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Langerscheidt F, Wied T, Al Kabbani MA, van Eimeren T, Wunderlich G, Zempel H. Genetic forms of tauopathies: inherited causes and implications of Alzheimer's disease-like TAU pathology in primary and secondary tauopathies. J Neurol 2024; 271:2992-3018. [PMID: 38554150 PMCID: PMC11136742 DOI: 10.1007/s00415-024-12314-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024]
Abstract
Tauopathies are a heterogeneous group of neurologic diseases characterized by pathological axodendritic distribution, ectopic expression, and/or phosphorylation and aggregation of the microtubule-associated protein TAU, encoded by the gene MAPT. Neuronal dysfunction, dementia, and neurodegeneration are common features of these often detrimental diseases. A neurodegenerative disease is considered a primary tauopathy when MAPT mutations/haplotypes are its primary cause and/or TAU is the main pathological feature. In case TAU pathology is observed but superimposed by another pathological hallmark, the condition is classified as a secondary tauopathy. In some tauopathies (e.g. MAPT-associated frontotemporal dementia (FTD), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and Alzheimer's disease (AD)) TAU is recognized as a significant pathogenic driver of the disease. In many secondary tauopathies, including Parkinson's disease (PD) and Huntington's disease (HD), TAU is suggested to contribute to the development of dementia, but in others (e.g. Niemann-Pick disease (NPC)) TAU may only be a bystander. The genetic and pathological mechanisms underlying TAU pathology are often not fully understood. In this review, the genetic predispositions and variants associated with both primary and secondary tauopathies are examined in detail, assessing evidence for the role of TAU in these conditions. We highlight less common genetic forms of tauopathies to increase awareness for these disorders and the involvement of TAU in their pathology. This approach not only contributes to a deeper understanding of these conditions but may also lay the groundwork for potential TAU-based therapeutic interventions for various tauopathies.
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Affiliation(s)
- Felix Langerscheidt
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Tamara Wied
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, Von-Liebig-Str. 20, 53359, Rheinbach, Germany
| | - Mohamed Aghyad Al Kabbani
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Thilo van Eimeren
- Multimodal Neuroimaging Group, Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Gilbert Wunderlich
- Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany.
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Pavithra S, Aich A, Chanda A, Zohra IF, Gawade P, Das RK. PER2 gene and its association with sleep-related disorders: A review. Physiol Behav 2024; 273:114411. [PMID: 37981094 DOI: 10.1016/j.physbeh.2023.114411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/12/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Abstract
The natural circadian rhythm in an individual governs the sleep-wake cycle over 24 h. Disruptions in this internal cycle can lead to major health hazards and sleep disorders. Reports suggest that at least 50 % of people worldwide suffer from sleep-related disorders. An increase in screen time, especially in the wake of the COVID-19 pandemic, is one of the external causative factors for this condition. While many factors govern the circadian clock and its aberrance, the PER2 gene has been strongly linked to chronotypes by many researchers. The current paper provides an extensive examination of key Single Nucleotide Polymorphisms within the PER2 gene and their potential connection to four major types of sleep disorders. This study investigates whether these SNPs play a causative role in sleep disorders or if they are solely associated with these conditions. Additionally, we explore whether these genetic variations exert a lifelong influence on these sleep patterns or if external triggers contribute to the development of sleep disorders. This gene is a crucial regulator of the circadian cycle responsible for the transcription of other clock genes. It regulates a variety of physiological systems such as metabolism, sleep, body temperature, blood pressure, endocrine, immunological, cardiovascular, and renal function. We aim to establish some clarity to the multifaceted nature of this gene, which is often overlooked, and seek to establish the mechanistic role of PER2 gene mutations in sleep disorders. This will improve further understanding, assessment, and treatment of these conditions in future.
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Affiliation(s)
- S Pavithra
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India; Centre for Biomaterials, Cellular & Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Adrija Aich
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Adrita Chanda
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Ifsha Fatima Zohra
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Pranotee Gawade
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Raunak Kumar Das
- Centre for Biomaterials, Cellular & Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
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Tu M, Saputo S. From Beginning to End: Expanding the SERINC3 Interactome Through an in silico Analysis. Bioinform Biol Insights 2022; 16:11779322221092944. [PMID: 35494555 PMCID: PMC9052817 DOI: 10.1177/11779322221092944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/07/2022] [Indexed: 11/15/2022] Open
Abstract
The serine incorporator (SERINC) family of proteins are a family of multipass transmembrane proteins associated with biosynthesis of serine-containing phospholipids and sphingolipids. Humans have 5 paralogs, SERINC1-5, which have been linked to disease including variable expression in tumor lines and possessing activity as restriction factors against HIV-1. Despite recent studies, the cellular function of SERINC proteins have yet to be fully elucidated. The goal of this study as to investigate the role of SERINC3 by expanding upon its interactome. We used a variety of bioinformatic tools to identify cellular factors that interact with SERINC3 and assessed how sequence variation might alter these interactions. Analysis of the promoter region indicates that SERINC3 is putatively regulated by transcription factors involved in tissue-specific development. Analysis of the unique 3′-untranslated region of one variant of HsSERINC3 revealed that this region serves as a conserved site of regulation by both RNA binding proteins and miRNA. In addition, SERINC3 is putatively regulated at the protein level by several posttranslational modifications. Our results show that extra-membrane portions of SERINC3 are subject to variation in the coding sequence as well as areas of relatively low conservation. Overall, our data suggest that regions of low homology as well as presence of variations in the nucleotide and protein sequences of HsSERINC3 suggest that these variations may lead to aberrant function and alternative regulatory mechanisms in homologs. The functional consequences of these sequence and structural variations need to be explored systematically to fully appreciate the role of SERINC3 in both health and disease.
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Affiliation(s)
- Mckenzie Tu
- Department of Chemistry and Biochemistry, SUNY Brockport, Brockport, NY, USA
| | - Sarah Saputo
- Department of Chemistry and Biochemistry, SUNY Brockport, Brockport, NY, USA
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Debnath M, Dey S, Sreenivas N, Pal PK, Yadav R. Genetic and Epigenetic Constructs of Progressive Supranuclear Palsy. Ann Neurosci 2022; 29:177-188. [PMID: 36419517 PMCID: PMC9676335 DOI: 10.1177/09727531221089396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/20/2022] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Progressive supranuclear palsy (PSP) is a rapidly progressive primary tauopathy characterized by vertical gaze palsy, postural instability, and mild dementia. PSP shows high clinical and pathologic heterogeneity. Although a few risk factors exist, such as advanced age and environmental toxins, the precise etiology remains largely elusive. Compelling evidence now suggests that genetic background plays a pivotal role in the pathogenetic pathways of PSP. Notably, PSP is genetically and phenotypically a complex disorder. Given the tau pathology, several studies in the past have identified microtubule-associated protein tau (MAPT) gene mutations/variations and its haplotype as the major genetic risk factor of PSP, both in the sporadic and the familial forms. Subsequently, genome-wide association studies (GWAS) also identified several novel risk variants. However, these genetic risk determinants fail to explain the pathogenetic basis of PSP and its phenotypic spectrum in majority of the cases. Some genetic variants are known to confer the risk, while others seem to act as modifier genes. SUMMARY Besides the complex genetic basis of PSP, the pathobiological mechanisms, differential diagnosis, and management of patients with PSP have further been complicated by genetic conditions that mimic the phenotypes of PSP. This is now becoming increasingly apparent that interactions between genetic and environmental factors significantly contribute to PSP development. Further, the effect of environmental factors seems to be mediated through epigenetic modifications. KEY MESSAGE Herein, we provide a comprehensive overview of the genetic and epigenetic constructs of PSP and highlight the relevance of genetic and epigenetic findings in the pathobiology of PSP.
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Affiliation(s)
- Monojit Debnath
- Department of Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
- These two authors have contributed equally
| | - Saikat Dey
- Department of Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
- These two authors have contributed equally
| | - Nikhitha Sreenivas
- Department of Human Genetics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
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A protein with broad functions: damage-specific DNA-binding protein 2. Mol Biol Rep 2022; 49:12181-12192. [PMID: 36190612 PMCID: PMC9712371 DOI: 10.1007/s11033-022-07963-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/17/2022] [Indexed: 02/01/2023]
Abstract
Damage-specific DNA-binding protein 2 (DDB2) was initially identified as a component of the damage-specific DNA-binding heterodimeric complex, which cooperates with other proteins to repair UV-induced DNA damage. DDB2 is involved in the occurrence and development of cancer by affecting nucleotide excision repair (NER), cell apoptosis, and premature senescence. DDB2 also affects the sensitivity of cancer cells to radiotherapy and chemotherapy. In addition, a recent study found that DDB2 is a pathogenic gene for hepatitis and encephalitis. In recent years, there have been few relevant literature reports on DDB2, so there is still room for further research about it. In this paper, the molecular mechanisms of different biological processes involving DDB2 are reviewed in detail to provide theoretical support for research on drugs that can target DDB2.
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Stamelou M, Respondek G, Giagkou N, Whitwell JL, Kovacs GG, Höglinger GU. Evolving concepts in progressive supranuclear palsy and other 4-repeat tauopathies. Nat Rev Neurol 2021; 17:601-620. [PMID: 34426686 DOI: 10.1038/s41582-021-00541-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Tauopathies are classified according to whether tau deposits predominantly contain tau isoforms with three or four repeats of the microtubule-binding domain. Those in which four-repeat (4R) tau predominates are known as 4R-tauopathies, and include progressive supranuclear palsy, corticobasal degeneration, argyrophilic grain disease, globular glial tauopathies and conditions associated with specific MAPT mutations. In these diseases, 4R-tau deposits are found in various cell types and anatomical regions of the brain and the conditions share pathological, pathophysiological and clinical characteristics. Despite being considered 'prototype' tauopathies and, therefore, ideal for studying neuroprotective agents, 4R-tauopathies are still severe and untreatable diseases for which no validated biomarkers exist. However, advances in research have addressed the issues of phenotypic overlap, early clinical diagnosis, pathophysiology and identification of biomarkers, setting a road map towards development of treatments. New clinical criteria have been developed and large cohorts with early disease are being followed up in prospective studies. New clinical trial readouts are emerging and biomarker research is focused on molecular pathways that have been identified. Lessons learned from failed trials of neuroprotective drugs are being used to design new trials. In this Review, we present an overview of the latest research in 4R-tauopathies, with a focus on progressive supranuclear palsy, and discuss how current evidence dictates ongoing and future research goals.
