene predispose the development of PD (odds ratio (OR) – 3.27 (p = 0.000004) and OR = 3.46 (p = 0.00008) for risk alleles and genotype respectively) and rs1799977 in the MLH1 gene (OR = 1.88 (p = 0.0004) and OR = 2.42 (p = 0.00007) respectively); heterozygotes have a protective effect (OR = 0.33 (p = 0.0007) and OR = 0.46 (p = 0.0007) for ATM and MLH1, respectively). The rare rs1805800 allele in the NBN gene (OR = 1.62 (p = 0.019)) and a homozygous genotype for it (OR = 2.28 (p = 0.016)) also predispose to PD. Associations with PD of the ATM, MLH1, NBN genes were revealed for the first time.Conclusion. Mitochondrial dysfunction is one of the key factors in the pathogenesis of PD, while at least two of the three protein products of associated genes are involved in the development of mitochondrial dysfunction. Accordingly, it can be assumed that associated genes are involved in the pathogenesis of PD precisely through mitochondrial dysfunction.
Collapse
|
6
|
Kovanda A, Rački V, Bergant G, Georgiev D, Flisar D, Papić E, Brankovic M, Jankovic M, Svetel M, Teran N, Maver A, Kostic VS, Novakovic I, Pirtošek Z, Rakuša M, Vuletić V, Peterlin B. A multicenter study of genetic testing for Parkinson’s disease in the clinical setting. NPJ Parkinsons Dis 2022; 8:149. [PMCID: PMC9636217 DOI: 10.1038/s41531-022-00408-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
Parkinson’s disease (PD) guidelines lack clear criteria for genetic evaluation. We assessed the yield and rationale of genetic testing for PD in a routine clinical setting on a multicenter cohort of 149 early-onset and familial patients by exome sequencing and semi-quantitative multiplex ligation-dependent probe amplification of evidence-based PD-associated gene panel. We show that genetic testing for PD should be considered for both early-onset and familial patients alike, and a clinical yield of about 10% in the Caucasian population can be expected.
Collapse
Affiliation(s)
- Anja Kovanda
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Valentino Rački
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Gaber Bergant
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Dejan Georgiev
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia ,grid.8954.00000 0001 0721 6013Artificial Intelligence Lab, Faculty of Computer and Information Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Dušan Flisar
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Eliša Papić
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marija Brankovic
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Marina Svetel
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Nataša Teran
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Vladimir S. Kostic
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- grid.7149.b0000 0001 2166 9385Institute of Human Genetics and Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zvezdan Pirtošek
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia ,grid.8954.00000 0001 0721 6013Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Martin Rakuša
- grid.412415.70000 0001 0685 1285Department of Neurology, University Medical Centre Maribor, Maribor, Slovenia
| | - Vladimira Vuletić
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Borut Peterlin
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
7
|
Kukkle PL, Geetha TS, Chaudhary R, Sathirapongsasuti JF, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Oliver M, Sunil M, Mootor MFE, Kapil S, Mandloi N, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Sakthivel Murugan SM, Peterson AS, Stawiski EW, Seshagiri S, Gupta R, Ramprasad VL, Prai PRAOI. Genome-Wide Polygenic Score Predicts Large Number of High Risk Individuals in Monogenic Undiagnosed Young Onset Parkinson's Disease Patients from India. Adv Biol (Weinh) 2022; 6:e2101326. [PMID: 35810474 DOI: 10.1002/adbi.202101326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
Parkinson's disease (PD) is a genetically heterogeneous neurodegenerative disease with poorly defined environmental influences. Genomic studies of PD patients have identified disease-relevant monogenic genes, rare variants of significance, and polygenic risk-associated variants. In this study, whole genome sequencing data from 90 young onset Parkinson's disease (YOPD) individuals are analyzed for both monogenic and polygenic risk. The genetic variant analysis identifies pathogenic/likely pathogenic variants in eight of the 90 individuals (8.8%). It includes large homozygous coding exon deletions in PRKN and SNV/InDels in VPS13C, PLA2G6, PINK1, SYNJ1, and GCH1. Eleven rare heterozygous GBA coding variants are also identified in 13 (14.4%) individuals. In 34 (56.6%) individuals, one or more variants of uncertain significance (VUS) in PD/PD-relevant genes are observed. Though YOPD patients with a prioritized pathogenic variant show a low polygenic risk score (PRS), patients with prioritized VUS or no significant rare variants show an increased PRS odds ratio for PD. This study suggests that both significant rare variants and polygenic risk from common variants together may contribute to the genesis of PD. Further validation using a larger cohort of patients will confirm the interplay between monogenic and polygenic variants and their use in routine genetic PD diagnosis and risk assessment.
Collapse
Affiliation(s)
- Prashanth Lingappa Kukkle
- Department of Neurology, Manipal Hospital, Miller Road, Bangalore, 560052, India.,Department of Neurology, Parkinson's Disease and Movement Disorders Clinic, Bangalore, 560010, India.,Department of Neurology, All India Institute of Medical Sciences, Rishikesh, 249201, India
| | - Thenral S Geetha
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Ruchi Chaudhary
- Research Department, MedGenome Inc., 348 Hatch Drive, Foster City, CA, 94404, USA
| | | | - Vinay Goyal
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110608, India.,Department of Neurology, Medanta Hospital, New Delhi, 110047, India.,Department of Neurology, Medanta, The Medicity, Gurgaon, 122006, India
| | | | - Hrishikesh Kumar
- Department of Neurology, Institute of Neurosciences Kolkata, Kolkata, 700007, India
| | - Rupam Borgohain
- Department of Neurology, Nizams Institute of Medical Sciences (NIMS), Hyderabad, 500082, India
| | - Adreesh Mukherjee
- Department of Neurology, Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, 700020, India
| | - Merina Oliver
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Meeta Sunil
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | | | - Shruti Kapil
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Nitin Mandloi
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Pettarusp M Wadia
- Department of Neurology, Jaslok Hospital and Research Centre, Mumbai, 400026, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Soaham Desai
- Department of Neurology, Shree Krishna Hospital and Pramukhswami Medical College, Bhaikaka University, Karamsad, 388325, India
| | - Niraj Kumar
- Department of Neurology, All India Institute of Medical Sciences, Rishikesh, 249201, India
| | - Atanu Biswas
- Department of Neurology, Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, 700020, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Uday B Muthane
- Department of Neurology, Parkinson and Ageing Research Foundation, Bangalore, 560095, India
| | - Shymal Kumar Das
- Department of Neurology, Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, 700020, India
| | | | - Andrew S Peterson
- Research Department, MedGenome Inc., 348 Hatch Drive, Foster City, CA, 94404, USA
| | - Eric W Stawiski
- Research Department, MedGenome Inc., 348 Hatch Drive, Foster City, CA, 94404, USA
| | | | - Ravi Gupta
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | - Vedam L Ramprasad
- Research and Diagnostics Department, MedGenome Labs Pvt Ltd, Bangalore, 560099, India
| | | |
Collapse
|
8
|
Ruffini N, Klingenberg S, Heese R, Schweiger S, Gerber S. The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Front Aging Neurosci 2022; 14:866886. [PMID: 35832065 PMCID: PMC9271745 DOI: 10.3389/fnagi.2022.866886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.
