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Bouter Y, Kacprowski T, Weissmann R, Dietrich K, Borgers H, Brauß A, Sperling C, Wirths O, Albrecht M, Jensen LR, Kuss AW, Bayer TA. Deciphering the molecular profile of plaques, memory decline and neuron loss in two mouse models for Alzheimer's disease by deep sequencing. Front Aging Neurosci 2014; 6:75. [PMID: 24795628 PMCID: PMC3997018 DOI: 10.3389/fnagi.2014.00075] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
One of the central research questions on the etiology of Alzheimer’s disease (AD) is the elucidation of the molecular signatures triggered by the amyloid cascade of pathological events. Next-generation sequencing allows the identification of genes involved in disease processes in an unbiased manner. We have combined this technique with the analysis of two AD mouse models: (1) The 5XFAD model develops early plaque formation, intraneuronal Aβ aggregation, neuron loss, and behavioral deficits. (2) The Tg4–42 model expresses N-truncated Aβ4–42 and develops neuron loss and behavioral deficits albeit without plaque formation. Our results show that learning and memory deficits in the Morris water maze and fear conditioning tasks in Tg4–42 mice at 12 months of age are similar to the deficits in 5XFAD animals. This suggested that comparative gene expression analysis between the models would allow the dissection of plaque-related and -unrelated disease relevant factors. Using deep sequencing differentially expressed genes (DEGs) were identified and subsequently verified by quantitative PCR. Nineteen DEGs were identified in pre-symptomatic young 5XFAD mice, and none in young Tg4–42 mice. In the aged cohort, 131 DEGs were found in 5XFAD and 56 DEGs in Tg4–42 mice. Many of the DEGs specific to the 5XFAD model belong to neuroinflammatory processes typically associated with plaques. Interestingly, 36 DEGs were identified in both mouse models indicating common disease pathways associated with behavioral deficits and neuron loss.
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Affiliation(s)
- Yvonne Bouter
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen , Goettingen , Germany
| | - Tim Kacprowski
- Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald , Greifswald , Germany ; Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Greifswald , Germany
| | - Robert Weissmann
- Human Molecular Genetics, Department for Human Genetics of the Institute for Genetics and Functional Genomics, Institute for Human Genetics, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald , Greifswald , Germany
| | - Katharina Dietrich
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen , Goettingen , Germany
| | - Henning Borgers
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen , Goettingen , Germany
| | - Andreas Brauß
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen , Goettingen , Germany
| | - Christian Sperling
- Human Molecular Genetics, Department for Human Genetics of the Institute for Genetics and Functional Genomics, Institute for Human Genetics, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald , Greifswald , Germany
| | - Oliver Wirths
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen , Goettingen , Germany
| | - Mario Albrecht
- Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald , Greifswald , Germany ; Institute for Knowledge Discovery, Graz University of Technology , Graz , Austria
| | - Lars R Jensen
- Human Molecular Genetics, Department for Human Genetics of the Institute for Genetics and Functional Genomics, Institute for Human Genetics, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald , Greifswald , Germany
| | - Andreas W Kuss
- Human Molecular Genetics, Department for Human Genetics of the Institute for Genetics and Functional Genomics, Institute for Human Genetics, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald , Greifswald , Germany
| | - Thomas A Bayer
- Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen , Goettingen , Germany
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Andreoli V, Trecroci F, La Russa A, Cittadella R, Liguori M, Spadafora P, Caracciolo M, Di Palma G, Colica C, Gambardella A, Quattrone A. Presenilin enhancer-2 gene: identification of a novel promoter mutation in a patient with early-onset familial Alzheimer's disease. Alzheimers Dement 2012; 7:574-8. [PMID: 22055974 DOI: 10.1016/j.jalz.2011.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 01/28/2011] [Accepted: 02/08/2011] [Indexed: 10/15/2022]
Abstract
UNLABELLED γ-Secretase proteins complex cleaves the amyloid precursor protein (APP) to generate amyloid-β (Aβ) peptides. Considerable evidence suggests that alterations in genes encoding these proteins exert their influence on the pathogenesis of familial Alzheimer's disease (FAD). Presenilin enhancer-2 gene (PEN-2) is a necessary component of the γ-Secretase complex. Recently, it has been shown that PEN-2 mutations could be involved in Alzheimer's disease (AD). We performed a mutational screening of all PEN-2 coding and promoter regions in a FAD cohort derived from Southern Italy. Four hundred and fifty-two subjects (FAD: 97; CONTROLS 355) were recruited for this study. We identified for the first time in a key region necessary for the promoter activity a novel 3 bp deletion in a subject with early-FAD. Our genetic data demonstrate that the mutant allele may influence the transcriptional activity of the PEN-2 gene. Although the effective role of the PEN-2 promoter deletion in AD is not entirely clear, these findings might lead to more studies on its functional and genetic role.