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Affiliation(s)
- Maria Stamelou
- Parkinson's Disease and Movement Disorders Dept, HYGEIA Hospital, Athens, Greece. .,European University of Cyprus, Nicosia, Cyprus. .,Philipps University, Marburg, Germany.
| | - Gesine Respondek
- Department of Neurology, Hanover Medical School, Hanover, Germany
| | - Nikolaos Giagkou
- Parkinson's Disease and Movement Disorders Dept, HYGEIA Hospital, Athens, Greece
| | | | - Gabor G Kovacs
- Department of Laboratory Medicine and Pathobiology and Tanz Centre for Research in Neurodegenerative Disease (CRND), University of Toronto, Toronto, Ontario, Canada.,Laboratory Medicine Program and Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
| | - Günter U Höglinger
- Department of Neurology, Hanover Medical School, Hanover, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
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Wen Y, Zhou Y, Jiao B, Shen L. Genetics of Progressive Supranuclear Palsy: A Review. JOURNAL OF PARKINSON'S DISEASE 2021; 11:93-105. [PMID: 33104043 PMCID: PMC7990399 DOI: 10.3233/jpd-202302] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/26/2020] [Indexed: 02/06/2023]
Abstract
Progressive supranuclear palsy (PSP) is an atypical parkinsonism with prominent 4R-tau neuropathology, and the classical clinical phenotype is characterized by vertical supranuclear gaze palsy, unprovoked falls, akinetic-rigid syndrome and cognitive decline. Though PSP is generally regarded as sporadic, there is increasing evidence suggesting that a series of common and rare genetic variants impact on sporadic and familial forms of PSP. To date, more than 10 genes have been reported to show a potential association with PSP. Among these genes, the microtubule-associated protein tau (MAPT) is the risk locus with the strongest effect size on sporadic PSP in the case-control genome-wide association studies (GWAS). Additionally, MAPT mutations are the most common cause of familial PSP while the leucine-rich repeat kinase 2 (LRRK2) is a rare monogenic cause of PSP, and several other gene mutations may mimic the PSP phenotype, like the dynactin subunit 1 (DCTN1). In total, 15 MAPT mutations have been identified in cases with PSP, and the mean age at onset is much earlier than in cases carrying LRRK2 or DCTN1 mutations. GWAS have further identified several risk loci of PSP, proposing molecular pathways related to PSP. The present review focused on genetic studies on PSP and summarized genetic factors of PSP, which may help to elucidate the underlying pathogenesis and provide new perspectives for therapeutic strategies.
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Affiliation(s)
- Yafei Wen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Yafang Zhou
- Department of Geriatrics Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, PR China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, Hunan, PR China
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Chu BB, Keys KL, German CA, Zhou H, Zhou JJ, Sobel EM, Sinsheimer JS, Lange K. Iterative hard thresholding in genome-wide association studies: Generalized linear models, prior weights, and double sparsity. Gigascience 2020; 9:giaa044. [PMID: 32491161 PMCID: PMC7268817 DOI: 10.1093/gigascience/giaa044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/27/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Consecutive testing of single nucleotide polymorphisms (SNPs) is usually employed to identify genetic variants associated with complex traits. Ideally one should model all covariates in unison, but most existing analysis methods for genome-wide association studies (GWAS) perform only univariate regression. RESULTS We extend and efficiently implement iterative hard thresholding (IHT) for multiple regression, treating all SNPs simultaneously. Our extensions accommodate generalized linear models, prior information on genetic variants, and grouping of variants. In our simulations, IHT recovers up to 30% more true predictors than SNP-by-SNP association testing and exhibits a 2-3 orders of magnitude decrease in false-positive rates compared with lasso regression. We also test IHT on the UK Biobank hypertension phenotypes and the Northern Finland Birth Cohort of 1966 cardiovascular phenotypes. We find that IHT scales to the large datasets of contemporary human genetics and recovers the plausible genetic variants identified by previous studies. CONCLUSIONS Our real data analysis and simulation studies suggest that IHT can (i) recover highly correlated predictors, (ii) avoid over-fitting, (iii) deliver better true-positive and false-positive rates than either marginal testing or lasso regression, (iv) recover unbiased regression coefficients, (v) exploit prior information and group-sparsity, and (vi) be used with biobank-sized datasets. Although these advances are studied for genome-wide association studies inference, our extensions are pertinent to other regression problems with large numbers of predictors.
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Affiliation(s)
- Benjamin B Chu
- Department of Computational Medicine, University of California, Los Angeles, 621 Charles E Young Dr S, Los Angeles, CA, 90095, USA
| | - Kevin L Keys
- Department of Medicine, University of California, San Francisco, 1701 Divisadero St, San Francisco, CA, 94115, USA
- Berkeley Institute of Data Science, University of California, Berkeley, 190 Doe Library, Berkeley, CA 94720, USA
| | - Christopher A German
- Department of Biostatistics, University of California, Los Angeles, 650 Charles E Young Dr S, Los Angeles, CA, 90095, USA
| | - Hua Zhou
- Department of Biostatistics, University of California, Los Angeles, 650 Charles E Young Dr S, Los Angeles, CA, 90095, USA
| | - Jin J Zhou
- Division of Epidemiology and Biostatistics, University of Arizona, 1295 N. Martin Ave. Tucson, AZ, 85724, USA
| | - Eric M Sobel
- Department of Computational Medicine, University of California, Los Angeles, 621 Charles E Young Dr S, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, 695 Charles E Young Dr S, Los Angeles, CA, 90095 USA
| | - Janet S Sinsheimer
- Department of Computational Medicine, University of California, Los Angeles, 621 Charles E Young Dr S, Los Angeles, CA, 90095, USA
- Department of Biostatistics, University of California, Los Angeles, 650 Charles E Young Dr S, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, 695 Charles E Young Dr S, Los Angeles, CA, 90095 USA
| | - Kenneth Lange
- Department of Computational Medicine, University of California, Los Angeles, 621 Charles E Young Dr S, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, 695 Charles E Young Dr S, Los Angeles, CA, 90095 USA
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Mehdizadeh M, Ashtari N, Jiao X, Rahimi Balaei M, Marzban A, Qiyami-Hour F, Kong J, Ghavami S, Marzban H. Alteration of the Dopamine Receptors' Expression in the Cerebellum of the Lysosomal Acid Phosphatase 2 Mutant (Naked-Ataxia ( NAX)) Mouse. Int J Mol Sci 2020; 21:E2914. [PMID: 32326360 PMCID: PMC7215910 DOI: 10.3390/ijms21082914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022] Open
Abstract
A spontaneous mutation in the lysosomal acid phosphatase (Acp2) enzyme (nax: naked-ataxia) in experimental mice results in delayed hair appearance and severe cytoarchitectural impairments of the cerebellum, such as a Purkinje cell (PC) migration defect. In our previous investigation, our team showed that Acp2 expression plans a significant role in cerebellar development. On the other hand, the dopaminergic system is also a player in central nervous system (CNS) development, including cerebellar structure and function. In the current investigation, we have explored how Acp2 can be involved in the regulation of the dopaminergic pathway in the cerebellum via the regulation of dopamine receptor expression and patterning. We provided evidence about the distribution of different dopamine receptors in the developing cerebellum by comparing the expression of dopamine receptors on postnatal days (P) 5 and 17 between nax mice and wild-type (wt) littermates. To this aim, immunohistochemistry and Western blot analysis were conducted using five antibodies against dopamine receptors (DRD1, -2, -3, -4, and -5) accompanied by RNAseq data. Our results revealed that DRD1, -3, and -4 gene expressions significantly increased in nax cerebella but not in wt, while gene expressions of all 5 receptors were evident in PCs of both wt and nax cerebella. DRD3 was strongly expressed in the PCs' somata and cerebellar nuclei neurons at P17 in nax mice, which was comparable to the expression levels in the cerebella of wt littermates. In addition, DRD3 was expressed in scattered cells in a granular layer reminiscent of Golgi cells and was observed in the wt cerebella but not in nax mice. DRD4 was expressed in a subset of PCs and appeared to align with the unique parasagittal stripes pattern. This study contributes to our understanding of alterations in the expression pattern of DRDs in the cerebellum of nax mice in comparison to their wt littermates, and it highlights the role of Acp2 in regulating the dopaminergic system.
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Affiliation(s)
- Mehdi Mehdizadeh
- Cellular and Molecular Research Center, Department of Anatomy, Faculty of Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran; (M.M.); (F.Q.-H.); (J.K.); (S.G.)
| | - Niloufar Ashtari
- Department of Human Anatomy and Cell Science, The Children’s Hospital Research Institute of Manitoba (CHRIM), Max Rady College of Medicine, Rady Faculty of Health science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (N.A.); (X.J.); (M.R.B.)
| | - Xiaodan Jiao
- Department of Human Anatomy and Cell Science, The Children’s Hospital Research Institute of Manitoba (CHRIM), Max Rady College of Medicine, Rady Faculty of Health science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (N.A.); (X.J.); (M.R.B.)
| | - Maryam Rahimi Balaei
- Department of Human Anatomy and Cell Science, The Children’s Hospital Research Institute of Manitoba (CHRIM), Max Rady College of Medicine, Rady Faculty of Health science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (N.A.); (X.J.); (M.R.B.)
| | - Asghar Marzban
- Department of Pediatrics, School of Medicine, Zanjan University of Medical Sciences, Zanjan 4513956111, Iran;
| | - Farshid Qiyami-Hour
- Cellular and Molecular Research Center, Department of Anatomy, Faculty of Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran; (M.M.); (F.Q.-H.); (J.K.); (S.G.)
| | - Jiming Kong
- Cellular and Molecular Research Center, Department of Anatomy, Faculty of Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran; (M.M.); (F.Q.-H.); (J.K.); (S.G.)
| | - Saeid Ghavami
- Cellular and Molecular Research Center, Department of Anatomy, Faculty of Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran; (M.M.); (F.Q.-H.); (J.K.); (S.G.)
- Research Institute in Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Hassan Marzban
- Cellular and Molecular Research Center, Department of Anatomy, Faculty of Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran; (M.M.); (F.Q.-H.); (J.K.); (S.G.)
- Department of Human Anatomy and Cell Science, The Children’s Hospital Research Institute of Manitoba (CHRIM), Max Rady College of Medicine, Rady Faculty of Health science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (N.A.); (X.J.); (M.R.B.)