Collapse
Affiliation(s)
- Nicolas Ruffini
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research, Leibniz Association, Mainz, Germany
| | - Susanne Klingenberg
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Raoul Heese
- Fraunhofer Institute for Industrial Mathematics (ITWM), Kaiserslautern, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| |
Collapse
|
9
|
Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell 2022; 185:2035-2056.e33. [PMID: 35688132 DOI: 10.1016/j.cell.2022.05.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022]
Abstract
Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that αS directly modulates processing bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N terminus of αS, but not other synucleins, dictates mutually exclusive binding either to cellular membranes or to P-bodies in the cytosol. αS associates with multiple decapping proteins in close proximity on the Edc4 scaffold. As αS pathologically accumulates, aberrant interaction with Edc4 occurs at the expense of physiologic decapping-module interactions. mRNA decay kinetics within PD-relevant pathways are correspondingly disrupted in PD patient neurons and brain. Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, our data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
Collapse
Affiliation(s)
- Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sumaiya Nazeen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Xiou H Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zoe Sheinkopf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shubhangi Sathyakumar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Souvarish Sarkar
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xin Jiang
- Yumanity Therapeutics, Boston, MA 02135, USA
| | - Xianjun Dong
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Genomics and Bioinformatics Hub, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew T Keeney
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics and Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON M5T 3M7, Canada
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | | | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| |
Collapse
|
10
|
Hua P, Zhao Y, Zeng Q, Li L, Ren J, Guo J, Tang B, Liu W. Genetic Analysis of Patients With Early-Onset Parkinson’s Disease in Eastern China. Front Aging Neurosci 2022; 14:849462. [PMID: 35645773 PMCID: PMC9131032 DOI: 10.3389/fnagi.2022.849462] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background Genetic factors play an important role in the pathogenesis of early-onset Parkinson’s disease (EOPD). To date, more than 20 pathogenic genes associated with Parkinson’s disease (PD) have been identified. This study aims to explore the mutation spectrum of EOPD and the clinical characteristics of mutation carriers in eastern China. Methods We recruited 155 unrelated EOPD patients, including 8 familial and 147 sporadic EOPD (age at onset ≤ 50 years). Overall, 24 known PD-associated genes were detected by whole exome sequencing and multiplex ligation-dependent probe amplification (MLPA) from patient samples. The genetic and clinical characteristics of pathogenic/likely pathogenic (P/LP) loci in this cohort were analyzed. Results Overall, 14 (9.03%) patients were detected with P/LP variants distributed in seven genes. The most frequent mutation occurred in PRKN (7/155, 4.52%), followed by LRRK2 (2/155, 1.29%), SNCA, CHCHD2, TMEM230, DNAJC13 and PLA2G6 (1/155, 0.64%, respectively). Exon rearrangement mutations accounted for 57.9% (11/19) of all mutations in PRKN. Four novel variants were detected: c.14T > C (p.M5T) in SNCA, c.297C > A (p.Y99X) in CHCHD2, c.2578C > T (p.R860C) in DNAJC13 and c.4C > T (p.Q2X) in TMEM230. We found the first case of LRRK2 c.6055G > A (p.G2019S) mutation in Chinese population. The median onset age of patients with P/LP mutations in autosomal recessive genes (PRKN and PLA2G6) was about 18.0 years earlier than patients without mutation. The proportion of patients with mutations were 63.64%, 27.03% and 9.68% when patients were stratified according to the age of onset at ≤ 30, ≤ 40 and ≤ 50 years, respectively. Conclusion Early-onset Parkinson’s disease patients from eastern China present a regional specific mutation spectrum. Analysis of larger patient cohorts is required to support these findings, and mechanistic studies of the four novel missense/non-sense mutations will clarify their role in the pathogenicity of EOPD.
Collapse
Affiliation(s)
- Ping Hua
- Department of Neurology, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lanting Li
- Department of Neurology, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
| | - Jingru Ren
- Department of Neurology, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Centre for Medical Genetics, Xiangya Hospital, School of Life Sciences, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, Centre for Medical Genetics, Xiangya Hospital, School of Life Sciences, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- Beisha Tang,
| | - Weiguo Liu
- Department of Neurology, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
- *Correspondence: Weiguo Liu,
| |
Collapse
|
11
|
Biallelic expansion in RFC1 as a rare cause of Parkinson's disease. NPJ Parkinsons Dis 2022; 8:6. [PMID: 35013364 PMCID: PMC8748909 DOI: 10.1038/s41531-021-00275-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
An intronic expansion (AAGGG)exp in the RFC1 gene has recently been shown to cause recessively inherited cerebellar ataxia, neuropathy, and vestibular areflexia syndrome and, furthermore, a few patients with ataxia and parkinsonism have been reported. We investigated 569 Finnish patients with medicated parkinsonism for RFC1 and found biallelic (AAGGG)exp in three non-consanguineous patients with clinically confirmed Parkinson’s disease without ataxia suggesting that RFC1-related disorders include Parkinson’s disease as well.
Collapse
|
12
|
Ho D, Schierding W, Farrow SL, Cooper AA, Kempa-Liehr AW, O’Sullivan JM. Machine Learning Identifies Six Genetic Variants and Alterations in the Heart Atrial Appendage as Key Contributors to PD Risk Predictivity. Front Genet 2022; 12:785436. [PMID: 35047012 PMCID: PMC8762216 DOI: 10.3389/fgene.2021.785436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease with a range of causes and clinical presentations. Over 76 genetic loci (comprising 90 SNPs) have been associated with PD by the most recent GWAS meta-analysis. Most of these PD-associated variants are located in non-coding regions of the genome and it is difficult to understand what they are doing and how they contribute to the aetiology of PD. We hypothesised that PD-associated genetic variants modulate disease risk through tissue-specific expression quantitative trait loci (eQTL) effects. We developed and validated a machine learning approach that integrated tissue-specific eQTL data on known PD-associated genetic variants with PD case and control genotypes from the Wellcome Trust Case Control Consortium. In so doing, our analysis ranked the tissue-specific transcription effects for PD-associated genetic variants and estimated their relative contributions to PD risk. We identified roles for SNPs that are connected with INPP5P, CNTN1, GBA and SNCA in PD. Ranking the variants and tissue-specific eQTL effects contributing most to the machine learning model suggested a key role in the risk of developing PD for two variants (rs7617877 and rs6808178) and eQTL associated transcriptional changes of EAF1-AS1 within the heart atrial appendage. Similarly, effects associated with eQTLs located within the Brain Cerebellum were also recognized to confer major PD risk. These findings were replicated in two additional, independent cohorts (the UK Biobank, and NeuroX) and thus warrant further mechanistic investigations to determine if these transcriptional changes could act as early contributors to PD risk and disease development.
Collapse
Affiliation(s)
- Daniel Ho
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Sophie L. Farrow
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Antony A. Cooper
- Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | | | - Justin M. O’Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
13
|
Lipponen J, Helisalmi S, Raivo J, Siitonen A, Doi H, Rusanen H, Lehtilahti M, Ryytty M, Laakso M, Tanaka F, Majamaa K, Kytövuori L. Molecular epidemiology of hereditary ataxia in Finland. BMC Neurol 2021; 21:382. [PMID: 34600502 PMCID: PMC8487109 DOI: 10.1186/s12883-021-02409-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetics of cerebellar ataxia is complex. Hundreds of causative genes have been identified, but only a few cause more than single cases. The spectrum of ataxia-causing genes differs considerably between populations. The aim of the study was to investigate the molecular epidemiology of ataxia in the Finnish population. PATIENTS AND METHODS All patients in hospital database were reviewed for the diagnosis of unspecified ataxia. Acquired ataxias and nongenetic ataxias such as those related to infection, trauma or stroke were excluded. Sixty patients with sporadic ataxia with unknown etiology and 36 patients with familial ataxia of unknown etiology were recruited in the study. Repeat expansions in the SCA genes (ATXN1, 2, 3, 7, 8/OS, CACNA1A, TBP), FXN, and RFC1 were determined. Point mutations in POLG, SPG7 and in mitochondrial DNA (mtDNA) were investigated. In addition, DNA from 8 patients was exome sequenced. RESULTS A genetic cause of ataxia was found in 33 patients (34.4%). Seven patients had a dominantly inherited repeat expansion in ATXN8/OS. Ten patients had mitochondrial ataxia resulting from mutations in nuclear mitochondrial genes POLG or RARS2, or from a point mutation m.8561C > G or a single deletion in mtDNA. Interestingly, five patients were biallelic for the recently identified pathogenic repeat expansion in RFC1. All the five patients presented with the phenotype of cerebellar ataxia, neuropathy, and vestibular areflexia (CANVAS). Moreover, screening of 54 patients with Charcot-Marie-Tooth neuropathy revealed four additional patients with biallelic repeat expansion in RFC1, but none of them had cerebellar symptoms. CONCLUSIONS Expansion in ATXN8/OS results in the majority of dominant ataxias in Finland, while mutations in RFC1 and POLG are the most common cause of recessive ataxias. Our results suggest that analysis of RFC1 should be included in the routine diagnostics of idiopathic ataxia and Charcot-Marie-Tooth polyneuropathy.