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Affiliation(s)
- Virginia Andreoli
- Institute of Neurological Sciences, National Research Council, Pianolago di Mangone, Cosenza, Italy.
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George AJ, Gordon L, Beissbarth T, Koukoulas I, Holsinger RMD, Perreau V, Cappai R, Tan SS, Masters CL, Scott HS, Li QX. A serial analysis of gene expression profile of the Alzheimer's disease Tg2576 mouse model. Neurotox Res 2010; 17:360-79. [PMID: 19760337 DOI: 10.1007/s12640-009-9112-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 06/22/2009] [Accepted: 08/31/2009] [Indexed: 10/20/2022]
Abstract
Serial analysis of gene expression (SAGE), a technique that allows for the simultaneous detection of expression levels of the entire genome without a priori knowledge of gene sequences, was used to examine the transcriptional expression pattern of the Tg2576 mouse model of Alzheimer's disease (AD). Pairwise comparison between the Tg2576 and nontransgenic SAGE libraries identified a number of differentially expressed genes in the Tg2576 SAGE library, some of which were not previously revealed by the microarray studies. Real-time PCR was used to validate a panel of genes selected from the SAGE analysis in the Tg2576 mouse brain, as well as the hippocampus and temporal cortex of sporadic AD and normal age-matched controls. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 5 (NDUFA5) and FXYD domain-containing ion transport regulator 6 (FXYD6) were found to be significantly decreased in the Tg2576 mouse brain and AD hippocampus. PTEN-induced putative kinase 1 (PINK1), phosphatidylethanolamine binding protein (PEBP), crystalline mu (CRYM), and neurogranin (NRGN) were significantly decreased in AD tissues. The gene ontologies represented in the Tg2576 data were statistically analyzed and demonstrated a significant under-representation of genes involved with G-protein-coupled receptor signaling and odorant binding, while genes significantly over-represented were focused on cellular communication and cellular physiological processes. The novel approach of profiling the Tg2576 mouse brain using SAGE has identified different genes that could subsequently be examined for their potential as peripheral diagnostic and prognostic markers for Alzheimer's disease.