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Heckman MG, Brennan RR, Labbé C, Soto AI, Koga S, DeTure MA, Murray ME, Petersen RC, Boeve BF, van Gerpen JA, Uitti RJ, Wszolek ZK, Rademakers R, Dickson DW, Ross OA. Association of MAPT Subhaplotypes With Risk of Progressive Supranuclear Palsy and Severity of Tau Pathology. JAMA Neurol 2020; 76:710-717. [PMID: 30882841 DOI: 10.1001/jamaneurol.2019.0250] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Importance The association between the microtubule-associated protein tau (MAPT) H1 haplotype and the risk of progressive supranuclear palsy (PSP) has been well documented. However, the specific H1 subhaplotypes that drive the association have not been evaluated in large studies, nor have they been studied in relation to neuropathologic severity of disease. Objective To comprehensively evaluate the associations of MAPT haplotypes with the risk of PSP and the severity of tau pathology using a large series of neuropathologically confirmed PSP cases. Design, Setting, and Participants A case-control study was used to investigate the associations between MAPT haplotypes and the risk of PSP, and a case series was conducted for examination of associations of MAPT haplotypes with the severity of tau pathology. All 802 neuropathologically confirmed PSP cases were obtained from a neurodegenerative disorders brain bank between January 1, 1998, and December 31, 2013, and 1312 clinical controls were obtained from the neurology department of the Mayo Clinic. Statistical analysis was performed from February 17 to December 12, 2018. Main Outcomes and Measures Presence of PSP in case-control analysis and semiquantitative tau pathology scores for neurofibrillary tangles, neuropil threads, tufted astrocytes, and oligodendroglial coiled bodies in PSP cases. Results For 802 patients with PSP (376 women and 426 men), the median age at death was 75 years (range, 52-98 years). For 1312 controls (701 women and 611 men), the median age at blood collection was 69 years (range, 45-92 years). After adjustment for multiple testing, known associations with risk of PSP were observed for the H2 and H1c haplotypes. Novel associations with PSP were observed for 3 H1 subhaplotypes, including H1d (odds ratio, 1.86; 95% CI, 1.43-2.42; P = 2 × 10-6), H1g (odds ratio, 3.64; 95% CI, 2.04-6.50; P = 2 × 10-6), and H1o (odds ratio, 2.60; 95% CI, 1.63-4.16; P = 2 × 10-5). Although not significant after multiple testing adjustment, 3 of these PSP risk haplotypes (H2, H1c, and H1d) were also nominally associated with measures of severity of tau pathology in PSP cases. Nominally significant associations with severity of tau pathology were also noted for the H1e and H1q haplotypes. Conclusions and Relevance This study has identified novel associations with risk of PSP for 3 MAPT H1 subhaplotypes. In addition, potential weaker associations between several haplotypes (including several PSP risk haplotypes) and severity of tau pathology were observed. These findings expand the current understanding of the role of MAPT haplotypic variation in susceptibility to and neuropathologic severity of PSP.
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Affiliation(s)
- Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, Florida
| | | | - Catherine Labbé
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
| | | | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
| | | | | | | | | | | | - Ryan J Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, Florida
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
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11
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Xenobiotics, Trace Metals and Genetics in the Pathogenesis of Tauopathies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17041269. [PMID: 32079163 PMCID: PMC7068520 DOI: 10.3390/ijerph17041269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/17/2022]
Abstract
Tauopathies are a disease group characterized by either pathological accumulation or release of fragments of hyperphosphorylated tau proteins originating from the central nervous system. The tau hypotheses of Parkinson’s and Alzheimer’s diseases contain a clinically diverse spectrum of tauopathies. Studies of case records of various tauopathies may reveal clinical phenotype characteristics of the disease. In addition, improved understanding of different tauopathies would disclose environmental factors, such as xenobiotics and trace metals, that can precipitate or modify the progression of the disorder. Important for diagnostics and monitoring of these disorders is a further development of adequate biomarkers, including refined neuroimaging, or proteomics. Our goal is to provide an in-depth review of the current literature regarding the pathophysiological roles of tau proteins and the pathogenic factors leading to various tauopathies, with the perspective of future advances in potential therapeutic strategies.
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12
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Murley AG, Jones PS, Coyle Gilchrist I, Bowns L, Wiggins J, Tsvetanov KA, Rowe JB. Metabolomic changes associated with frontotemporal lobar degeneration syndromes. J Neurol 2020; 267:2228-2238. [PMID: 32277260 PMCID: PMC7359154 DOI: 10.1007/s00415-020-09824-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Widespread metabolic changes are seen in neurodegenerative disease and could be used as biomarkers for diagnosis and disease monitoring. They may also reveal disease mechanisms that could be a target for therapy. In this study we looked for blood-based biomarkers in syndromes associated with frontotemporal lobar degeneration. METHODS Plasma metabolomic profiles were measured from 134 patients with a syndrome associated with frontotemporal lobar degeneration (behavioural variant frontotemporal dementia n = 30, non fluent variant primary progressive aphasia n = 26, progressive supranuclear palsy n = 45, corticobasal syndrome n = 33) and 32 healthy controls. RESULTS Forty-nine of 842 metabolites were significantly altered in frontotemporal lobar degeneration syndromes (after false-discovery rate correction for multiple comparisons). These were distributed across a wide range of metabolic pathways including amino acids, energy and carbohydrate, cofactor and vitamin, lipid and nucleotide pathways. The metabolomic profile supported classification between frontotemporal lobar degeneration syndromes and controls with high accuracy (88.1-96.6%) while classification accuracy was lower between the frontotemporal lobar degeneration syndromes (72.1-83.3%). One metabolic profile, comprising a range of different pathways, was consistently identified as a feature of each disease versus controls: the degree to which a patient expressed this metabolomic profile was associated with their subsequent survival (hazard ratio 0.74 [0.59-0.93], p = 0.0018). CONCLUSIONS The metabolic changes in FTLD are promising diagnostic and prognostic biomarkers. Further work is required to replicate these findings, examine longitudinal change, and test their utility in differentiating between FTLD syndromes that are pathologically distinct but phenotypically similar.
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Affiliation(s)
- Alexander G Murley
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - P Simon Jones
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Lucy Bowns
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Julie Wiggins
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Kamen A Tsvetanov
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - James B Rowe
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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13
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Giagkou N, Höglinger GU, Stamelou M. Progressive supranuclear palsy. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2019; 149:49-86. [PMID: 31779824 DOI: 10.1016/bs.irn.2019.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Progressive supranuclear palsy (PSP) is a neurodegenerative disease characterized pathologically by 4 repeat tau deposition in various cell types and anatomical regions. Richardson's syndrome (RS) is the initially described and one of the clinical phenotypes associated with PSP pathology, characterized by vertical supranuclear gaze paly in particular downwards, postural instability with early falls and subcortical frontal dementia. PSP can manifest as several other clinical phenotypes, including PSP-parkinsonism, -pure akinesia with gait freezing, -frontotemporal dementia, - corticobasal syndrome, - speech/language impairment. RS can also have a pathologic diagnosis other than PSP, including corticobasal degeneration, FTD-TDP-43 and others. New clinical diagnostic criteria take into account this phenotypic variability in an attempt to diagnose the disease earlier, given the current lack of a validated biomarker. At present, therapeutic options for PSP are symptomatic and insufficient. Recent large neuroprotective trials have failed to provide a positive clinical outcome, however, have led to the design of better studies that are ongoing and hold promise for a neuroprotective treatment for PSP.
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Affiliation(s)
- Nikolaos Giagkou
- Parkinson's Disease and Movement Disorders Department, HYGEIA Hospital, Athens, Greece
| | - Günter U Höglinger
- Department for Neurology Hannover Medical School (MHH), Hannover, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Maria Stamelou
- Parkinson's Disease and Movement Disorders Department, HYGEIA Hospital, Athens, Greece; Aiginiteion Hospital, First Department of Neurology, University of Athens, Greece; Clinic for Neurology, Philipps University, Marburg, Germany
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14
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Stamelou M, Giagkou N, Höglinger GU. One decade ago, one decade ahead in progressive supranuclear palsy. Mov Disord 2019; 34:1284-1293. [DOI: 10.1002/mds.27788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
- Maria Stamelou
- Parkinson's disease and Movement Disorders DepartmentHYGEIA Hospital Athens Greece
- Neurology ClinicPhilipps University Marburg Germany
- First Department of Neurology, Aiginiteion HospitalUniversity of Athens Athens Greece
| | - Nikolaos Giagkou
- Parkinson's disease and Movement Disorders DepartmentHYGEIA Hospital Athens Greece
| | - Günter U Höglinger
- Department of NeurologyTechnische Universität München Munich Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich Germany
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15
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Chen Z, Chen JA, Shatunov A, Jones AR, Kravitz SN, Huang AY, Lawrence L, Lowe JK, Lewis CM, Payan CAM, Lieb W, Franke A, Deloukas P, Amouyel P, Tzourio C, Dartigues JF, Ludolph A, Bensimon G, Leigh PN, Bronstein JM, Coppola G, Geschwind DH, Al-Chalabi A. Genome-wide survey of copy number variants finds MAPT duplications in progressive supranuclear palsy. Mov Disord 2019; 34:1049-1059. [PMID: 31059154 DOI: 10.1002/mds.27702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/01/2019] [Accepted: 02/26/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Progressive supranuclear palsy is a neurodegenerative tauopathy manifesting clinically as a progressive akinetic-rigid syndrome. In this study, we sought to identify genetic variants influencing PSP susceptibility through a genome-wide association analysis of a cohort of well-characterized patients who had participated in the Neuroprotection and Natural History in Parkinson Plus Syndromes and Blood Brain Barrier in Parkinson Plus Syndromes studies. METHODS We genotyped single-nucleotide polymorphisms in 283 PSP cases from the United Kingdom, Germany, and France and compared these with genotypes from 4472 controls. Copy number variants were identified from genotyping data. RESULTS We observed associations on chromosome 17 within or close to the MAPT gene and explored the genetic architecture at this locus. We confirmed the previously reported association of rs1768208 in the MOBP gene (P = 3.29 × 10-13 ) and rs1411478 in STX6 (P = 3.45 × 10-10 ). The population-attributable risk from the MAPT, MOBP, and STX6 single-nucleotide polymorphisms was found to be 0.37, 0.26, and 0.08, respectively. In addition, we found 2 instances of copy number variants spanning the MAPT gene in patients with PSP. These copy number variants include tau but few other genes within the chromosome 17 haplotype region, providing additional support for the direct pathogenicity of MAPT in PSP. CONCLUSIONS Clinicians should also be aware of MAPT duplication as a possible genetic cause of PSP, especially in patients presenting with young age at onset. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Zhongbo Chen
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Jason A Chen
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Stephanie N Kravitz
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Alden Y Huang
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Lauren Lawrence
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jennifer K Lowe
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
| | - Christine A M Payan
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factor and Molecular Determinants of Aging Diseases, Labex-Distalz, Lille, France
| | - Christophe Tzourio
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Jean-François Dartigues
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Oberer Eselsberg, Ulm, Germany
| | - Gilbert Bensimon
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - P Nigel Leigh
- Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, UK
| | - Jeff M Bronstein
- Program in Movement Disorders, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Giovanni Coppola
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
- Department of Human Genetics, University of California, Los Angeles, California, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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16
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Progressive supranuclear palsy and multiple system atrophy: clinicopathological concepts and therapeutic challenges. Curr Opin Neurol 2019; 31:448-454. [PMID: 29746401 DOI: 10.1097/wco.0000000000000581] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW This update discusses novel aspects on clinicopathological concepts and therapeutic challenges in progressive supranuclear palsy (PSP) and multiple system atrophy (MSA), arising from publications of the last 1.5 years. RECENT FINDINGS The clinical criteria for diagnosis of PSP have been revised. Clinical variability of pathologically defined PSP and MSA makes the development of mature biomarkers for early diagnosis and biomarker-based trial design indispensable. Novel molecular techniques for biomarker supported diagnosis of PSP and MSA and for monitoring disease progression are being studied. Research in the pathophysiology of both diseases generates gradual progress in the understanding of the underlying processes. Several promising disease-modifying therapeutic approaches for PSP and MSA are now moving into clinical trials. SUMMARY Recent research generates insights in the pathophysiological relevant processes and raises hope for earlier clinical diagnosis and disease-modifying therapies of patients with PSP and MSA.