Collapse
Affiliation(s)
- Joonas Lipponen
- Research Unit of Clinical Neuroscience, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Seppo Helisalmi
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Joose Raivo
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ari Siitonen
- Research Unit of Clinical Neuroscience, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Harri Rusanen
- Research Unit of Clinical Neuroscience, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Maria Lehtilahti
- Research Unit of Clinical Neuroscience, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Mervi Ryytty
- Research Unit of Clinical Neuroscience, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Laura Kytövuori
- Research Unit of Clinical Neuroscience, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, 90014, Oulu, Finland. .,Department of Neurology, Oulu University Hospital, Oulu, Finland.
| |
Collapse
|
14
|
Recent ultra-rare inherited variants implicate new autism candidate risk genes. Nat Genet 2021; 53:1125-1134. [PMID: 34312540 DOI: 10.1038/s41588-021-00899-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/18/2021] [Indexed: 01/28/2023]
Abstract
Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation contributes significantly to risk. Using whole-genome sequencing data from 3,474 families, we investigate another source of large-effect risk variation, ultra-rare variants. We report and replicate a transmission disequilibrium of private, likely gene-disruptive (LGD) variants in probands but find that 95% of this burden resides outside of known DNM-enriched genes. This variant class more strongly affects multiplex family probands and supports a multi-hit model for autism. Candidate genes with private LGD variants preferentially transmitted to probands converge on the E3 ubiquitin-protein ligase complex, intracellular transport and Erb signaling protein networks. We estimate that these variants are approximately 2.5 generations old and significantly younger than other variants of similar type and frequency in siblings. Overall, private LGD variants are under strong purifying selection and appear to act on a distinct set of genes not yet associated with autism.
Collapse
|
15
|
Mahmood A, Shah AA, Umair M, Wu Y, Khan A. Recalling the pathology of Parkinson's disease; lacking exact figure of prevalence and genetic evidence in Asia with an alarming outcome: A time to step-up. Clin Genet 2021; 100:659-677. [PMID: 34195994 DOI: 10.1111/cge.14019] [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: 04/23/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 11/26/2022]
Abstract
Parkinson's disease (PD) is the second most common and progressive neurodegenerative disease globally, with major symptoms like bradykinesia, impaired posture, and tremor. Several genetic and environmental factors have been identified but elucidating the main factors have been challenging due to the disease's complex nature. Diagnosis, prognosis, and management of such diseases are challenging and require effective targeted attention in developing countries. Recently, PD is growing rapidly in many crowded Asian countries as an alarming threat with inadequate knowledge of its prevalence, genetic architecture, and geographic distribution. This study gave an in-depth overview of the prevalence, incidence and genomic/genetics studies published so far in the Asian population. To the best of our knowledge, PD has increased significantly in several Asian countries, including China, South Korea, Japan, Thailand, and Israel over the past few years, requiring a greater level of care and attention. Genetic screening of families with PD at national levels and establishing an official database of PD cases are essential to get a comprehensive and conclusive view of the exact prevalence and genetic diversity of PD in the Asian population to properly manage and treat the disease.
Collapse
Affiliation(s)
- Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdul-Aziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Yiming Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Amjad Khan
- Faculty of Science, Department of Biological Sciences, University of Lakki Marwat, Lakki Marwat, Pakistan
| |
Collapse
|
16
|
Day JO, Mullin S. The Genetics of Parkinson's Disease and Implications for Clinical Practice. Genes (Basel) 2021; 12:genes12071006. [PMID: 34208795 PMCID: PMC8304082 DOI: 10.3390/genes12071006] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
The genetic landscape of Parkinson’s disease (PD) is characterised by rare high penetrance pathogenic variants causing familial disease, genetic risk factor variants driving PD risk in a significant minority in PD cases and high frequency, low penetrance variants, which contribute a small increase of the risk of developing sporadic PD. This knowledge has the potential to have a major impact in the clinical care of people with PD. We summarise these genetic influences and discuss the implications for therapeutics and clinical trial design.
Collapse
Affiliation(s)
- Jacob Oliver Day
- Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK;
| | - Stephen Mullin
- Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK;
- Department of Clinical and Movement Neurosciences, University College London Institute of Neurology, London WC1N 3BG, UK
- Correspondence:
| |
Collapse
|
17
|
Li B, Zhao G, Zhou Q, Xie Y, Wang Z, Fang Z, Lu B, Qin L, Zhao Y, Zhang R, Jiang L, Pan H, He Y, Wang X, Luo T, Zhang Y, Wang Y, Chen Q, Liu Z, Guo J, Tang B, Li J. Gene4PD: A Comprehensive Genetic Database of Parkinson's Disease. Front Neurosci 2021; 15:679568. [PMID: 33981200 PMCID: PMC8107430 DOI: 10.3389/fnins.2021.679568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/07/2021] [Indexed: 01/02/2023] Open
Abstract
Parkinson’s disease (PD) is a complex neurodegenerative disorder with a strong genetic component. A growing number of variants and genes have been reported to be associated with PD; however, there is no database that integrate different type of genetic data, and support analyzing of PD-associated genes (PAGs). By systematic review and curation of multiple lines of public studies, we integrate multiple layers of genetic data (rare variants and copy-number variants identified from patients with PD, associated variants identified from genome-wide association studies, differentially expressed genes, and differential DNA methylation genes) and age at onset in PD. We integrated five layers of genetic data (8302 terms) with different levels of evidences from more than 3,000 studies and prioritized 124 PAGs with strong or suggestive evidences. These PAGs were identified to be significantly interacted with each other and formed an interconnected functional network enriched in several functional pathways involved in PD, suggesting these genes may contribute to the pathogenesis of PD. Furthermore, we identified 10 genes were associated with a juvenile-onset (age ≤ 30 years), 11 genes were associated with an early-onset (age of 30–50 years), whereas another 10 genes were associated with a late-onset (age > 50 years). Notably, the AAOs of patients with loss of function variants in five genes were significantly lower than that of patients with deleterious missense variants, while patients with VPS13C (P = 0.01) was opposite. Finally, we developed an online database named Gene4PD (http://genemed.tech/gene4pd) which integrated published genetic data in PD, the PAGs, and 63 popular genomic data sources, as well as an online pipeline for prioritize risk variants in PD. In conclusion, Gene4PD provides researchers and clinicians comprehensive genetic knowledge and analytic platform for PD, and would also improve the understanding of pathogenesis in PD.
