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      Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease, and shows evidence for additional susceptibility genes

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          Abstract

          We undertook a two-stage genome-wide association study of Alzheimer's disease involving over 16,000 individuals. In stage 1 (3,941 cases and 7,848 controls), we replicated the established association with the APOE locus (most significant SNP: rs2075650, p= 1.8×10 −157) and observed genome-wide significant association with SNPs at two novel loci: rs11136000 in the CLU or APOJ gene (p= 1.4×10 −9) and rs3851179, a SNP 5′ to the PICALM gene (p= 1.9×10 −8). Both novel associations were supported in stage 2 (2,023 cases and 2,340 controls), producing compelling evidence for association with AD in the combined dataset (rs11136000: p= 8.5×10 −10, odds ratio= 0.86; rs3851179: p= 1.3×10 −9, odds ratio= 0.86). We also observed more variants associated at p< 1×10 −5 than expected by chance (p=7.5×10 −6), including polymorphisms at the BIN1, DAB1 and CR1 loci.

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          Most cited references45

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          Transport pathways for clearance of human Alzheimer's amyloid beta-peptide and apolipoproteins E and J in the mouse central nervous system.

          Amyloid beta-peptide (Abeta) clearance from the central nervous system (CNS) maintains its low levels in brain. In Alzheimer's disease, Abeta accumulates in brain possibly because of its faulty CNS clearance and a deficient efflux across the blood-brain barrier (BBB). By using human-specific enzyme-linked immunosorbent assays, we measured a rapid 30 mins efflux at the BBB and transport via the interstitial fluid (ISF) bulk flow of human-unlabeled Abeta and of Abeta transport proteins, apolipoprotein E (apoE) and apoJ in mice. We show (i) Abeta40 is cleared rapidly across the BBB via low-density lipoprotein receptor-related protein (LRP)1 at a rate of 0.21 pmol/min g ISF or 6-fold faster than via the ISF flow; (ii) Abeta42 is removed across the BBB at a rate 1.9-fold slower compared with Abeta40; (iii) apoE, lipid-poor isoform 3, is cleared slowly via the ISF flow and across the BBB (0.03-0.04 pmol/min g ISF), and after lipidation its transport at the BBB becomes barely detectable within 30 mins; (iv) apoJ is eliminated rapidly across the BBB (0.16 pmol/min g ISF) via LRP2. Clearance rates of unlabeled and corresponding 125I-labeled Abeta and apolipoproteins were almost identical, but could not be measured at low physiologic levels by mass spectrometry. Amyloid beta-peptide 40 binding to apoE3 reduced its efflux rate at the BBB by 5.7-fold, whereas Abeta42 binding to apoJ enhanced Abeta42 BBB clearance rate by 83%. Thus, Abeta, apoE, and apoJ are cleared from brain by different transport pathways, and apoE and apoJ may critically modify Abeta clearance at the BBB.
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            Endocytosis is required for synaptic activity-dependent release of amyloid-beta in vivo.

            Aggregation of amyloid-beta (Abeta) peptide into soluble and insoluble forms within the brain extracellular space is central to the pathogenesis of Alzheimer's disease. Full-length amyloid precursor protein (APP) is endocytosed from the cell surface into endosomes where it is cleaved to produce Abeta. Abeta is subsequently released into the brain interstitial fluid (ISF). We hypothesized that synaptic transmission results in more APP endocytosis, thereby increasing Abeta generation and release into the ISF. We found that inhibition of clathrin-mediated endocytosis immediately lowers ISF Abeta levels in vivo. Two distinct methods that increased synaptic transmission resulted in an elevation of ISF Abeta levels. Inhibition of endocytosis, however, prevented the activity-dependent increase in Abeta. We estimate that approximately 70% of ISF Abeta arises from endocytosis-associated mechanisms, with the vast majority of this pool also dependent on synaptic activity. These findings have implications for AD pathogenesis and may provide insights into therapeutic intervention.
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              Genome-wide association analysis reveals putative Alzheimer's disease susceptibility loci in addition to APOE.