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17
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Lee YC, Su CY, Lin YF, Lin CM, Fang CY, Lin YK, Hsiao M, Chen CL. Lysosomal acid phosphatase 2 is an unfavorable prognostic factor but is associated with better survival in stage II colorectal cancer patients receiving chemotherapy. Oncotarget 2017; 8:12120-12132. [PMID: 28076332 PMCID: PMC5355330 DOI: 10.18632/oncotarget.14552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/27/2016] [Indexed: 11/25/2022] Open
Abstract
Colorectal cancer (CRC) is one of the leading cancers worldwide. Surgery is the main therapeutic modality for stage II CRC. However, the implementation of adjuvant chemotherapy remains controversial and is not universally applied so far. In this study, we found that the protein expression of lysosomal acid phosphatase 2 (ACP2) was increased in CRC and that stage II CRC patients with high ACP2 expression showed a poorer outcome than those with low ACP2 expression (p = 0.004). To investigate this discrepancy, we analyzed the relation between ACP2 expression and several clinical cofactors. Among patients who received chemotherapy, those with an high expression of ACP2 showed better survival in both stage II and III CRC than those with low ACP2 expression. In stage II CRC patients, univariate analysis showed ACP2 expression and T stage to be cofactors significantly associated with overall survival (ACP2: p = 0.006; T stage: p = 0.034). Multivariate Cox proportion hazard model analysis also revealed ACP2 to be an independent prognostic factor for overall survival (ACP2: p = 0.006; T stage: p = 0.041). Furthermore, ACP2-knockdown CRC cells showed an increase in chemoresistance to 5-FU treatment and increased proliferation marker in the ACP2 knockdown clone. Taken together, our results suggested that ACP2 is an unfavorable prognostic factor for stage II CRC and may serve as a potential chemotherapy-sensitive marker to help identify a subset of stage II and III CRC patients for whom chemotherapy would improve survival.
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Affiliation(s)
- Yu-Chieh Lee
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Gastroenterology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Chia-Yu Su
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yuan-Feng Lin
- Graduate Institute of Clinical Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chun-Mao Lin
- Department of Biochemistry, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chih-Yeu Fang
- Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yen-Kuang Lin
- Biostatistics Center, Taipei Medical University, Taipei, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chi-Long Chen
- Department of Pathology, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pathology, Taipei Medical University Hospital, Taipei, Taiwan
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18
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Sousa I, Abrantes P, Francisco V, Teixeira G, Monteiro M, Neves J, Norte A, Robalo Cordeiro C, Moura e Sá J, Reis E, Santos P, Oliveira M, Sousa S, Fradinho M, Malheiro F, Negrão L, Feijó S, Oliveira SA. Multicentric Genome-Wide Association Study for Primary Spontaneous Pneumothorax. PLoS One 2016; 11:e0156103. [PMID: 27203581 PMCID: PMC4874577 DOI: 10.1371/journal.pone.0156103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/08/2016] [Indexed: 11/18/2022] Open
Abstract
Despite elevated incidence and recurrence rates for Primary Spontaneous Pneumothorax (PSP), little is known about its etiology, and the genetics of idiopathic PSP remains unexplored. To identify genetic variants contributing to sporadic PSP risk, we conducted the first PSP genome-wide association study. Two replicate pools of 92 Portuguese PSP cases and of 129 age- and sex-matched controls were allelotyped in triplicate on the Affymetrix Human SNP Array 6.0 arrays. Markers passing quality control were ranked by relative allele score difference between cases and controls (|RASdiff|), by a novel cluster method and by a combined Z-test. 101 single nucleotide polymorphisms (SNPs) were selected using these three approaches for technical validation by individual genotyping in the discovery dataset. 87 out of 94 successfully tested SNPs were nominally associated in the discovery dataset. Replication of the 87 technically validated SNPs was then carried out in an independent replication dataset of 100 Portuguese cases and 425 controls. The intergenic rs4733649 SNP in chromosome 8 (between LINC00824 and LINC00977) was associated with PSP in the discovery (P = 4.07E-03, ORC[95% CI] = 1.88[1.22–2.89]), replication (P = 1.50E-02, ORC[95% CI] = 1.50[1.08–2.09]) and combined datasets (P = 8.61E-05, ORC[95% CI] = 1.65[1.29–2.13]). This study identified for the first time one genetic risk factor for sporadic PSP, but future studies are warranted to further confirm this finding in other populations and uncover its functional role in PSP pathogenesis.
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Affiliation(s)
- Inês Sousa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Patrícia Abrantes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Vânia Francisco
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | - João Neves
- Centro Hospitalar do Porto, Porto, Portugal
| | - Ana Norte
- Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | | | - João Moura e Sá
- Centro Hospitalar de Vila Nova de Gaia, Vila Nova de Gaia, Portugal
| | | | - Patrícia Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Susana Sousa
- Hospital de São Bernardo (Centro Hospitalar de Setúbal, E.P.E.), Setúbal, Portugal
| | - Marta Fradinho
- Hospital Egas Moniz (Centro Hospitalar de Lisboa Ocidental), Lisboa, Portugal
| | | | - Luís Negrão
- Instituto Português do Sangue e da Transplantacão, Centro Regional de Sangue de Lisboa, Lisboa, Portugal
| | | | - Sofia A. Oliveira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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19
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Rahimi Balaei M, Jiao X, Ashtari N, Afsharinezhad P, Ghavami S, Marzban H. Cerebellar Expression of the Neurotrophin Receptor p75 in Naked-Ataxia Mutant Mouse. Int J Mol Sci 2016; 17:E115. [PMID: 26784182 PMCID: PMC4730356 DOI: 10.3390/ijms17010115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/07/2016] [Accepted: 01/11/2016] [Indexed: 01/08/2023] Open
Abstract
Spontaneous mutation in the lysosomal acid phosphatase 2 (Acp2) mouse (nax--naked-ataxia mutant mouse) correlates with severe cerebellar defects including ataxia, reduced size and abnormal lobulation as well as Purkinje cell (Pc) degeneration. Loss of Pcs in the nax cerebellum is compartmentalized and harmonized to the classic pattern of gene expression of the cerebellum in the wild type mouse. Usually, degeneration starts in the anterior and posterior zones and continues to the central and nodular zones of cerebellum. Studies have suggested that the p75 neurotrophin receptor (NTR) plays a role in Pc degeneration; thus, in this study, we investigated the p75NTR pattern and protein expression in the cerebellum of the nax mutant mouse. Despite massive Pc degeneration that was observed in the nax mouse cerebellum, p75NTR pattern expression was similar to the HSP25 pattern in nax mice and comparable with wild type sibling cerebellum. In addition, immunoblot analysis of p75NTR protein expression did not show any significant difference between nax and wild type sibling (p > 0.5). In comparison with wild type counterparts, p75NTR pattern expression is aligned with the fundamental cytoarchitecture organization of the cerebellum and is unchanged in the nax mouse cerebellum despite the severe neurodevelopmental disorder accompanied with Pc degeneration.
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Affiliation(s)
- Maryam Rahimi Balaei
- Department of Human Anatomy & Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Xiaodan Jiao
- Department of Human Anatomy & Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Niloufar Ashtari
- Department of Human Anatomy & Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Pegah Afsharinezhad
- Department of Human Anatomy & Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Saeid Ghavami
- Department of Human Anatomy & Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
- Health Policy Research Center, Shiraz University of Medical Science, Shiraz 713484579, Iran.
| | - Hassan Marzban
- Department of Human Anatomy & Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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20
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Scholz SW, Bras J. Genetics Underlying Atypical Parkinsonism and Related Neurodegenerative Disorders. Int J Mol Sci 2015; 16:24629-55. [PMID: 26501269 PMCID: PMC4632769 DOI: 10.3390/ijms161024629] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/01/2015] [Accepted: 10/09/2015] [Indexed: 12/14/2022] Open
Abstract
Atypical parkinsonism syndromes, such as dementia with Lewy bodies, multiple system atrophy, progressive supranuclear palsy and corticobasal degeneration, are neurodegenerative diseases with complex clinical and pathological features. Heterogeneity in clinical presentations, possible secondary determinants as well as mimic syndromes pose a major challenge to accurately diagnose patients suffering from these devastating conditions. Over the last two decades, significant advancements in genomic technologies have provided us with increasing insights into the molecular pathogenesis of atypical parkinsonism and their intriguing relationships to related neurodegenerative diseases, fueling new hopes to incorporate molecular knowledge into our diagnostic, prognostic and therapeutic approaches towards managing these conditions. In this review article, we summarize the current understanding of genetic mechanisms implicated in atypical parkinsonism syndromes. We further highlight mimic syndromes relevant to differential considerations and possible future directions.
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Affiliation(s)
- Sonja W Scholz
- Neurodegenerative Diseases Research Unit, Laboratory of Neurogenetics, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, 1800 Orleans Street, Baltimore, MD 21287, USA.
| | - Jose Bras
- Department of Molecular Neuroscience, University College London, Institute of Neurology, Queen Square House, London WC1N 3BG, UK.
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Im SY, Kim YE, Kim YJ. Genetics of Progressive Supranuclear Palsy. J Mov Disord 2015; 8:122-9. [PMID: 26413239 PMCID: PMC4572662 DOI: 10.14802/jmd.15033] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 12/21/2022] Open
Abstract
Progressive supranuclear palsy (PSP) is a neurodegenerative syndrome that is clinically characterized by progressive postural instability, supranuclear gaze palsy, parkinsonism and cognitive decline. Pathologically, diagnosis of PSP is based on characteristic features, such as neurofibrillary tangles, neutrophil threads, tau-positive astrocytes and their processes in basal ganglia and brainstem, and the accumulation of 4 repeat tau protein. PSP is generally recognized as a sporadic disorder; however, understanding of genetic background of PSP has been expanding rapidly. Here we review relevant publications to outline the genetics of PSP. Although only small number of familial PSP cases have been reported, the recognition of familial PSP has been increasing. In some familial cases of clinically probable PSP, PSP pathologies were confirmed based on NINDS neuropathological diagnostic criteria. Several mutations in MAPT, the gene that causes a form of familial frontotemporal lobar degeneration with tauopathy, have been identified in both sporadic and familial PSP cases. The H1 haplotype of MAPT is a risk haplotype for PSP, and within H1, a sub-haplotype (H1c) is associated with PSP. A recent genome-wide association study on autopsyproven PSP revealed additional PSP risk alleles in STX6 and EIF2AK3. Several heredodegenerative parkinsonian disorders are referred to as PSP-look-alikes because their clinical phenotype, but not their pathology, mimics PSP. Due to the fast development of genomics and bioinformatics, more genetic factors related to PSP are expected to be discovered. Undoubtedly, these studies will provide a better understanding of the pathogenesis of PSP and clues for developing therapeutic strategies.