Collapse
Affiliation(s)
- Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Mobile Health Ministry of Education-China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yali Xie
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenghuan Fang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Bin Lu
- Department of Pathogen Biology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lixia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yan He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaomeng Wang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Tengfei Luo
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yijing Wang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| |
Collapse
|
18
|
Kaiyrzhanov R, Aitkulova A, Vandrovcova J, Murphy D, Zharkinbekova N, Shashkin C, Akhmetzhanov V, Kaishibayeva G, Karimova A, Myrzayev Z, Murray M, Khaibullin T, Hardy J, Houlden H. A glimpse of the genetics of young-onset Parkinson's disease in Central Asia. Mol Genet Genomic Med 2021; 9:e1671. [PMID: 33818904 PMCID: PMC8222829 DOI: 10.1002/mgg3.1671] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Background Knowledge of the genetic background of many human diseases is currently lacking from genetically undiscovered regions, including Central Asia. Kazakhstan is the first Central Asian country where the genetic studies of Parkinson's disease (PD) have been emerging since it had become a member of the International Parkinson Disease Genomics Consortium. Here we report on the results of whole‐exome sequencing (WES) in 50 young‐onset PD (YOPD) cases from Kazakhstan. Methodology WES was performed on 50 unrelated individuals with YOPD from Kazakhstan. Exome data were screened for novel/ultra‐rare deleterious variants in known and candidate PD genes. Copy number variants and small indels were also called. Results Only three cases (6%) were found to be positive for known PD genes including two unrelated familial PD cases with LRRK2 p.(Arg1441Cys) and one case with a homozygous pathogenic PRKN p.(Arg84Trp) variant. Four cases had novel and ultra‐rare variants of uncertain significance in LRRK2, DNAJC13, and VPS35. Novel deleterious variants were found in candidate Mendelian PD genes including CSMD1, TNR, EIF4G1, and ATP13A3. Eight cases harbored the East Asian‐specific LRRK2 p.(Ala419Val) variant. Conclusions The low diagnostic yield in our study might imply that a significant proportion of YOPD cases in Central Asia remains unresolved. Therefore, a better understanding of the genetic architecture of PD among populations of Central Asian ancestry and the pathogenicity of numerous rare variants should be further investigated. WES is a valuable technique for large‐scale YOPD genetic studies in Central Asia.
Collapse
Affiliation(s)
- Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Akbota Aitkulova
- Department of Molecular Genetics, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Jana Vandrovcova
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | | | - Chingiz Shashkin
- Contemporary Neurology and Neurorehabilitation Clinic "Shashkin Clinic", Almaty, Kazakhstan
| | - Vadim Akhmetzhanov
- Department of Neurology, South Kazakhstan Medical Academy, Shymkent, Kazakhstan
| | - Gulnaz Kaishibayeva
- Institute of Neurology and Neurorehabilitation Named After Smagul Kaishibayev, Almaty, Kazakhstan
| | - Altynay Karimova
- Kazakh Medical University of Continuing Study, Almaty, Kazakhstan
| | - Zhanybek Myrzayev
- Contemporary Neurology and Neurorehabilitation Clinic "Shashkin Clinic", Almaty, Kazakhstan
| | - Malgorzata Murray
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Talgat Khaibullin
- Department of Neurology, Semey Medical University, Semey, Kazakhstan
| | - John Hardy
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| |
Collapse
|
19
|
Li B, Zhao G, Li K, Wang Z, Fang Z, Wang X, Luo T, Zhang Y, Wang Y, Chen Q, Huang Y, Dong L, Guo J, Tang B, Li J. Characterizing the Expression Patterns of Parkinson's Disease Associated Genes. Front Neurosci 2021; 15:629156. [PMID: 33867917 PMCID: PMC8049291 DOI: 10.3389/fnins.2021.629156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/12/2021] [Indexed: 01/13/2023] Open
Abstract
Background The expression pattern represents a quantitative phenotype that provides an in-depth view of the molecular mechanism in Parkinson’s disease (PD); however, the expression patterns of PD-associated genes (PAGs) and their relation to age at onset (AAO) remain unclear. Methods The known PD-causing genes and PD-risk genes, which were collected from latest published authoritative meta-analysis, were integrated as PAGs. The expression data from Genotype-Tissue Expression database, Allen Brian Map database, and BrainSpan database, were extracted to characterize the tissue specificity, inhibitory-excitatory neuron expression profile, and spatio-temporal expression pattern of PAGs, respectively. The AAO information of PD-causing gene was download from Gene4PD and MDSgene database. Results We prioritized 107 PAGs and found that the PAGs were more likely to be expressed in brain-related tissues than non-brain tissues and that more PAGs had higher expression levels in excitatory neurons than inhibitory neurons. In addition, we identified two spatio-temporal expression modules of PAGs in human brain: the first module showed a higher expression level in the adult period than in the prenatal period, and the second module showed the opposite features. It showed that more PAGs belong to the first module that the second module. Furthermore, we found that the median AAO of patients with mutations in PD-causing genes of the first module was lower than that of the second module. Conclusion In conclusion, this study provided comprehensive landscape of expression patterns, AAO features and their relationship for the first time, improving the understanding of pathogenesis, and precision medicine in PD.
Collapse
Affiliation(s)
- Bin Li
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Mobile Health Ministry of Education-China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Guihu Zhao
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Kuokuo Li
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Zheng Wang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenghuan Fang
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Xiaomeng Wang
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Tengfei Luo
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Yi Zhang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yijing Wang
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qian Chen
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanfeng Huang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lijie Dong
- Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Beisha Tang
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Jinchen Li
- Department of Geriatrics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics and Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| |
Collapse
|
20
|
Hunting for Familial Parkinson's Disease Mutations in the Post Genome Era. Genes (Basel) 2021; 12:genes12030430. [PMID: 33802862 PMCID: PMC8002626 DOI: 10.3390/genes12030430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/20/2022] Open
Abstract
Parkinson’s disease (PD) is typically sporadic; however, multi-incident families provide a powerful platform to discover novel genetic forms of disease. Their identification supports deciphering molecular processes leading to disease and may inform of new therapeutic targets. The LRRK2 p.G2019S mutation causes PD in 42.5–68% of carriers by the age of 80 years. We hypothesise similarly intermediately penetrant mutations may present in multi-incident families with a generally strong family history of disease. We have analysed six multiplex families for missense variants using whole exome sequencing to find 32 rare heterozygous mutations shared amongst affected members. Included in these mutations was the KCNJ15 p.R28C variant, identified in five affected members of the same family, two elderly unaffected members of the same family, and two unrelated PD cases. Additionally, the SIPA1L1 p.R236Q variant was identified in three related affected members and an unrelated familial case. While the evidence presented here is not sufficient to assign causality to these rare variants, it does provide novel candidates for hypothesis testing in other modestly sized families with a strong family history. Future analysis will include characterisation of functional consequences and assessment of carriers in other familial cases.
Collapse
|
21
|
Jiang Y, Yu M, Chen J, Zhou H, Sun W, Sun Y, Li F, Wei L, Pinkhardt EH, Zhang L, Yuan Y, Wang Z. Parkin is the most common causative gene in a cohort of mainland Chinese patients with sporadic early-onset Parkinson's disease. Brain Behav 2020; 10:e01765. [PMID: 32677319 PMCID: PMC7507393 DOI: 10.1002/brb3.1765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/06/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Genetic mutations associated with early-onset Parkinson's disease (EOPD) vary widely among different ethnicities. We detected the genes associated with EOPD in a Chinese cohort using next-generation sequencing (NGS) combined with multiplex ligation-dependent probe amplification (MLPA) and analyzed the phenotypic characteristics of the mutation carriers. METHODS Cohort of 23 sporadic EOPD patients (onset age ≤ 45 years) were recruited. Genetic causes were identified by a targeted NGS panel containing 136 known extrapyramidal disease-causative genes. Multiplications or deletions of PD-causing genes were detected using the MLPA method. Demographic and clinical data were obtained, analyzed, and compared between patients with and those without Parkin gene variants. RESULTS We identified 14 pathogenic or likely pathogenic variants (12 in Parkin, 1 in LRRK2, and 1 in VPS13C) in 10 patients (43.5%) and 8 rare variants of uncertain significance in 9 patients (39.1%). Parkin (34.8%) was the most common causative gene among our patients cohort, and exon deletion (62.5%) was the main type of variant. Patients with Parkin mutations had a younger age of onset, longer delay in diagnosis, slower disease progression, higher frequency of hyperreflexia, fatigue, and less hyposmia compared to patients without Parkin mutations. CONCLUSION Our results revealed a higher prevalence of Parkin mutations in Chinese sporadic EOPD patients, and notably, exon deletion was the most common type of mutation. EOPD patients with Parkin mutations showed unique clinical characteristics.