              Alzheimer's disease (AD) is a genetically complex and heterogeneous disorder. To date four genes have been established to either cause early-onset autosomal-dominant AD (APP, PSEN1, and PSEN2(1-4)) or to increase susceptibility for late-onset AD (APOE5). However, the heritability of late-onset AD is as high as 80%, (6) and much of the phenotypic variance remains unexplained to date. We performed a genome-wide association (GWA) analysis using 484,522 single-nucleotide polymorphisms (SNPs) on a large (1,376 samples from 410 families) sample of AD families of self-reported European descent. We identified five SNPs showing either significant or marginally significant genome-wide association with a multivariate phenotype combining affection status and onset age. One of these signals (p = 5.7 x 10(-14)) was elicited by SNP rs4420638 and probably reflects APOE-epsilon4, which maps 11 kb proximal (r2 = 0.78). The other four signals were tested in three additional independent AD family samples composed of nearly 2700 individuals from almost 900 families. Two of these SNPs showed significant association in the replication samples (combined p values 0.007 and 0.00002). The SNP (rs11159647, on chromosome 14q31) with the strongest association signal also showed evidence of association with the same allele in GWA data generated in an independent sample of approximately 1,400 AD cases and controls (p = 0.04). Although the precise identity of the underlying locus(i) remains elusive, our study provides compelling evidence for the existence of at least one previously undescribed AD gene that, like APOE-epsilon4, primarily acts as a modifier of onset age.
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                Author and article information

                Journal
                9216904
                2419
                Nat Genet
                Nat. Genet.
                Nature genetics
                1061-4036
                1546-1718
                2 March 2010
                06 September 2009
                October 2009
                01 April 2010
                : 41
                : 10
                : 1088-1093
                Affiliations
                [1 ] MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
                [2 ] NIHR Biomedical Research Centre for Mental Health at the South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Kings College, London, UK.
                [3 ] Department of Neuroscience, Institute of Psychiatry, Kings College, London, UK.
                [4 ] Institute of Public Health, University of Cambridge, Cambridge, UK.
                [5 ] Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
                [6 ] Mercer's Institute for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland.
                [7 ] Institute of Genetics, Queen's Medical Centre, University of Nottingham, NG7 2UH, UK.
                [8 ] Ageing Group, Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, UK.
                [9 ] Division of Clinical Neurosciences, School of Medicine, University of Southampton, Southampton, UK.
                [10 ] Clinical Neuroscience Research Group, Greater Manchester Neurosciences Centre, University of Manchester, Salford, UK.
                [11 ] Oxford Project to Investigate Memory and Ageing (OPTIMA), University of Oxford, Level 4, John Radcliffe Hospital, Oxford OX3 9DU, UK.
                [12 ] Dementia Research Group, University of Bristol Institute of Clinical Neurosciences, Frenchay Hospital, Bristol, UK.
                [13 ] Department of Molecular Neuroscience and Reta Lilla Weston Laboratories, Institute of Neurology, London, UK.
                [14 ] MRC Prion Unit, Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK.
                [15 ] Dementia Research Centre, Department of Neurodegenerative Diseases, University College London, Institute of Neurology, London, UK.
                [16 ] Department of Psychiatry, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany.
                [17 ] Institute of Primary Medical Care, University Medical Center Hamburg-Eppendorf, Germany.
                [18 ] Department of Psychiatry, Charité Berlin, Germany.
                [19 ] Department of Psychiatry and Psychotherapy, University of Erlangen-Nüremberg, Germany.
                [20 ] LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, University Duisburg-Essen, Germany.
                [21 ] Institute for Stroke and Dementia Reserach, Klinikum der Universität München, Marchioninistr. 15, 81377, Munich, Germany.
                [22 ] Department of Neurology, Klinikum der Universität München, Marchioninistr. 15, 81377, Munich, Germany.
                [23 ] Department of Geriatric Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Square J5, D-68161 Mannheim, Germany.
                [24 ] Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Laboratory of Neuroimaging & Biomarker Research, Trinity College, University of Dublin, Ireland.
                [25 ] Alzheimer Memorial Center and Geriatric Psychiatry Branch, Department of Psychiatry, Ludwig-Maximilian University, Munich, Germany.
                [26 ] Centre for Geriatric Medicine and Section of Gerontopsychiatry and Neuropsychology, Medical School, University of Freiburg, Germany.
                [27 ] Departments of Psychiatry, Neurology and Genetics, Washington University School of Medicine, St Louis, MO 63110, US.
                [28 ] Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
                [29 ] Neurodegenerative Brain Diseases group, Department of Molecular Genetics, VIB, Antwerpen, Belgium.
                [30 ] Institute Born-Bunge and University of Antwerp; Antwerpen, Belgium.
                [31 ] Memory Clinic and Department of Neurology, ZNA Middelheim, Antwerpen, Belgium.
                [32 ] Department of Mental Health Sciences, University College London, UK.
                [33 ] The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
                [34 ] MRC Centre for Neurodegeneration Research, Department of Clinical Neuroscience, King's College London, Institute of Psychiatry, London, SE5 8AF, UK.
                [35 ] 3rd Department of Neurology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
                [36 ] Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.
                [37 ] Department of Genomics, Life & Brain Center, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany.
                [38 ] Institute of Human Genetics, University of Bonn, Wilhelmstr. 31, D-53111 Bonn, Germany.
                [39 ] Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Hufelandstr. 55, D-45147 Essen, Germany.
                [40 ] Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
                [41 ] Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany.
                [42 ] Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224, USA.
                [43 ] Division of Biomedical Statistics and Informatics, Mayo Clinic and Mayo Foundation, Rochester, Minnesota 55905, USA.
                Author notes
                [] Corresponding authors
                [*]