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Affiliation(s)
- Sun Young Im
- Department of Neurology, Hallym University College of Medicine, Anyang, Korea
| | - Young Eun Kim
- Department of Neurology, Hallym University College of Medicine, Anyang, Korea
| | - Yun Joong Kim
- Department of Neurology, Hallym University College of Medicine, Anyang, Korea ; ILSONG Institute of Life Science, Hallym University, Anyang, Korea ; Hallym Institute of Translational Genomics & Bioinformatics, Anyang, Korea
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Xavier JM, Shahram F, Sousa I, Davatchi F, Matos M, Abdollahi BS, Sobral J, Nadji A, Oliveira M, Ghaderibarim F, Shafiee NM, Oliveira SA. FUT2: filling the gap between genes and environment in Behçet's disease? Ann Rheum Dis 2015; 74:618-24. [PMID: 24326010 DOI: 10.1136/annrheumdis-2013-204475] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVES To identify new susceptibility loci for Behçet's disease (BD), we performed a genome-wide association study (GWAS) using DNA pooling. METHODS Two replicate pools of 292 Iranian BD cases and of 294 age- and sex-matched controls were allelotyped in quadruplicate on the Affymetrix Genome-Wide Human SNP Array 6.0. Of the 51 top markers, 47 were technically validated through individually genotyping. Replication of validated single nucleotide polymorphisms (SNPs) was performed in an independent Iranian dataset (684 cases and 532 controls). RESULTS In addition to the well-established HLA-B locus, rs7528842 in a gene desert on chromosome 1p21.2, and rs632111 at the 3'UTR of FUT2 were associated in both the discovery and replication datasets (individually and in combination). However, only the FUT2 SNP was associated in a previous GWAS for BD in Turkish people. Fine-mapping of FUT2 in the full Iranian dataset showed additional associations in five coding SNPs (2.97E-06 CONCLUSIONS This study suggests for the first time a putative link between a specific gene and environment in the aetiopathogenesis of BD. The non-secretor phenotype affects mucosal glycosylation, which may explain its known association with dysbiosis and altered susceptibility to infections. A different antigenic stimulation in early life and consequent increased propensity for autoimmunity and inflammation may contribute to BD development.
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Affiliation(s)
- Joana M Xavier
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Farhad Shahram
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Inês Sousa
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Fereydoun Davatchi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mafalda Matos
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Bahar Sadeghi Abdollahi
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - João Sobral
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Abdolhadi Nadji
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Manuela Oliveira
- Centro de Investigação Matemática e Aplicaçóes - CIMA, Universidade de Évora, Évora, Portugal
| | - Fahmida Ghaderibarim
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Niloofar Mojarad Shafiee
- Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sofia A Oliveira
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Colosimo C, Bak TH, Bologna M, Berardelli A. Fifty years of progressive supranuclear palsy. J Neurol Neurosurg Psychiatry 2014; 85:938-44. [PMID: 24013274 DOI: 10.1136/jnnp-2013-305740] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Carlo Colosimo
- Department of Neurology and Psychiatry, "Sapienza" University, Rome, Italy
| | - Thomas H Bak
- School of Philosophy, Psychology and Language Sciences (PPLS) & Centre for Clinical Brain Sciences (CCBS), University of Edinburgh, Edinburgh, UK
| | | | - Alfredo Berardelli
- Department of Neurology and Psychiatry, "Sapienza" University, Rome, Italy Neuromed Institute IRCCS, Pozzilli (IS), Italy
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Shi M, Umbach DM, Weinberg CR. Disentangling pooled triad genotypes for association studies. Ann Hum Genet 2014; 78:345-56. [PMID: 24962618 DOI: 10.1111/ahg.12073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 05/05/2014] [Indexed: 11/30/2022]
Abstract
Association studies that genotype affected offspring and their parents (triads) offer robustness to genetic population structure while enabling assessments of maternal effects, parent-of-origin effects, and gene-by-environment interaction. We propose case-parents designs that use pooled DNA specimens to make economical use of limited available specimens. One can markedly reduce the number of genotyping assays required by randomly partitioning the case-parent triads into pooling sets of h triads each and creating three pools from every pooling set, one pool each for mothers, fathers, and offspring. Maximum-likelihood estimation of relative risk parameters proceeds via log-linear modeling using the expectation-maximization algorithm. The approach can assess offspring and maternal genetic effects and accommodate genotyping errors and missing genotypes. We compare the power of our proposed analysis for testing offspring and maternal genetic effects to that based on a difference approach and that of the gold standard based on individual genotypes, under a range of allele frequencies, missing parent proportions, and genotyping error rates. Power calculations show that the pooling strategies cause only modest reductions in power if genotyping errors are low, while reducing genotyping costs and conserving limited specimens.
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Affiliation(s)
- Min Shi
- Biostatistics Branch, NIEHS, NIH, DHHS, Research Triangle Park, NC, USA
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Bailey K, Rahimi Balaei M, Mehdizadeh M, Marzban H. Spatial and temporal expression of lysosomal acid phosphatase 2 (ACP2) reveals dynamic patterning of the mouse cerebellar cortex. THE CEREBELLUM 2014; 12:870-81. [PMID: 23780826 DOI: 10.1007/s12311-013-0502-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Acp2 gene encodes lysosomal acid phosphatase 2 (ACP2), an isoenzyme that hydrolyzes orthophosphoric monoesters to alcohol and phosphate. Mutations in this gene compromise lysosomal function and cause acid phosphatase deficiency. Loss of Acp2 in the brain causes defects in the cerebellum. Here, we performed an in-depth protein expression analysis in the mouse cerebellum to understand how Acp2 controls cellular function in the developing and adult brain. We have found that during development, ACP2 expression marks the caudal midbrain and cerebellum, two regions that are linked by multiple signaling mechanisms during embryogenesis. By around P8, ACP2 was localized predominantly to the somata of Purkinje cells, the principal neurons of the cerebellar cortex. During the second postnatal week, we found that ACP2 expression expanded into the dendrites and axon terminals of Purkinje cells. However, at 2 weeks of age, only a subset of Purkinje cells strongly express ACP2. Further expression analyses revealed that in the mature cerebellum, ACP2 expression divided Purkinje cells into a pattern of molecular zones that are associated with the functional topography of sensory-motor circuitry. These data suggest that ACP2 expression is dynamically regulated during development, and in the adult, it may function within a complex architecture that is linked to cerebellar modular organization.
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Affiliation(s)
- Karen Bailey
- Department of Human Anatomy and Cell Science, Manitoba Institute of Child Health (MICH), Faculty of Medicine, University of Manitoba, Winnipeg, MB, Canada
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Bailey K, Rahimi Balaei M, Mannan A, Del Bigio MR, Marzban H. Purkinje cell compartmentation in the cerebellum of the lysosomal Acid phosphatase 2 mutant mouse (nax - naked-ataxia mutant mouse). PLoS One 2014; 9:e94327. [PMID: 24722417 PMCID: PMC3983142 DOI: 10.1371/journal.pone.0094327] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/15/2014] [Indexed: 12/11/2022] Open
Abstract
The Acp2 gene encodes the beta subunit of lysosomal acid phosphatase, which is an isoenzyme that hydrolyzes orthophosphoric monoesters. In mice, a spontaneous mutation in Acp2 results in severe cerebellar defects. These include a reduced size, abnormal lobulation, and an apparent anterior cerebellar disorder with an absent or hypoplastic vermis. Based on differential gene expression in the cerebellum, the mouse cerebellar cortex can normally be compartmentalized anteroposteriorly into four transverse zones and mediolaterally into parasagittal stripes. In this study, immunohistochemistry was performed using various Purkinje cell compartmentation markers to examine their expression patterns in the Acp2 mutant. Despite the abnormal lobulation and anterior cerebellar defects, zebrin II and PLCβ4 showed similar expression patterns in the nax mutant and wild type cerebellum. However, fewer stripes were found in the anterior zone of the nax mutant, which could be due to a lack of Purkinje cells or altered expression of the stripe markers. HSP25 expression was uniform in the central zone of the nax mutant cerebellum at around postnatal day (P) 18–19, suggesting that HSP25 immunonegative Purkinje cells are absent or delayed in stripe pattern expression compared to the wild type. HSP25 expression became heterogeneous around P22–23, with twice the number of parasagittal stripes in the nax mutant compared to the wild type. Aside from reduced size and cortical disorganization, both the posterior zone and nodular zone in the nax mutant appeared less abnormal than the rest of the cerebellum. From these results, it is evident that the anterior zone of the nax mutant cerebellum is the most severely affected, and this extends beyond the primary fissure into the rostral central zone/vermis. This suggests that ACP2 has critical roles in the development of the anterior cerebellum and it may regulate anterior and central zone compartmentation.