Collapse
Affiliation(s)
- Yanyan Jiang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Jing Chen
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Hong Zhou
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Wei Sun
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yunchuang Sun
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Fan Li
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Luhua Wei
- Department of Neurology, Peking University First Hospital, Beijing, China
| | | | - Lin Zhang
- Department of Neurology, UC Davis Medical Center, Sacramento, CA, USA
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| |
Collapse
|
22
|
Qiu X, He H, Huang Y, Wang J, Xiao Y. Genome-wide identification of m 6A-associated single-nucleotide polymorphisms in Parkinson's disease. Neurosci Lett 2020; 737:135315. [PMID: 32827573 DOI: 10.1016/j.neulet.2020.135315] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/05/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
N6-methyladenosine (m6A)-associated single nucleotide polymorphisms (SNPs) play a vital role in several neurological diseases. However, little is known about the relationship between m6A modification and Parkinson's disease (PD). We investigated potential functional variants of m6A-SNPs from large-scale genome-wide association studies (GWAS) in PD patients. The candidate m6A-SNPs were further assessed by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We identified 12 m6A-SNPs that were significantly associated with PD risk. Further, eQTL and expression analyses identified five of these m6A-SNPs (rs75072999 of GAK, rs1378602, rs4924839 and rs8071834 of ALKBH5, and rs1033500 of C6orf10) that were associated with altered gene expression in PD. Our results suggest that m6A-SNPs could play a role in PD risk. Future studies are needed to confirm these PD-associated m6A-SNPs and elucidate their mechanisms.
Collapse
Affiliation(s)
- Xiaohui Qiu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Honghu He
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yanning Huang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jin Wang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
| | - Yousheng Xiao
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
| |
Collapse
|
23
|
Bandres-Ciga S, Diez-Fairen M, Kim JJ, Singleton AB. Genetics of Parkinson's disease: An introspection of its journey towards precision medicine. Neurobiol Dis 2020; 137:104782. [PMID: 31991247 PMCID: PMC7064061 DOI: 10.1016/j.nbd.2020.104782] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/15/2020] [Accepted: 01/24/2020] [Indexed: 12/15/2022] Open
Abstract
A substantial proportion of risk for Parkinson's disease (PD) is driven by genetics. Progress in understanding the genetic basis of PD has been significant. So far, highly-penetrant rare genetic alterations in SNCA, LRRK2, VPS35, PRKN, PINK1, DJ-1 and GBA have been linked with typical familial PD and common genetic variability at 90 loci have been linked to risk for PD. In this review, we outline the journey thus far of PD genetics, highlighting how significant advances have improved our knowledge of the genetic basis of PD risk, onset and progression. Despite remarkable progress, our field has yet to unravel how genetic risk variants disrupt biological pathways and molecular networks underlying the pathobiology of the disease. We highlight that currently identified genetic risk factors only represent a fraction of the likely genetic risk for PD. Identifying the remaining genetic risk will require us to diversify our efforts, performing genetic studies across different ancestral groups. This work will inform us on the varied genetic basis of disease across populations and also aid in fine mapping discovered loci. If we are able to take this course, we foresee that genetic discoveries in PD will directly influence our ability to predict disease and aid in defining etiological subtypes, critical steps for the implementation of precision medicine for PD.
Collapse
Affiliation(s)
- Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada 18016, Spain.
| | - Monica Diez-Fairen
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Fundació Docència i Recerca Mútua Terrassa and Movement Disorders Unit, Department of Neurology, University Hospital Mútua Terrassa, Terrassa 08221, Barcelona, Spain
| | - Jonggeol Jeff Kim
- 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.
| |
Collapse
|
24
|
Lee DSM, Ghanem LR, Barash Y. Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations. Nat Commun 2020; 11:527. [PMID: 31988292 PMCID: PMC6985247 DOI: 10.1038/s41467-020-14404-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/03/2020] [Indexed: 11/17/2022] Open
Abstract
G-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5' and 3' UTRs are selectively constrained, and enriched for cis-eQTLs and RNA-binding protein (RBP) interactions. Using over 15,000 whole-genome sequences, we find that negative selection acting on central guanines of UTR pG4s is comparable to that of missense variation in protein-coding sequences. At multiple GWAS-implicated SNPs within pG4 UTR sequences, we find robust allelic imbalance in gene expression across diverse tissue contexts in GTEx, suggesting that variants affecting G-quadruplex formation within UTRs may also contribute to phenotypic variation. Our results establish UTR G4s as important cis-regulatory elements and point to a link between disruption of UTR pG4 and disease.
Collapse
Affiliation(s)
- David S M Lee
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Louis R Ghanem
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
25
|
Gialluisi A, Reccia MG, Tirozzi A, Nutile T, Lombardi A, De Sanctis C, Varanese S, Pietracupa S, Modugno N, Simeone A, Ciullo M, Esposito T. Whole Exome Sequencing Study of Parkinson Disease and Related Endophenotypes in the Italian Population. Front Neurol 2020; 10:1362. [PMID: 31998221 PMCID: PMC6965311 DOI: 10.3389/fneur.2019.01362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022] Open
Abstract
Parkinson Disease (PD) is a complex neurodegenerative disorder characterized by large genetic heterogeneity and missing heritability. Since the genetic background of PD can partly vary among ethnicities and neurological scales have been scarcely investigated in a PD setting, we performed an exploratory Whole Exome Sequencing (WES) analysis of 123 PD patients from mainland Italy, investigating scales assessing motor (UPDRS), cognitive (MoCA), and other non-motor symptoms (NMS). We performed variant prioritization, followed by targeted association testing of prioritized variants in 446 PD cases and 211 controls. Then we ran Exome-Wide Association Scans (EWAS) within sequenced PD cases (N = 113), testing both motor and non-motor PD endophenotypes, as well as their associations with Polygenic Risk Scores (PRS) influencing brain subcortical volumes. We identified a variant associated with PD, rs201330591 in GTF2H2 (5q13; alternative T allele: OR [CI] = 8.16[1.08; 61.52], FDR = 0.048), which was not replicated in an independent cohort of European ancestry (1,148 PD cases, 503 controls). In the EWAS, polygenic analyses revealed statistically significant multivariable associations of amygdala- [β(SE) = -0.039(0.013); FDR = 0.039] and caudate-PRS [0.043(0.013); 0.028] with motor symptoms. All subcortical PRSs in a multivariable model notably increased the variance explained in motor (adjusted-R2 = 38.6%), cognitive (32.2%) and other non-motor symptoms (28.9%), compared to baseline models (~20%). Although, the small sample size warrants further replications, these findings suggest shared genetic architecture between PD symptoms and subcortical structures, and provide interesting clues on PD genetic and neuroimaging features.