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Affiliation(s)
- Amee J George
- Department of Pathology, The University of Melbourne and The Mental Health Research Institute of Victoria, Parkville, VIC 3052, Australia
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A new integrative model of cerebral activation, deactivation and default mode function in Alzheimer’s disease. Eur J Nucl Med Mol Imaging 2008; 35 Suppl 1:S12-24. [DOI: 10.1007/s00259-007-0698-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Evin G, Sernee MF, Masters CL. Inhibition of gamma-secretase as a therapeutic intervention for Alzheimer's disease: prospects, limitations and strategies. CNS Drugs 2006; 20:351-72. [PMID: 16696577 DOI: 10.2165/00023210-200620050-00002] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genetic and experimental evidence points to amyloid-beta (Abeta) peptide as the culprit in Alzheimer's disease pathogenesis. This protein fragment abnormally accumulates in the brain cortex and hippocampus of patients with Alzheimer's disease, and self-aggregates to form toxic oligomers causing neurodegeneration.Abeta is heterogeneous and produced from a precursor protein (amyloid precursor protein [APP]) by two sequential proteolytic cleavages that involve beta- and gamma-secretases. This latter enzyme represents a potentially attractive drug target since it dictates the solubility of the generated Abeta fragment by creating peptides of various lengths, namely Abeta(40) and Abeta(42), the longest being the most aggregating. gamma-Secretase comprises a molecular complex of four integral membrane proteins - presenilin, nicastrin, APH-1 and PEN-2 - and its molecular mechanism remains under extensive scrutiny. The ratio of Abeta(42) over Abeta(40) is increased by familial Alzheimer's disease mutations occurring in the presenilin genes or in APP, near the gamma-secretase cleavage site. Potent gamma-secretase inhibitors have been identified by screening drug libraries or by designing aspartyl protease transition-state analogues based on the APP substrate cleavage site. Most of these compounds are not specific for gamma-secretase cleavage of APP, and equally inhibit the processing of other gamma-secretase substrates, such as Notch and a subset of cell-surface receptors and proteins involved in embryonic development, haematopoiesis, cell adhesion and cell/cell contacts. Therefore, current research aims at finding compounds that show selectivity for APP cleavage, and particularly that inhibit the formation of the aggregating form, Abeta(42). Compounds that target the substrate docking site rather than the enzyme active site are also being investigated as an alternative strategy. The finding that some NSAID analogues preferentially inhibit the formation of Abeta(42) over Abeta(40) and do not affect Notch processing has opened a new therapeutic window. The progress in design of selective inhibitors as well as recent results obtained in animal studies prove that gamma-secretase remains among the best targets for the therapeutic control of amyloid build-up in Alzheimer's disease. The full understanding of gamma-secretase regulation may yet uncover new therapeutic leads.
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Affiliation(s)
- Geneviève Evin
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.
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Genetics of Alzheimer's disease. NEURODEGENER DIS 2005. [DOI: 10.1017/cbo9780511544873.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Bertram L, Hsiao M, Mullin K, Parkinson M, Menon R, Moscarillo TJ, Blacker D, Tanzi RE. ACAT1 is not associated with Alzheimer's disease in two independent family-based samples. Mol Psychiatry 2005; 10:522-4. [PMID: 15768051 DOI: 10.1038/sj.mp.4001646] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Seripa D, Matera MG, Dal Forno G, Gravina C, Masullo C, Daniele A, Binetti G, Bonvicini C, Squitti R, Palermo MT, Davis DG, Antuono P, Wekstein DR, Dobrina A, Gennarelli M, Fazio VM. Genotypes and haplotypes in the IL-1 gene cluster: analysis of two genetically and diagnostically distinct groups of Alzheimer patients. Neurobiol Aging 2005; 26:455-64. [PMID: 15653174 DOI: 10.1016/j.neurobiolaging.2004.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2003] [Revised: 03/24/2004] [Accepted: 04/12/2004] [Indexed: 11/30/2022]
Abstract