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Affiliation(s)
- Karen Bailey
- Department of Human Anatomy and Cell Science, Manitoba Institute of Child Health (MICH), Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maryam Rahimi Balaei
- Department of Human Anatomy and Cell Science, Manitoba Institute of Child Health (MICH), Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ashraf Mannan
- Institute of Human Genetics, University Medical Center Goettingen, Georg-August University, Goettingen, Germany
| | - Marc R. Del Bigio
- Department of Human Anatomy and Cell Science, Manitoba Institute of Child Health (MICH), Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hassan Marzban
- Department of Human Anatomy and Cell Science, Manitoba Institute of Child Health (MICH), Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Zhang K, Huentelman MJ, Rao F, Sun EI, Corneveaux JJ, Schork AJ, Wei Z, Waalen J, Miramontes-Gonzalez JP, Hightower CM, Maihofer AX, Mahata M, Pastinen T, Ehret GB, Schork NJ, Eskin E, Nievergelt CM, Saier MH, O'Connor DT. Genetic implication of a novel thiamine transporter in human hypertension. J Am Coll Cardiol 2014; 63:1542-55. [PMID: 24509276 DOI: 10.1016/j.jacc.2014.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/29/2013] [Accepted: 01/07/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVES This study coupled 2 strategies-trait extremes and genome-wide pooling-to discover a novel blood pressure (BP) locus that encodes a previously uncharacterized thiamine transporter. BACKGROUND Hypertension is a heritable trait that remains the most potent and widespread cardiovascular risk factor, although details of its genetic determination are poorly understood. METHODS Representative genomic deoxyribonucleic acid (DNA) pools were created from male and female subjects in the highest- and lowest-fifth percentiles of BP in a primary care population of >50,000 patients. The peak associated single-nucleotide polymorphisms were typed in individual DNA samples, as well as in twins/siblings phenotyped for cardiovascular and autonomic traits. Biochemical properties of the associated transporter were evaluated in cellular assays. RESULTS After chip hybridization and calculation of relative allele scores, the peak associations were typed in individual samples, revealing an association between hypertension, systolic BP, and diastolic BP and the previously uncharacterized solute carrier SLC35F3. The BP genetic association at SLC35F3 was validated by meta-analysis in an independent sample from the original source population, as well as the International Consortium for Blood Pressure Genome-Wide Association Studies (across North America and western Europe). Sequence homology to a putative yeast thiamine (vitamin B1) transporter prompted us to express human SLC35F3 in Escherichia coli, which catalyzed [(3)H]-thiamine uptake. SLC35F3 risk-allele homozygotes (T/T) displayed decreased erythrocyte thiamine content on microbiological assay. In twin pairs, the SLC35F3 risk allele predicted heritable cardiovascular traits previously associated with thiamine deficiency, including elevated cardiac stroke volume with decreased vascular resistance, and elevated pressor responses to environmental (cold) stress. Allelic expression imbalance confirmed that cis variation at the human SLC35F3 locus influenced expression of that gene, and the allelic expression imbalance peak coincided with the hypertension peak. CONCLUSIONS Novel strategies were coupled to position a new hypertension-susceptibility locus, uncovering a previously unsuspected thiamine transporter whose genetic variants predicted several disturbances in cardiac and autonomic function. The results have implications for the pathogenesis and treatment of systemic hypertension.
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Affiliation(s)
- Kuixing Zhang
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Matthew J Huentelman
- Division of Neurogenomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Fangwen Rao
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Eric I Sun
- Department of Biology, UCSD, La Jolla, California
| | - Jason J Corneveaux
- Division of Neurogenomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Andrew J Schork
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Zhiyun Wei
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Jill Waalen
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | | | - C Makena Hightower
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Adam X Maihofer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California; Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Manjula Mahata
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Tomi Pastinen
- Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Georg B Ehret
- Center for Complex Disease Genomics, McKusick-Nathans, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Nicholas J Schork
- Department of Psychiatry, UCSD, La Jolla, California; Departments of Computer Science and Human Genetics, University of California at Los Angeles, Los Angeles, California
| | - Eleazar Eskin
- Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Caroline M Nievergelt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California; Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | | | - Daniel T O'Connor
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California; Veterans Affairs San Diego Healthcare System, San Diego, California; Department of Pharmacology and the Institute for Genomic Medicine, UCSD, La Jolla, California.
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Ferrari R, Ryten M, Simone R, Trabzuni D, Nicolaou N, Nicolaou N, Hondhamuni G, Ramasamy A, Vandrovcova J, Weale ME, Lees AJ, Momeni P, Hardy J, de Silva R. Assessment of common variability and expression quantitative trait loci for genome-wide associations for progressive supranuclear palsy. Neurobiol Aging 2014; 35:1514.e1-12. [PMID: 24503276 PMCID: PMC4104112 DOI: 10.1016/j.neurobiolaging.2014.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/06/2014] [Accepted: 01/08/2014] [Indexed: 12/22/2022]
Abstract
Progressive supranuclear palsy is a rare parkinsonian disorder with characteristic neurofibrillary pathology consisting of hyperphosphorylated tau protein. Common variation defining the microtubule associated protein tau gene (MAPT) H1 haplotype strongly contributes to disease risk. A recent genome-wide association study (GWAS) revealed 3 novel risk loci on chromosomes 1, 2, and 3 that primarily implicate STX6, EIF2AK3, and MOBP, respectively. Genetic associations, however, rarely lead to direct identification of the relevant functional allele. More often, they are in linkage disequilibrium with the causative polymorphism(s) that could be a coding change or affect gene expression regulatory motifs. To identify any such changes, we sequenced all coding exons of those genes directly implicated by the associations in progressive supranuclear palsy cases and analyzed regional gene expression data from control brains to identify expression quantitative trait loci within 1 Mb of the risk loci. Although we did not find any coding variants underlying the associations, GWAS-associated single-nucleotide polymorphisms at these loci are in complete linkage disequilibrium with haplotypes that completely overlap with the respective genes. Although implication of EIF2AK3 and MOBP could not be fully assessed, we show that the GWAS single-nucleotide polymorphism rs1411478 (STX6) is a strong expression quantitative trait locus with significantly lower expression of STX6 in white matter in carriers of the risk allele.
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Affiliation(s)
- Raffaele Ferrari
- Laboratory of Neurogenetics, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Roberto Simone
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Daniah Trabzuni
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Nayia Nicolaou
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Naiya Nicolaou
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Geshanthi Hondhamuni
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Adaikalavan Ramasamy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - Jana Vandrovcova
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Michael E Weale
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - Andrew J Lees
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK
| | - Parastoo Momeni
- Laboratory of Neurogenetics, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - John Hardy
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Rohan de Silva
- Reta Lila Weston Institute, UCL Institute of Neurology, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.
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Sepe S, Payan-Gomez C, Milanese C, Hoeijmakers JH, Mastroberardino PG. Nucleotide excision repair in chronic neurodegenerative diseases. DNA Repair (Amst) 2013; 12:568-77. [PMID: 23726220 DOI: 10.1016/j.dnarep.2013.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Impaired DNA repair involving the nucleotide excision repair (NER)/transcription-coupled repair (TCR) pathway cause human pathologies associated with severe neurological symptoms. These clinical observations suggest that defective NER/TCR might also play a critical role in chronic neurodegenerative disorders (ND), such as Alzheimer's and Parkinson's disease. Involvement of NER/TCR in these disorders is also substantiated by the evidence that aging constitutes the principal risk factor for chronic ND and that this DNA repair mechanism is very relevant for the aging process itself. Our understanding of the exact role of NER/TCR in chronic ND, however, is extremely rudimentary; while there is no doubt that defective NER/TCR can lead to neuronal death, evidence for its participation in the etiopathogenesis of ND is inconclusive thus far. Here we summarize the experimental observations supporting a role for NER/TCR in chronic ND and suggest questions and lines of investigation that might help in addressing this important issue. We also present a preliminary yet unprecedented meta-analysis on human brain microarray data to understand the expression levels of the various NER factors in the anatomical areas relevant for chronic ND pathogenesis. In summary, this review intends to highlight elements supporting a role of NER/TCR in these devastating disorders and to propose potential strategies of investigation.
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Affiliation(s)
- Sara Sepe
- Department of Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Damaged DNA binding protein 2 in reactive oxygen species (ROS) regulation and premature senescence. Int J Mol Sci 2012; 13:11012-11026. [PMID: 23109835 PMCID: PMC3472727 DOI: 10.3390/ijms130911012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/22/2012] [Accepted: 08/28/2012] [Indexed: 11/16/2022] Open
Abstract
Premature senescence induced by DNA damage or oncogene is a critical mechanism of tumor suppression. Reactive oxygen species (ROS) have been implicated in the induction of premature senescence response. Several pathological disorders such as cancer, aging and age related neurological abnormalities have been linked to ROS deregulation. Here, we discuss how Damaged DNA binding Protein-2 (DDB2), a nucleotide excision repair protein, plays an important role in ROS regulation by epigenetically repressing the antioxidant genes MnSOD and Catalase. We further revisit a model in which DDB2 plays an instrumental role in DNA damage induced ROS accumulation, ROS induced premature senescence and inhibition of skin tumorigenesis.
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Abstract
PURPOSE OF REVIEW Atypical parkinsonian disorders (APDs) comprise a heterogenous group of disorders including multiple system atrophy (MSA), dementia with Lewy bodies (DLB), progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD). Based on literature published in 2010, we here review recent advances in the APD field. RECENT FINDINGS Genome-wide association studies have provided robust evidence of increased disease risk conferred by synuclein and tau gene variants in MSA and PSP. Furthermore, advanced imaging tools have been established in the differential diagnosis and as surrogate markers of disease activity in patients with APDs. Finally, although therapeutic options are still disappointing, translational research into disease-modifying strategies has accelerated with the increasing availability of transgenic animal models, particularly for MSA. SUMMARY Remarkable progress has been achieved in the field of APDs, and advances in the genetics, molecular biology and neuroimaging of these disorders will continue to facilitate intensified clinical trial activity.
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Wenning GK, Litvan I, Tolosa E. Milestones in atypical and secondary Parkinsonisms. Mov Disord 2011; 26:1083-95. [DOI: 10.1002/mds.23713] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Deng L, Tang X, Chen W, Lin J, Lai Z, Liu Z, Zhang D. Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy. GENOMICS PROTEOMICS & BIOINFORMATICS 2011; 8:256-61. [PMID: 21382594 PMCID: PMC5054161 DOI: 10.1016/s1672-0229(10)60027-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Population genomic approaches, which take advantages of high-throughput genotyping, are powerful yet costly methods to scan for selective sweeps. DNA-pooling strategies have been widely used for association studies because it is a cost-effective alternative to large-scale individual genotyping. Here, we performed an SNP-MaP (single nucleotide polymorphism microarrays and pooling) analysis using samples from Eurasia to evaluate the efficiency of pooling strategy in genome-wide scans for selection. By conducting simulations of allelotype data, we first demonstrated that the boxplot with average heterozygosity (HET) is a promising method to detect strong selective sweeps with a moderate level of pooling error. Based on this, we used a sliding window analysis of HET to detect the large contiguous regions (LCRs) putatively under selective sweeps from Eurasia datasets. This survey identified 63 LCRs in a European population. These signals were further supported by the integrated haplotype score (iHS) test using HapMap II data. We also confirmed the European-specific signatures of positive selection from several previously identified genes(KEL, TRPV5, TRPV6, EPHB6). In summary, our results not only revealed the high credibility of SNP-MaP strategy in scanning for selective sweeps, but also provided an insight into the population differentiation.
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Affiliation(s)
- Libin Deng
- Facuity of Basic Medical Science, Nanchang University, Nanchang 330006, China
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Huang W, Kirkpatrick BW, Rosa GJM, Khatib H. A genome-wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle. Anim Genet 2010; 41:570-8. [DOI: 10.1111/j.1365-2052.2010.02046.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Uebe S, Pasutto F, Krumbiegel M, Schanze D, Ekici AB, Reis A. GPFrontend and GPGraphics: graphical analysis tools for genetic association studies. BMC Bioinformatics 2010; 11:472. [PMID: 20858257 PMCID: PMC2949897 DOI: 10.1186/1471-2105-11-472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 09/21/2010] [Indexed: 11/10/2022] Open
Abstract
Background Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Results Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Conclusions Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.