Collapse
Affiliation(s)
| | | | | | - Teresa Nutile
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | | | | | | | | | | | - Antonio Simeone
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Marina Ciullo
- IRCCS Neuromed, Pozzilli, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Teresa Esposito
- IRCCS Neuromed, Pozzilli, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| |
Collapse
|
26
|
Finnish Parkinson's disease study integrating protein-protein interaction network data with exome sequencing analysis. Sci Rep 2019; 9:18865. [PMID: 31827228 PMCID: PMC6906405 DOI: 10.1038/s41598-019-55479-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/29/2019] [Indexed: 12/30/2022] Open
Abstract
Variants associated with Parkinson’s disease (PD) have generally a small effect size and, therefore, large sample sizes or targeted analyses are required to detect significant associations in a whole exome sequencing (WES) study. Here, we used protein-protein interaction (PPI) information on 36 genes with established or suggested associations with PD to target the analysis of the WES data. We performed an association analysis on WES data from 439 Finnish PD subjects and 855 controls, and included a Finnish population cohort as the replication dataset with 60 PD subjects and 8214 controls. Single variant association (SVA) test in the discovery dataset yielded 11 candidate variants in seven genes, but the associations were not significant in the replication cohort after correction for multiple testing. Polygenic risk score using variants rs2230288 and rs2291312, however, was associated to PD with odds ratio of 2.7 (95% confidence interval 1.4–5.2; p < 2.56e-03). Furthermore, an analysis of the PPI network revealed enriched clusters of biological processes among established and candidate genes, and these functional networks were visualized in the study. We identified novel candidate variants for PD using a gene prioritization based on PPI information, and described why these variants may be involved in the pathogenesis of PD.
Collapse
|
27
|
Olsen AL, Feany MB. Glial α-synuclein promotes neurodegeneration characterized by a distinct transcriptional program in vivo. Glia 2019; 67:1933-1957. [PMID: 31267577 DOI: 10.1002/glia.23671] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/29/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022]
Abstract
α-Synucleinopathies are neurodegenerative diseases that are characterized pathologically by α-synuclein inclusions in neurons and glia. The pathologic contribution of glial α-synuclein in these diseases is not well understood. Glial α-synuclein may be of particular importance in multiple system atrophy (MSA), which is defined pathologically by glial cytoplasmic α-synuclein inclusions. We have previously described Drosophila models of neuronal α-synucleinopathy, which recapitulate key features of the human disorders. We have now expanded our model to express human α-synuclein in glia. We demonstrate that expression of α-synuclein in glia alone results in α-synuclein aggregation, death of dopaminergic neurons, impaired locomotor function, and autonomic dysfunction. Furthermore, co-expression of α-synuclein in both neurons and glia worsens these phenotypes as compared to expression of α-synuclein in neurons alone. We identify unique transcriptomic signatures induced by glial as opposed to neuronal α-synuclein. These results suggest that glial α-synuclein may contribute to the burden of pathology in the α-synucleinopathies through a cell type-specific transcriptional program. This new Drosophila model system enables further mechanistic studies dissecting the contribution of glial and neuronal α-synuclein in vivo, potentially shedding light on mechanisms of disease that are especially relevant in MSA but also the α-synucleinopathies more broadly.
Collapse
Affiliation(s)
- Abby L Olsen
- Department of Neurology, Brigham and Women's Hospital, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
28
|
Trinh J, Lohmann K, Baumann H, Balck A, Borsche M, Brüggemann N, Dure L, Dean M, Volkmann J, Tunc S, Prasuhn J, Pawlack H, Imhoff S, Lill CM, Kasten M, Bauer P, Rolfs A, Klein C. Utility and implications of exome sequencing in early‐onset Parkinson's disease. Mov Disord 2018; 34:133-137. [DOI: 10.1002/mds.27559] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Joanne Trinh
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Katja Lohmann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Hauke Baumann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Alexander Balck
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Max Borsche
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Leon Dure
- Department of Neurology University of Alabama at Birmingham Birmingham Alabama USA
| | - Marissa Dean
- Department of Neurology University of Alabama at Birmingham Birmingham Alabama USA
| | - Jens Volkmann
- Departement of Neurology Universitatsklinikum Würzburg Würzburg Germany
| | - Sinem Tunc
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Jannik Prasuhn
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Heike Pawlack
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Sophie Imhoff
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | | | - Meike Kasten
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Psychiatry University of Lübeck Lübeck Germany
| | - Peter Bauer
- Centogene AG, Institute for Rare Diseases Rostock Germany
| | - Arndt Rolfs
- Centogene AG, Institute for Rare Diseases Rostock Germany
- Albrecht Kossel Institute for Neuroregeneration University Hospital Rostock Rostock Germany
| | - Christine Klein
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | | |
Collapse
|
29
|
Chen AH, Ge W, Metcalf W, Jakobsson E, Mainzer LS, Lipka AE. An assessment of true and false positive detection rates of stepwise epistatic model selection as a function of sample size and number of markers. Heredity (Edinb) 2018; 122:660-671. [PMID: 30443009 PMCID: PMC6462028 DOI: 10.1038/s41437-018-0162-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/19/2018] [Accepted: 10/28/2018] [Indexed: 12/21/2022] Open
Abstract
Association studies have been successful at identifying genomic regions associated with important traits, but routinely employ models that only consider the additive contribution of an individual marker. Because quantitative trait variability typically arises from multiple additive and non-additive sources, utilization of statistical approaches that include main and two-way interaction marker effects of several loci in one model could lead to unprecedented characterization of these sources. Here we examine the ability of one such approach, called the Stepwise Procedure for constructing an Additive and Epistatic Multi-Locus model (SPAEML), to detect additive and epistatic signals simulated using maize and human marker data. Our results revealed that SPAEML was capable of detecting quantitative trait nucleotides (QTNs) at sample sizes as low as n = 300 and consistently specifying signals as additive and epistatic for larger sizes. Sample size and minor allele frequency had a major influence on SPAEML's ability to distinguish between additive and epistatic signals, while the number of markers tested did not. We conclude that SPAEML is a useful approach for providing further elucidation of the additive and epistatic sources contributing to trait variability when applied to a small subset of genome-wide markers located within specific genomic regions identified using a priori analyses.
Collapse
Affiliation(s)
- Angela H Chen
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Weihao Ge
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - William Metcalf
- Department of Computer Sciences, Rose-Hulman Institute of Technology, Terre Haute, IN, 47803, USA
| | - Eric Jakobsson
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Liudmila Sergeevna Mainzer
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| |
Collapse
|
30
|
Pan H, Shen JY, Du JJ, Cui SS, Liu J, Lin YQ, He YX, Fu Y, Gao C, Li G, Chen SD, Ma JF. Lack of Association Between DNMT3B Polymorphisms and Sporadic Parkinson's Disease in a Han Chinese Population. Neurosci Bull 2018; 34:867-869. [PMID: 29761417 PMCID: PMC6129251 DOI: 10.1007/s12264-018-0233-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/03/2018] [Indexed: 11/24/2022] Open
Affiliation(s)
- Hong Pan
- Laboratory of Neurodegenerative Diseases, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jun-Yi Shen
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Juan-Juan Du
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shi-Shuang Cui
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jin Liu
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yi-Qi Lin
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yi-Xi He
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yang Fu
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chao Gao
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Gen Li
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Sheng-Di Chen
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jian-Fang Ma
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| |
Collapse
|
31
|
Chew EGY, Liany H, Tan LCS, Au WL, Prakash KM, Annuar AA, Chan AYY, Lim SY, Mok V, Chung SJ, Song K, Liu J, Foo JN, Tan EK. Evaluation of novel Parkinson's disease candidate genes in the Chinese population. Neurobiol Aging 2018; 74:235.e1-235.e4. [PMID: 30337193 DOI: 10.1016/j.neurobiolaging.2018.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 11/30/2022]
Abstract
Recent whole-exome sequencing studies in European patients with Parkinson's disease (PD) have identified potential risk variants across 33 novel PD candidate genes. We aim to determine if these reported candidate genes are similarly implicated in Asians by assessing common, rare, and novel nonsynonymous coding variants by sequencing all 33 genes in 198 Chinese samples and genotyping coding variants in an independent set of 9756 Chinese samples. We carried out further targeted sequencing of CD36 in an additional 576 Chinese and Korean samples. We found that only 8 of 43 reported risk variants were polymorphic in our Chinese samples. We identified several heterozygotes for rare loss-of-function mutations, including the reported CD36 p.Gln74Ter variant, in both cases and controls. We also observed 2 potential compound heterozygotes among PD cases for rare loss-of-function mutations in CD36 and SSPO. The other reported variants were common in East Asians and not associated with PD, completely absent, or only found in controls. Therefore, the 33 reported candidate genes and associated variants are unlikely to confer significant PD risk in the East Asian population.