Increased risk of Alzheimer's disease (AD) has been associated with polymorphisms in the IL-1 gene cluster, and in particular with the IL-1alpha-889 T/T genotype. However, this association is still unclear, and needs further investigation. In order to clarify the role of these polymorphisms in the complex pathogenesis of AD we examined genotype and haplotype frequencies of the two C-to-T SNPs at position -889 and -551 in the IL-1alpha and IL-1beta genes, respectively, and of the 86 bp VNTR intron-2 polymorphisms in the IL-1Ra gene. The analysis was performed in two genetically and diagnostically distinct groups of sporadic AD from Italy and the USA. In the Italian group a significant association between the IL-1alpha-889 T/T genotype and AD (OR=3.022, 95% CI: 1.001-9.119) was found, whereas no difference was found in the group from the USA. Results were also compared with previously published studies that analyzed the same IL-1 polymorphisms in AD. In both groups, the analysis of the estimated haplotypes shows that AD patients and controls who carry the IL-1beta-511 C allele, were also more frequently carriers of the IL-1Ra 1 allele (haplotypes -C-1). The total frequency of the two -C-1 haplotypes (C-C-1 plus T-C-1) was about one half of the total frequency of the eight estimated haplotypes. This was confirmed by significant linkage disequilibrium between these two loci in both the Italian and USA groups. In the Italian group a weak association of the T-C-2 haplotype with the disease (OR=1.648, 95% CI: 1.519-1.788) was also found, whereas in the USA group no difference was found. Although ours and other published data on different samples of Caucasian and non-Caucasian AD show a great heterogeneity in the frequencies of the IL-1alpha-889, the IL-1beta-511 and the IL-1Ra VNTR gene polymorphisms, we confirm the role of the IL-1alpha-889 T/T genotype as a risk factor for sporadic AD, and show the presence of an allelic association between IL-1beta C and IL-1Ra 1 alleles in both the Italian and the USA groups, confirmed by the presence of significant levels of linkage disequilibrium between these two loci.
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Affiliation(s)
- Davide Seripa
- Laboratory of Gene Therapy, I.R.C.C.S. Casa Sollievo della Sofferenza, Padre Pio da Pietrelcina Foundation, San Giovanni Rotondo, FG, Italy.
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Weiner DM, Goodman MW, Colpitts TM, Feddock MA, Duggento KL, Nash NR, Levey AI, Brann MR. Functional Screening of Drug Target Genes. ACTA ACUST UNITED AC 2004; 4:119-28. [PMID: 15059034 DOI: 10.2165/00129785-200404020-00006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
BACKGROUND AND OBJECTIVES A number of recent studies surveying single nucleotide polymorphisms within the exonic regions of human genes have revealed a significant number of such variants, including many non-synonymous variants. This highlights the need to directly identify, within individual clinically well-defined patients, those variants that alter protein function as well as structure. We report on the development of a novel phenotypic screening process that combines high-throughput molecular cloning techniques with functional expression utilizing the cell-based assay R-SAT. METHODS We applied the phenotypic screening process to an analysis of the m1 muscarinic acetylcholine receptor (CHRM1) gene in a cohort of 74 individuals, including 48 diagnosed with neurodegenerative disease, primarily Alzheimer disease, who have been stratified according to their clinical response to the acetylcholinesterase inhibitor donepezil. Phenotypic screening of the CHRM1 gene involved PCR-based amplification from genomic DNA and heterologous expression in mammalian cells. RESULTS Phenotypic screening yielded functional responses to the agonist carbachol displaying a mean potency (-pEC(50)+/- standard deviation) of 5.8 +/- 0.2, which did not differ from that observed with expression of the wild-type receptor gene (6.0 +/- 0.3). No altered levels of constitutive receptor activity were observed. Dideoxy sequencing did not reveal any non-synonymous variants in the coding exon of this gene within this clinical cohort, while detecting three synonymous variants. CONCLUSION The results confirm that the m1 receptor gene (CHRM1) is not highly polymorphic in the human population, suggesting that genetic variation within the coding exon of this gene is not a contributing factor to the clinical variability observed during treatment of dementia with cholinergic enhancement therapies.
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Affiliation(s)
- David M Weiner
- ACADIA Pharmaceuticals, Inc., San Diego, California 92121, USA.