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Affiliation(s)
- Steffen Uebe
- Institute of Human Genetics, University of Erlangen-Nuremberg, Schwabachanlage 10, 91054 Erlangen, Germany
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Lind PA, Macgregor S, Vink JM, Pergadia ML, Hansell NK, de Moor MHM, Smit AB, Hottenga JJ, Richter MM, Heath AC, Martin NG, Willemsen G, de Geus EJC, Vogelzangs N, Penninx BW, Whitfield JB, Montgomery GW, Boomsma DI, Madden PAF. A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations. Twin Res Hum Genet 2010; 13:10-29. [PMID: 20158304 DOI: 10.1375/twin.13.1.10] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Persistent tobacco use and excessive alcohol consumption are major public health concerns worldwide. Both alcohol and nicotine dependence (AD, ND) are genetically influenced complex disorders that exhibit a high degree of comorbidity. To identify gene variants contributing to one or both of these addictions, we first conducted a pooling-based genomewide association study (GWAS) in an Australian population, using Illumina Infinium 1M arrays. Allele frequency differences were compared between pooled DNA from case and control groups for: (1) AD, 1224 cases and 1162 controls; (2) ND, 1273 cases and 1113 controls; and (3) comorbid AD and ND, 599 cases and 488 controls. Secondly, we carried out a GWAS in independent samples from the Netherlands for AD and for ND. Thirdly, we performed a meta-analysis of the 10,000 most significant AD- and ND-related SNPs from the Australian and Dutch samples. In the Australian GWAS, one SNP achieved genomewide significance (p < 5 x 10(-8)) for ND (rs964170 in ARHGAP10 on chromosome 4, p = 4.43 x 10(-8)) and three others for comorbid AD/ND (rs7530302 near MARK1 on chromosome 1 (p = 1.90 x 10(-9)), rs1784300 near DDX6 on chromosome 11 (p = 2.60 x 10(-9)) and rs12882384 in KIAA1409 on chromosome 14 (p = 4.86 x 10(-8))). None of the SNPs achieved genomewide significance in the Australian/Dutch meta-analysis, but a gene network diagram based on the top-results revealed overrepresentation of genes coding for ion-channels and cell adhesion molecules. Further studies will be required before the detailed causes of comorbidity between AD and ND are understood.
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Affiliation(s)
- Penelope A Lind
- Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia.
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Stamelou M, de Silva R, Arias-Carrión O, Boura E, Höllerhage M, Oertel WH, Müller U, Höglinger GU. Rational therapeutic approaches to progressive supranuclear palsy. Brain 2010; 133:1578-90. [PMID: 20472654 DOI: 10.1093/brain/awq115] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Progressive supranuclear palsy is a sporadic and progressive neurodegenerative disease, most often presenting as a symmetric, akinetic-rigid syndrome with postural instability, vertical supranuclear gaze palsy and frontal lobe deficits. It belongs to the family of tauopathies and involves both cortical and subcortical structures. Although the exact pathophysiology is not yet fully understood, several lines of evidence point to a crucial contribution from both genetic predisposition and mitochondrial dysfunction. Recently gained insights into the pathophysiology of this disease have led to several hypothesis-driven therapeutic approaches aiming at disease-modification rather than mere symptomatic neurotransmitter-replacement therapy. Agents targeting mitochondrial dysfunction have already shown a positive effect in a phase II study and further studies to verify and expand these results are ongoing. Clinical studies with agents targeting tau dysfunction such as tau-kinase inhibitors, tau-aggregation inhibitors and microtubule stabilizers are in preparation or ongoing. This review presents the current pathophysiological concepts driving these exciting therapeutic developments.
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Affiliation(s)
- Maria Stamelou
- Department of Neurology, Philipps University, Rudolf-Bultmann Str. 8, D-35033 Marburg, Germany
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Cowperthwaite MC, Mohanty D, Burnett MG. Genome-wide association studies: a powerful tool for neurogenomics. Neurosurg Focus 2010; 28:E2. [PMID: 20043717 DOI: 10.3171/2010.10.focus09186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As their power and utility increase, genome-wide association (GWA) studies are poised to become an important element of the neurosurgeon's toolkit for diagnosing and treating disease. In this paper, the authors review recent findings and discuss issues associated with gathering and analyzing GWA data for the study of neurological diseases and disorders, including those of neurosurgical importance. Their goal is to provide neurosurgeons and other clinicians with a better understanding of the practical and theoretical issues associated with this line of research. A modern GWA study involves testing hundreds of thousands of genetic markers across an entire genome, often in thousands of individuals, for any significant association with a particular disease. The number of markers assayed in a study presents several practical and theoretical issues that must be considered when planning the study. Genome-wide association studies show great promise in our understanding of the genes underlying common neurological diseases and disorders, as well as in leading to a new generation of genetic tests for clinicians.
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A Genomewide Association Study of Nicotine and Alcohol Dependence in Australian and Dutch Populations. Twin Res Hum Genet 2010. [DOI: 10.1017/s183242740002003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Persistent tobacco use and excessive alcohol consumption are major public health concerns worldwide. Both alcohol and nicotine dependence (AD, ND) are genetically influenced complex disorders that exhibit a high degree of comorbidity. To identify gene variants contributing to one or both of these addictions, we first conducted a pooling-based genomewide association study (GWAS) in an Australian population, using Illumina Infinium 1M arrays. Allele frequency differences were compared between pooled DNA from case and control groups for: (1) AD, 1224 cases and 1162 controls; (2) ND, 1273 cases and 1113 controls; and (3) comorbid AD and ND, 599 cases and 488 controls. Secondly, we carried out a GWAS in independent samples from the Netherlands for AD and for ND. Thirdly, we performed a meta-analysis of the 10, 000 most significant AD- and ND-related SNPs from the Australian and Dutch samples. In the Australian GWAS, one SNP achieved genomewide significance (p < 5 x 10-8) for ND (rs964170 in ARHGAPlOon chromosome 4, p = 4.43 x 10”8) and three others for comorbid AD/ND (rs7530302 near MARK1 on chromosome 1 (p = 1.90 x 10-9), rs1784300 near DDX6 on chromosome 11 (p = 2.60 x 10-9) and rs12882384 in KIAA1409 on chromosome 14 (p = 4.86 x 10-8)). None of the SNPs achieved genomewide significance in the Australian/Dutch meta-analysis, but a gene network diagram based on the top-results revealed overrepre-sentation of genes coding for ion-channels and cell adhesion molecules. Further studies will be requirec before the detailed causes of comorbidity between AC and ND are understood.
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Höllerhage M, Matusch A, Champy P, Lombès A, Ruberg M, Oertel WH, Höglinger GU. Natural lipophilic inhibitors of mitochondrial complex I are candidate toxins for sporadic neurodegenerative tau pathologies. Exp Neurol 2009; 220:133-42. [PMID: 19682988 DOI: 10.1016/j.expneurol.2009.08.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 07/22/2009] [Accepted: 08/05/2009] [Indexed: 12/21/2022]
Abstract
Annonacin, a natural lipophilic inhibitor of mitochondrial complex I has been implicated in the etiology of a sporadic neurodegenerative tauopathy in Guadeloupe. We therefore studied further compounds representing the broad biochemical spectrum of complex I inhibitors to which humans are potentially exposed. We determined their lipophilicity, their effect on complex I activity in submitochondrial particles, and their effect on cellular ATP levels, neuronal cell death and somatodendritic redistribution of phosphorylated tau protein (AD2 antibody against pS396/pS404-tau) in primary cultures of fetal rat striatum. The 24 compounds tested were lipophilic (logP range 0.9-8.5; exception: MPP(+) logP=-1.35) and potent complex I inhibitors (IC(50) range 0.9 nM-2.6 mM). They all decreased ATP levels (EC(50) range 1.9 nM-54.2 microM), induced neuronal cell death (EC(50) range 1.1 nM-54.5 microM) and caused the redistribution of AD2(+) tau from axons to the cell body (EC(5) range 0.6 nM-33.3 microM). The potency of the compounds to inhibit complex I correlated with their potency to induce tau redistribution (r=0.80, p<0.001). In conclusion, we propose that the widely distributed lipophilic complex I inhibitors studied here might be implicated in the induction of tauopathies with global prevalence.
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Kirov G, Zaharieva I, Georgieva L, Moskvina V, Nikolov I, Cichon S, Hillmer A, Toncheva D, Owen MJ, O'Donovan MC. A genome-wide association study in 574 schizophrenia trios using DNA pooling. Mol Psychiatry 2009; 14:796-803. [PMID: 18332876 DOI: 10.1038/mp.2008.33] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cost of genome-wide association (GWA) studies can be prohibitively high when large samples are genotyped. We conducted a GWA study on schizophrenia (SZ) and to reduce the cost, we used DNA pooling. We used a parent-offspring trios design to avoid the potential problems of population stratification. We constructed pools from 605 unaffected controls, 574 SZ patients and a third pool from all the parents of the patients. We hybridized each pool eight times on Illumina HumanHap550 arrays. We estimated the allele frequencies of each pool from the averaged intensities of the arrays. The significance level of results in the trios sample was estimated on the basis of the allele frequencies in cases and non-transmitted pseudocontrols, taking into account the technical variability of the data. We selected the highest ranked SNPs for individual genotyping, after excluding poorly performing SNPs and those that showed a trend in the opposite direction in the control pool. We genotyped 63 SNPs in 574 trios and analysed the results with the transmission disequilibrium test. Forty of those were significant at P<0.05, with the best result at P=1.2 x 10(-6) for rs11064768. This SNP is within the gene CCDC60, a coiled-coil domain gene. The third best SNP (P=0.00016) is rs893703, within RBP1, a candidate gene for schizophrenia.
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Affiliation(s)
- G Kirov
- Department of Psychological Medicine, Cardiff University, Henry Wellcome Building, Cardiff, UK.