Collapse
Affiliation(s)
| | - Herty Liany
- Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Louis C S Tan
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore; Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Wing-Lok Au
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
| | - Kumar-M Prakash
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
| | - Azlina Ahmad Annuar
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Anne Y Y Chan
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, Gerald Choa Neuroscience Centre, Division of Neurology, Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR, China
| | - Shen-Yang Lim
- Division of Neurology, Department of Medicine, and the Mah Pooi Soo and Tan Chin Nam Centre for Parkinson's and Related Disorders, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vincent Mok
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, Gerald Choa Neuroscience Centre, Division of Neurology, Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR, China
| | - Sun Ju Chung
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Ulsan, Korea
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jia Nee Foo
- Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | - Eng-King Tan
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore; Duke-National University of Singapore Medical School, Singapore, Singapore.
| |
Collapse
|
32
|
Kumar S, Yadav N, Pandey S, Thelma BK. Advances in the discovery of genetic risk factors for complex forms of neurodegenerative disorders: contemporary approaches, success, challenges and prospects. J Genet 2018. [DOI: 10.1007/s12041-018-0953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
33
|
Emelyanov AK, Usenko TS, Tesson C, Senkevich KA, Nikolaev MA, Miliukhina IV, Kopytova AE, Timofeeva AA, Yakimovsky AF, Lesage S, Brice A, Pchelina SN. Mutation analysis of Parkinson's disease genes in a Russian data set. Neurobiol Aging 2018; 71:267.e7-267.e10. [PMID: 30146349 DOI: 10.1016/j.neurobiolaging.2018.06.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/24/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
Abstract
Common variants and risk factors related to familial and sporadic cases of Parkinson's disease (PD) in diverse populations have been identified at numerous genomic loci. In this study, genetic analysis was performed through a screening of LRRK2 G2019S, GBA mutations (L444P, N370S), and common variants (E326K, T369M) in 762 PD patients and in 400 controls. Next-generation sequencing analysis of 22 PD-related genes in 28 early-onset PD cases from North-Western region of Russia was performed. The frequency of LRRK2 G2019S mutation was 5.8% in familial and 0.5% in sporadic PD cases. The frequency of GBA mutations (L444P, N370S) in PD patients was higher compared to controls (odds ratio [OR] = 6.9, 95% confidence interval [CI], 0.9-53.13, p = 0.031), particularly in patients with early-onset compared to late-onset PD (OR = 3.90 [95% CI, 1.2-13.2], p = 0.009). The frequency of E326K and T369M was twice higher among PD patients than in controls (OR = 2.24, 95% CI 1.05-4.79, p = 0.033). However, the screening of 22 PD-related genes using our novel panel of gene resequencing in our series of 28 early-onset PD failed to identify any mutations. LRRK2 and GBA mutations were found to be common risk factors for PD in North-Western region of Russia.
Collapse
Affiliation(s)
- Anton K Emelyanov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia
| | - Tatiana S Usenko
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia; CT, SL, AB Sorbonne Universités, UPMC Université, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Christelle Tesson
- CT, SL, AB Sorbonne Universités, UPMC Université, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Konstantin A Senkevich
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia; Institute of Experimental Medicine, St. Petersburg, Russia
| | - Mikhail A Nikolaev
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia
| | - Irina V Miliukhina
- First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia; Institute of Experimental Medicine, St. Petersburg, Russia
| | - Alena E Kopytova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Saint-Petersburg, Russia
| | - Alla A Timofeeva
- First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia
| | - Andrey F Yakimovsky
- First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia
| | - Suzanne Lesage
- CT, SL, AB Sorbonne Universités, UPMC Université, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Alexis Brice
- CT, SL, AB Sorbonne Universités, UPMC Université, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Sofya N Pchelina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia; Institute of Experimental Medicine, St. Petersburg, Russia.
| |
Collapse
|
34
|
Kumar S, Yadav N, Pandey S, Thelma BK. Advances in the discovery of genetic risk factors for complex forms of neurodegenerative disorders: contemporary approaches, success, challenges and prospects. J Genet 2018; 97:625-648. [PMID: 30027900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Neurodegenerative diseases constitute a large proportion of disorders in elderly, majority being sporadic in occurrence with ∼5-10% familial. A strong genetic component underlies the Mendelian forms but nongenetic factors together with genetic vulnerability contributes to the complex sporadic forms. Several gene discoveries in the familial forms have provided novel insights into the pathogenesis of neurodegeneration with implications for treatment. Conversely, findings from genetic dissection of the sporadic forms, despite large genomewide association studies and more recently whole exome and whole genome sequencing, have been limited. This review provides a concise account of the genetics that we know, the pathways that they implicate, the challenges that are faced and the prospects that are envisaged for the sporadic, complex forms of neurodegenerative diseases, taking four most common conditions, namely Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington disease as examples. Poor replication across studies, inability to establish genotype-phenotype correlations and the overall failure to predict risk and/or prevent disease in this group poses a continuing challenge. Among others, clinical heterogeneity emerges as the most important impediment warranting newer approaches. Advanced computational and system biology tools to analyse the big data are being generated and the alternate strategy such as subgrouping of case-control cohorts based on deep phenotyping using the principles of Ayurveda to overcome current limitation of phenotype heterogeneity seem to hold promise. However, at this point, with advances in discovery genomics and functional analysis of putative determinants with translation potential for the complex forms being minimal, stem cell therapies are being attempted as potential interventions. In this context, the possibility to generate patient derived induced pluripotent stem cells, mutant/gene/genome correction through CRISPR/Cas9 technology and repopulating the specific brain regions with corrected neurons, which may fulfil the dream of personalized medicine have been mentioned briefly. Understanding disease pathways/biology using this technology, with implications for development of novel therapeutics are optimistic expectations in the near future.
Collapse
Affiliation(s)
- Sumeet Kumar
- Department of Genetics, University of Delhi South Campus, New Delhi 110 021, India.