                These authors contributed equally to this work

                Author Contributions

                JW (Cardiff), MJO, MOD directed this study, assisted by RA, PH, and PAH. DH and JW (Cardiff) took primary responsibility for drafting the manuscript assisted by RA, PH, RS, AG, MOD and MJO. JW (Cardiff), RA, PH, RS, AG, KD, AW, NJ, CT, AS, ARM, SL (IOP), JP, PP, MKL, CB, DCR, MG, BL, AL, KM (Notts), KSB, PAP, DC, BM, ST, CH, DM, ADS, SL (Bristol) PGK, JH, SM (UCL), NF, MR, JC, WM, FJ, BS, HvB, IH, JK, JW (Essen), MD, LF, AMG, JSK, CC, PN, JCM, KM (WashU), GL, NJB, HG and AM contributed towards clinical sample collection, ascertainment, diagnosis and preparation of samples from the ‘610 group’ from the stage 1 ‘discovery sample’ and in some cases also provided stage 2 ‘follow up’ samples. RA and PH were responsible for the coordination, collection, transit and selection of samples for genotyping from the ‘610 group’. RG (Sanger) and PD were responsible for procedures related to genotyping the 610 group on the Illumina platform. AA, CES, ABS, RG (NIA), TWM, MMN, SM, KJ, NK, HW, MMC, SVP and SGY were involved in clinical sample collection, ascertainment, diagnosis, preparation of samples and genotyping of ‘collaborative samples’ included in Stage 1 (i.e. samples other than the ‘610 group’). KS, KB, SE, PDD, CVB and MT contributed towards sample collection, diagnosis and preparation of case-control material for the stage 2 ‘replication sample’. Replication genotyping was coordinated and performed by RA, assisted by RS and AG. JSP developed the database for the GWA project in which the data were stored. DH completed statistical quality control and produced association statistics, under the supervision of MH (Cardiff), VM and PAH. All authors discussed the results and approved the manuscript.

                Article
                UKMS27833
                10.1038/ng.440
                2845877
                19734902
                36e9979f-682d-436b-90d5-5f3bd1b93ee4

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                History
                Funding
                Funded by: Wellcome Trust :
                Award ID: 082604 || WT
                Funded by: Wellcome Trust :
                Award ID: 064354 || WT
                Funded by: Medical Research Council :
                Award ID: G0300429(66813) || MRC_
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                Genetics
                Genetics

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