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Ludolph AC, Kassubek J, Landwehrmeyer BG, Mandelkow E, Mandelkow EM, Burn DJ, Caparros-Lefebvre D, Frey KA, de Yebenes JG, Gasser T, Heutink P, Höglinger G, Jamrozik Z, Jellinger KA, Kazantsev A, Kretzschmar H, Lang AE, Litvan I, Lucas JJ, McGeer PL, Melquist S, Oertel W, Otto M, Paviour D, Reum T, Saint-Raymond A, Steele JC, Tolnay M, Tumani H, van Swieten JC, Vanier MT, Vonsattel JP, Wagner S, Wszolek ZK. Tauopathies with parkinsonism: clinical spectrum, neuropathologic basis, biological markers, and treatment options. Eur J Neurol 2009; 16:297-309. [PMID: 19364361 DOI: 10.1111/j.1468-1331.2008.02513.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tauopathies with parkinsonism represent a spectrum of disease entities unified by the pathologic accumulation of hyperphosphorylated tau protein fragments within the central nervous system. These pathologic characteristics suggest shared pathogenetic pathways and possible molecular targets for disease-modifying therapeutic interventions. Natural history studies, for instance, in progressive supranuclear palsy, frontotemporal dementia with parkinsonism linked to chromosome 17, corticobasal degeneration, and Niemann-Pick disease type C as well as in amyotrophic lateral sclerosis/Parkinson-dementia complex permit clinical characterization of the disease phenotypes and are crucial to the development and validation of biological markers for differential diagnostics and disease monitoring, for example, by use of neuroimaging or proteomic approaches. The wide pathologic and clinical spectrum of the tauopathies with parkinsonism is reviewed in this article, and perspectives on future advances in the understanding of the pathogenesis are given, together with potential therapeutic strategies.
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Affiliation(s)
- A C Ludolph
- Department of Neurology, University of Ulm, Ulm, Germany.
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Affiliation(s)
- John Hardy
- Institute of Neurology, University College London, London, United Kingdom. at
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44
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Camuzat A, Romana M, Dürr A, Feingold J, Brice A, Ruberg M, Lannuzel A. The PSP-associated MAPT H1 subhaplotype in Guadeloupean atypical parkinsonism. Mov Disord 2009; 23:2384-91. [PMID: 18785640 DOI: 10.1002/mds.22297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The aim of this study was to determine whether the H1 subhaplotype in MAPT associated with progressive supranuclear palsy (PSP) in Caucasians confers risk for PSP-like atypical parkinsonism in Guadeloupe, a tauopathy. Guadeloupean controls and patients with atypical and idiopathic parkinsonism and ethnically and age-matched controls were genotyped for H1 and H2 alleles, then for the H1 subhaplotype associated with PSP in Caucasians, using previously described haplotype-tagging single nucleotide polymorphisms (Ht-SNPs) in linkage disequilibrium at the MAPT locus. Most Guadeloupean controls and patients were homozygous for the H1 allele; only 5% were heterozygous for the H2 allele, consistent with the European contribution to the racial admixture in Guadeloupe, but equivalent to the frequency found in Caucasian PSP patients. The frequencies of the Ht-SNPs used to determine the PSP-associated H1 subhaplotype in both Guadeloupean controls and parkinsonians were similar, indicating that the H1 subhaplotype associated with PSP in Caucasians was not a risk factor for PSP-like atypical parkinsonism in Guadeloupe. Interestingly, they were also similar to the frequencies in Caucasian PSP patients. The major H1 subhaplotype in Guadeloupe, determined by analysis of linkage desequibrium, differed from the major Caucasian subhaplotype, but corresponded to minor alleles previously described.
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Affiliation(s)
- Agnès Camuzat
- INSERM, UMR_S 679, Neurology and Experimental Therapeutics, Paris, France
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45
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Ludolph AC, Kassubek J, Landwehrmeyer BG, Mandelkow E, Mandelkow EM, Burn DJ, Caparros-Lefebvre D, Frey KA, de Yebenes JG, Gasser T, Heutink P, Höglinger G, Jamrozik Z, Jellinger KA, Kazantsev A, Kretzschmar H, Lang AE, Litvan I, Lucas JJ, McGeer PL, Melquist S, Oertel W, Otto M, Paviour D, Reum T, Saint-Raymond A, Steele JC, Tolnay M, Tumani H, van Swieten JC, Vanier MT, Vonsattel JP, Wagner S, Wszolek ZK. Tauopathies with parkinsonism: clinical spectrum, neuropathologic basis, biological markers, and treatment options. Eur J Neurol 2009. [PMID: 19364361 DOI: 10.1111/j.l468-1331.2008.02513.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Tauopathies with parkinsonism represent a spectrum of disease entities unified by the pathologic accumulation of hyperphosphorylated tau protein fragments within the central nervous system. These pathologic characteristics suggest shared pathogenetic pathways and possible molecular targets for disease-modifying therapeutic interventions. Natural history studies, for instance, in progressive supranuclear palsy, frontotemporal dementia with parkinsonism linked to chromosome 17, corticobasal degeneration, and Niemann-Pick disease type C as well as in amyotrophic lateral sclerosis/Parkinson-dementia complex permit clinical characterization of the disease phenotypes and are crucial to the development and validation of biological markers for differential diagnostics and disease monitoring, for example, by use of neuroimaging or proteomic approaches. The wide pathologic and clinical spectrum of the tauopathies with parkinsonism is reviewed in this article, and perspectives on future advances in the understanding of the pathogenesis are given, together with potential therapeutic strategies.
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Affiliation(s)
- A C Ludolph
- Department of Neurology, University of Ulm, Ulm, Germany.
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46
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Cruchaga C, Vidal-Taboada JM, Ezquerra M, Lorenzo E, Martinez-Lage P, Blazquez M, Tolosa E, Pastor P. 5′-upstream variants of CRHR1 and MAPT genes associated with age at onset in progressive supranuclear palsy and cortical basal degeneration. Neurobiol Dis 2009; 33:164-70. [DOI: 10.1016/j.nbd.2008.09.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 09/11/2008] [Accepted: 09/30/2008] [Indexed: 11/29/2022] Open
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Bossé Y, Bacot F, Montpetit A, Rung J, Qu HQ, Engert JC, Polychronakos C, Hudson TJ, Froguel P, Sladek R, Desrosiers M. Identification of susceptibility genes for complex diseases using pooling-based genome-wide association scans. Hum Genet 2009; 125:305-18. [PMID: 19184112 DOI: 10.1007/s00439-009-0626-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 01/08/2009] [Indexed: 11/30/2022]
Abstract
The success of genome-wide association studies (GWAS) to identify risk loci of complex diseases is now well-established. One persistent major hurdle is the cost of those studies, which make them beyond the reach of most research groups. Performing GWAS on pools of DNA samples may be an effective strategy to reduce the costs of these studies. In this study, we performed pooling-based GWAS with more than 550,000 SNPs in two case-control cohorts consisting of patients with Type II diabetes (T2DM) and with chronic rhinosinusitis (CRS). In the T2DM study, the results of the pooling experiment were compared to individual genotypes obtained from a previously published GWAS. TCF7L2 and HHEX SNPs associated with T2DM by the traditional GWAS were among the top ranked SNPs in the pooling experiment. This dataset was also used to refine the best strategy to correctly identify SNPs that will remain significant based on individual genotyping. In the CRS study, the top hits from the pooling-based GWAS located within ten kilobases of known genes were validated by individual genotyping of 1,536 SNPs. Forty-one percent (598 out of the 1,457 SNPs that passed quality control) were associated with CRS at a nominal P value of 0.05, confirming the potential of pooling-based GWAS to identify SNPs that differ in allele frequencies between two groups of subjects. Overall, our results demonstrate that a pooling experiment on high-density genotyping arrays can accurately determine the minor allelic frequency as compared to individual genotyping and produce a list of top ranked SNPs that captures genuine allelic differences between a group of cases and controls. The low cost associated with a pooling-based GWAS clearly justifies its use in screening for genetic determinants of complex diseases.
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Affiliation(s)
- Yohan Bossé
- Laval Hospital Research Center, Laval University, Pavillon Margeritte-d'Youville, chemin Sainte-Foy, Quebec, QC, Canada.
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Zhao Y, Wang S. Optimal DNA pooling-based two-stage designs in case-control association studies. Hum Hered 2008; 67:46-56. [PMID: 18931509 DOI: 10.1159/000164398] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 01/03/2007] [Indexed: 11/19/2022] Open
Abstract
Study cost remains the major limiting factor for genome-wide association studies due to the necessity of genotyping a large number of SNPs for a large number of subjects. Both DNA pooling strategies and two-stage designs have been proposed to reduce genotyping costs. In this study, we propose a cost-effective, two-stage approach with a DNA pooling strategy. During stage I, all markers are evaluated on a subset of individuals using DNA pooling. The most promising set of markers is then evaluated with individual genotyping for all individuals during stage II. The goal is to determine the optimal parameters (pi(p)(sample ), the proportion of samples used during stage I with DNA pooling; and pi(p)(marker ), the proportion of markers evaluated during stage II with individual genotyping) that minimize the cost of a two-stage DNA pooling design while maintaining a desired overall significance level and achieving a level of power similar to that of a one-stage individual genotyping design. We considered the effects of three factors on optimal two-stage DNA pooling designs. Our results suggest that, under most scenarios considered, the optimal two-stage DNA pooling design may be much more cost-effective than the optimal two-stage individual genotyping design, which use individual genotyping during both stages.
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Affiliation(s)
- Yihong Zhao
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, N.Y., USA
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49
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Abstract
The analysis of genome wide variation offers the possibility of unravelling the genes involved in the pathogenesis of disease. Genome wide association studies are also particularly useful for identifying and validating targets for therapeutic intervention as well as for detecting markers for drug efficacy and side effects. The cost of such large-scale genetic association studies may be reduced substantially by the analysis of pooled DNA from multiple individuals. However, experimental errors inherent in pooling studies lead to a potential increase in the false positive rate and a loss in power compared to individual genotyping. Here we quantify various sources of experimental error using empirical data from typical pooling experiments and corresponding individual genotyping counts using two statistical methods. We provide analytical formulas for calculating these different errors in the absence of complete information, such as replicate pool formation, and for adjusting for the errors in the statistical analysis. We demonstrate that DNA pooling has the potential of estimating allele frequencies accurately, and adjusting the pooled allele frequency estimates for differential allelic amplification considerably improves accuracy. Estimates of the components of error show that differential allelic amplification is the most important contributor to the error variance in absolute allele frequency estimation, followed by allele frequency measurement and pool formation errors. Our results emphasise the importance of minimising experimental errors and obtaining correct error estimates in genetic association studies.
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Affiliation(s)
- A Jawaid
- Research & Development Genetics, AstraZeneca Pharmaceuticals, Macclesfield Cheshire SK104TG, UK.
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50
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Neale BM, Purcell S. The positives, protocols, and perils of genome-wide association. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:1288-94. [PMID: 18500721 DOI: 10.1002/ajmg.b.30747] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genome-wide association aims to comprehensively survey genetic variation for the purposes of disease and trait mapping. We provide a brief history of the development of genetic technology necessary to realize genome-wide association. From there we identify and review the publicly available resources for conducting such work including the molecular technologies, genomic databases, and analytic tools. Following on from the analytic tools, we highlight common analytic considerations, ranging from study design, quality control, and data cleaning to association analysis and replication. We conclude with a look toward future developments such as the analysis of copy number variation and integration of expression and epigenetic phenomenon into genome-wide association.
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Affiliation(s)
- Benjamin M Neale
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, UK.
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