| | | | | | | |
Collapse
|
35
|
Chew EG, Foo JN, Tan EK. Identifying genes in Parkinson disease: state of the art. Med J Aust 2018; 208:381-382. [PMID: 29764346 DOI: 10.5694/mja17.01254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/28/2018] [Indexed: 11/17/2022]
Affiliation(s)
- Elaine Gy Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jia Nee Foo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | | |
Collapse
|
36
|
Burke EA, Frucht SJ, Thompson K, Wolfe LA, Yokoyama T, Bertoni M, Huang Y, Sincan M, Adams DR, Taylor RW, Gahl WA, Toro C, Malicdan MCV. Biallelic mutations in mitochondrial tryptophanyl-tRNA synthetase cause Levodopa-responsive infantile-onset Parkinsonism. Clin Genet 2018; 93:712-718. [PMID: 29120065 PMCID: PMC5828974 DOI: 10.1111/cge.13172] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/30/2017] [Accepted: 11/05/2017] [Indexed: 12/30/2022]
Abstract
Mitochondrial aminoacyl‐tRNA synthetases (mtARSs) are essential, ubiquitously expressed enzymes that covalently attach amino acids to their corresponding tRNA molecules during translation of mitochondrial genes. Deleterious variants in the mtARS genes cause a diverse array of phenotypes, many of which involve the nervous system. Moreover, distinct mutations in mtARSs often cause different clinical manifestations. Recently, the gene encoding mitochondrial tryptophanyl tRNA synthetase (WARS2) was reported to cause 2 different neurological phenotypes, a form of autosomal recessive intellectual disability and a syndrome of severe infantile‐onset leukoencephalopathy. Here, we report the case of a 17‐year‐old boy with compound heterozygous mutations in WARS2 (p.Trp13Gly, p.Ser228Trp) who presented with infantile‐onset, Levodopa‐responsive Parkinsonism at the age of 2 years. Analysis of patient‐derived dermal fibroblasts revealed decreased steady‐state WARS2 protein and normal OXPHOS content. Muscle mitochondrial studies suggested mitochondrial proliferation without obvious respiratory chain deficiencies at the age of 9 years. This case expands the phenotypic spectrum of WARS2 deficiency and emphasizes the importance of mitochondrial protein synthesis in the pathogenesis of Parkinsonism.
Collapse
Affiliation(s)
- E A Burke
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland
| | - S J Frucht
- Movement Disorders Division, School of Medicine, New York University Langone, New York, New York
| | - K Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - L A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - T Yokoyama
- Section of Human Biochemical Genetics, Medical Genetics Branch, NHGRI, NIH, Bethesda, Maryland
| | - M Bertoni
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland
| | - Y Huang
- Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - M Sincan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland
| | - D R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - R W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - W A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland.,Section of Human Biochemical Genetics, Medical Genetics Branch, NHGRI, NIH, Bethesda, Maryland
| | - C Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - M C V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| |
Collapse
|
37
|
Schormair B, Kemlink D, Mollenhauer B, Fiala O, Machetanz G, Roth J, Berutti R, Strom TM, Haslinger B, Trenkwalder C, Zahorakova D, Martasek P, Ruzicka E, Winkelmann J. Diagnostic exome sequencing in early-onset Parkinson's disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson's disease. Clin Genet 2018; 93:603-612. [PMID: 28862745 DOI: 10.1111/cge.13124] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/18/2022]
Abstract
Parkinson's disease (PD) is a genetically heterogeneous disorder and new putative disease genes are discovered constantly. Therefore, whole-exome sequencing could be an efficient approach to genetic testing in PD. To evaluate its performance in early-onset sporadic PD, we performed diagnostic exome sequencing in 80 individuals with manifestation of PD symptoms at age 40 or earlier and a negative family history of PD. Variants in validated and candidate disease genes and risk factors for PD and atypical Parkinson syndromes were annotated, followed by further analysis for selected variants. We detected pathogenic variants in Mendelian genes in 6.25% of cases and high-impact risk factor variants in GBA in 5% of cases, resulting in overall maximum diagnostic yield of 11.25%. One individual was compound heterozygous for variants affecting canonical splice sites in VPS13C, confirming the causal role of protein-truncating variants in this gene linked to autosomal-recessive early-onset PD. Despite the low diagnostic yield of exome sequencing in sporadic early-onset PD, the confirmation of the recently discovered VPS13C gene highlights its advantage over using predefined gene panels.
Collapse
Affiliation(s)
- B Schormair
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - D Kemlink
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine and General University Hospital in Prague, Charles University in Prague, Prague, Czech Republic
| | - B Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany.,Institute of Neuropathology and Department of Neurosurgery, University Medical Center Göttingen, Göttingen, Germany
| | - O Fiala
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine and General University Hospital in Prague, Charles University in Prague, Prague, Czech Republic.,Institute of Neuropsychiatric Care (INEP), Prague, Czech Republic
| | | | - J Roth
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine and General University Hospital in Prague, Charles University in Prague, Prague, Czech Republic
| | - R Berutti
- Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | - T M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | - B Haslinger
- Neurologische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | | | - D Zahorakova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine and General University Hospital in Prague, Charles University in Prague, Prague, Czech Republic
| | - P Martasek
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine and General University Hospital in Prague, Charles University in Prague, Prague, Czech Republic
| | - E Ruzicka
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine and General University Hospital in Prague, Charles University in Prague, Prague, Czech Republic
| | - J Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany.,Neurologische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| |
Collapse
|
38
|
Genetic risk factors in Finnish patients with Parkinson's disease. Parkinsonism Relat Disord 2017; 45:39-43. [PMID: 29029963 DOI: 10.1016/j.parkreldis.2017.09.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/30/2017] [Accepted: 09/28/2017] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Variation contributing to the risk of Parkinson's disease (PD) has been identified in several genes and at several loci including GBA, SMPD1, LRRK2, POLG1, CHCHD10 and MAPT, but the frequencies of risk variants seem to vary according to ethnic background. Our aim was to analyze how variation in these genes contributes to PD in the Finnish population. METHODS The subjects consisted of 527 Finnish patients with early-onset PD, 325 patients with late-onset PD and 403 population controls. We screened for known genetic risk variants in GBA, SMPD1, LRRK2, POLG1, CHCHD10 and MAPT. In addition, DNA from 225 patients with early-onset Parkinson's disease was subjected to whole exome sequencing (WES). RESULTS We detected a significant difference in the length variation of the CAG repeat in POLG1 between patients with early-onset PD compared to controls. The p.N370S and p.L444P variants in GBA contributed to a relative risk of 3.8 in early-onset PD and 2.5 in late-onset PD. WES revealed five variants in LRRK2 and SMPD1 that were found in the patients but not in the Finnish ExAC sequences. These are possible risk variants that require further confirmation. The p.G2019S variant in LRRK2, common in North African Arabs and Ashkenazi Jews, was not detected in any of the 849 PD patients. CONCLUSIONS The POLG1 CAG repeat length variation and the GBA p.L444P variant are associated with PD in the Finnish population.
Collapse
|
39
|
Wang YA, Kammenga JE, Harvey SC. Genetic variation in neurodegenerative diseases and its accessibility in the model organism Caenorhabditis elegans. Hum Genomics 2017; 11:12. [PMID: 28545550 PMCID: PMC5445269 DOI: 10.1186/s40246-017-0108-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/12/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Neurodegenerative diseases (NGDs) such as Alzheimer's and Parkinson's are debilitating and largely untreatable conditions strongly linked to age. The clinical, neuropathological, and genetic components of NGDs indicate that neurodegeneration is a complex trait determined by multiple genes and by the environment. MAIN BODY The symptoms of NGDs differ among individuals due to their genetic background, and this variation affects the onset and progression of NGD and NGD-like states. Such genetic variation affects the molecular and cellular processes underlying NGDs, leading to differential clinical phenotypes. So far, we have a limited understanding of the mechanisms of individual background variation. Here, we consider how variation between genetic backgrounds affects the mechanisms of aging and proteostasis in NGD phenotypes. We discuss how the nematode Caenorhabditis elegans can be used to identify the role of variation between genetic backgrounds. Additionally, we review advances in C. elegans methods that can facilitate the identification of NGD regulators and/or networks. CONCLUSION Genetic variation both in disease genes and in regulatory factors that modulate onset and progression of NGDs are incompletely understood. The nematode C. elegans represents a valuable system in which to address such questions.
Collapse
Affiliation(s)
- Yiru Anning Wang
- Biomolecular Research Group, School of Human and Life Science, Canterbury Christ Church University, Canterbury, CT1 1QU UK
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Jan Edward Kammenga
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Simon Crawford Harvey
- Biomolecular Research Group, School of Human and Life Science, Canterbury Christ Church University, Canterbury, CT1 1QU UK
| |
Collapse
|