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Bloom FE. Presidential address. Science as a way of life: perplexities of a physician-scientist. Science 2003; 300:1680-5. [PMID: 12805530 DOI: 10.1126/science.1085535] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Floyd E Bloom
- Department of Neuro- pharmacology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Bertram L, Saunders AJ, Mullin K, Sampson A, Moscarillo TJ, Basset SS, Go RCP, Blacker D, Tanzi RE. No association between marker D10S1423 and Alzheimer's disease. Mol Psychiatry 2003; 8:571-3. [PMID: 12851634 DOI: 10.1038/sj.mp.4001355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Alzheimer's disease afflicts every tenth human aged over 65. Despite the dramatic progress that has been made in understanding the disease, the exact cause of Alzheimer's disease is still unknown. Most gene mutations associated with Alzheimer's disease point at the same culprits: amyloid precursor protein and ultimately amyloid beta. The enigmatic proteases alpha-,beta-, and gamma-secretase are the three executioners of amyloid precursor protein processing, and disruption of their delicate balance is suspected to result in Alzheimer's disease. Significant progress has been made in the selective control of these proteases, regardless of the availability of structural information. Not even the absence of a robust cell-free assay for gamma-secretase could hamper the identification of nonpeptidic inhibitors of this enzyme for long. Within five years, four distinctly different structural moieties were developed and the first drug candidates are in clinical trials. Unfortunately, selective inhibition of amyloid beta formation remains a crucial issue because fundamental fragments of the gamma-secretase complex are important for other signaling events. This problem makes beta-secretase inhibition and alpha-secretase induction even more appealing.
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Affiliation(s)
- Boris Schmidt
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry TU Darmstadt, Petersenstrasse 22 64287 Darmstadt, Germany.
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Goodman AB, Pardee AB. Evidence for defective retinoid transport and function in late onset Alzheimer's disease. Proc Natl Acad Sci U S A 2003; 100:2901-5. [PMID: 12604774 PMCID: PMC151438 DOI: 10.1073/pnas.0437937100] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hypothesis of this article is that late onset Alzheimer's disease (AD) is influenced by the availability in brain of retinoic acid (RA), the final product of the vitamin A (retinoid) metabolic cascade. Genetic, metabolic, and environmental/dietary evidence is cited supporting this hypothesis. Significant genetic linkages to AD are demonstrated for markers close to four of the six RA receptors, RA receptor G at 12q13, retinoid X receptor B at 6p21.3, retinoid X receptor G at 1q21, and RA receptor A at 17q21. Three of the four retinol-binding proteins at 3q23 and 10q23 and the RA-degrading cytochrome P450 enzymes at 10q23 and 2p13 map to AD linkages. Synthesis of the evidence supports retinoid hypofunction and impaired transport as contributing factors. These findings suggest testable experiments to determine whether increasing the availability of retinoid in brain, possibly through pharmacologic targeting of the RA receptors and the cytochrome P450 RA-inactivating enzymes, can prevent or decrease amyloid plaque formation.
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MESH Headings
- Age of Onset
- Aging
- Alleles
- Alzheimer Disease/genetics
- Alzheimer Disease/metabolism
- Brain/metabolism
- Chromosome Mapping
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 10
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 3
- Chromosomes, Human, Pair 6
- Genetic Linkage
- Humans
- Protein Transport
- Retinoids/metabolism
- Tretinoin/metabolism
- Up-Regulation
- Vitamin A/metabolism
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Abstract
A remarkable rise in life expectancy during the past century has made Alzheimer's disease (AD) the most common form of progressive cognitive failure in humans. Compositional analyses of the classical brain lesions, the senile (amyloid) plaques and neurofibrillary tangles, preceded and has guided the search for genetic alterations. Four genes have been unequivocally implicated in inherited forms of AD, and mutations or polymorphisms in these genes cause excessive cerebral accumulation of the amyloid beta-protein and subsequent neuronal and glial pathology in brain regions important for memory and cognition. This understanding of the genotype-to-phenotype conversions of familial AD has led to the development of pharmacological strategies to lower amyloid beta-protein levels as a way of treating or preventing all forms of the disease.
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Affiliation(s)
- Dennis J Selkoe
- Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
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