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Hernández-Lorenzo L, García-Gutiérrez F, Solbas-Casajús A, Corrochano S, Matías-Guiu JA, Ayala JL. Genetic-based patient stratification in Alzheimer's disease. Sci Rep 2024; 14:9970. [PMID: 38693203 PMCID: PMC11063050 DOI: 10.1038/s41598-024-60707-1] [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: 12/19/2023] [Accepted: 04/26/2024] [Indexed: 05/03/2024] Open
Abstract
Alzheimer's disease (AD) shows a high pathological and symptomatological heterogeneity. To study this heterogeneity, we have developed a patient stratification technique based on one of the most significant risk factors for the development of AD: genetics. We addressed this challenge by including network biology concepts, mapping genetic variants data into a brain-specific protein-protein interaction (PPI) network, and obtaining individualized PPI scores that we then used as input for a clustering technique. We then phenotyped each obtained cluster regarding genetics, sociodemographics, biomarkers, fluorodeoxyglucose-positron emission tomography (FDG-PET) imaging, and neurocognitive assessments. We found three clusters defined mainly by genetic variants found in MAPT, APP, and APOE, considering known variants associated with AD and other neurodegenerative disease genetic architectures. Profiling of these clusters revealed minimal variation in AD symptoms and pathology, suggesting different biological mechanisms may activate the neurodegeneration and pathobiological patterns behind AD and result in similar clinical and pathological presentations, even a shared disease diagnosis. Lastly, our research highlighted MAPT, APP, and APOE as key genes where these genetic distinctions manifest, suggesting them as potential targets for personalized drug development strategies to address each AD subgroup individually.
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Affiliation(s)
- Laura Hernández-Lorenzo
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Fernando García-Gutiérrez
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain
| | - Ana Solbas-Casajús
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain
| | - Silvia Corrochano
- Department of Neurology, San Carlos Research Institute (IdSSC), Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Jordi A Matías-Guiu
- Department of Neurology, San Carlos Research Institute (IdSSC), Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Jose L Ayala
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain
- Instituto de Tecnología del Conocimiento, Universidad Complutense de Madrid, 28040, Madrid, Spain
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Bonomi CG, Bruno M, Colona VL, Bengala M, Martorana A. A case of hereditary dementia: Is it Alzheimer's disease or not? J Neurol Sci 2024; 458:122947. [PMID: 38448253 DOI: 10.1016/j.jns.2024.122947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Affiliation(s)
| | - Matilde Bruno
- Memory Clinic, University of Rome Tor Vergata, Viale Oxford 81, 00133 Roma, Italy
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Mario Bengala
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
| | - Alessandro Martorana
- Memory Clinic, University of Rome Tor Vergata, Viale Oxford 81, 00133 Roma, Italy.
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Xiao X, Liu H, Zhou L, Liu X, Xu T, Zhu Y, Yang Q, Hao X, Liu Y, Zhang W, Zhou Y, Wang J, Li J, Jiao B, Shen L, Liao X. The associations of APP, PSEN1, and PSEN2 genes with Alzheimer's disease: A large case-control study in Chinese population. CNS Neurosci Ther 2022; 29:122-128. [PMID: 36217304 PMCID: PMC9804049 DOI: 10.1111/cns.13987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/28/2022] [Indexed: 02/06/2023] Open
Abstract
AIM The associations of non-pathogenic variants of APP, PSEN1, and PSEN2 with Alzheimer's disease (AD) remain unclear. This study is aimed at determining the role of these variants in AD. METHODS Our study recruited 1154 AD patients and 2403 controls. APP, PSEN1, PSEN2, and APOE were sequenced using a targeted panel. Variants were classified into common or rare variants with the minor allele frequencies (MAF) cutoff of 0.01. Common variant (MAF≥0.01)-based association test was performed by PLINK 1.9, and gene-based (MAF <0.01) association analysis was conducted using Sequence Kernel Association Test-Optimal (SKAT-O test). Additionally, using PLINK 1.9, we performed AD endophenotypes association studies. RESULTS A common variant, PSEN2 rs11405, was suggestively associated with AD risk (p = 1.08 × 10-2 ). The gene-based association analysis revealed that the APP gene exhibited a significant association with AD (p = 1.43 × 10-2 ). In the AD endophenotypes association studies, APP rs459543 was nominally correlated with CSF Aβ42 level (p = 7.91 × 10-3 ). CONCLUSION Our study indicated that non-pathogenic variants in PSEN2 and APP may be involved in AD pathogenesis in the Chinese population.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Hui Liu
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Lu Zhou
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xixi Liu
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Tianyan Xu
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yuan Zhu
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Qijie Yang
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xiaoli Hao
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yingzi Liu
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Weiwei Zhang
- Bioinformatics Center && National Clinical Research Center for Geriatric DisordersCentral South UniversityChangshaChina,Department of Radiology, Xiangya HospitalCentral South UniversityChangshaChina,Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaChina,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaChina,Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaChina
| | - Yafang Zhou
- Bioinformatics Center && National Clinical Research Center for Geriatric DisordersCentral South UniversityChangshaChina,Department of Geriatrics, Xiangya HospitalCentral South UniversityChangshaChina,Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaChina,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaChina,Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaChina
| | - Junling Wang
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina,Bioinformatics Center && National Clinical Research Center for Geriatric DisordersCentral South UniversityChangshaChina,Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaChina,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaChina,Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaChina
| | - Jinchen Li
- Bioinformatics Center && National Clinical Research Center for Geriatric DisordersCentral South UniversityChangshaChina
| | - Bin Jiao
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina,Bioinformatics Center && National Clinical Research Center for Geriatric DisordersCentral South UniversityChangshaChina,Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaChina,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaChina,Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaChina
| | - Lu Shen
- Department of Neurology, Xiangya HospitalCentral South UniversityChangshaChina,Bioinformatics Center && National Clinical Research Center for Geriatric DisordersCentral South UniversityChangshaChina,Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaChina,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaChina,Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaChina,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan ProvinceChangshaChina
| | - Xinxin Liao
- Bioinformatics Center && National Clinical Research Center for Geriatric DisordersCentral South UniversityChangshaChina,Department of Geriatrics, Xiangya HospitalCentral South UniversityChangshaChina,Engineering Research Center of Hunan Province in Cognitive Impairment DisordersCentral South UniversityChangshaChina,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic DiseasesChangshaChina,Key Laboratory of Hunan Province in Neurodegenerative DisordersCentral South UniversityChangshaChina
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Leveille E, Ross OA, Gan-Or Z. Tau and MAPT genetics in tauopathies and synucleinopathies. Parkinsonism Relat Disord 2021; 90:142-154. [PMID: 34593302 DOI: 10.1016/j.parkreldis.2021.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
MAPT encodes the microtubule-associated protein tau, which is the main component of neurofibrillary tangles (NFTs) and found in other protein aggregates. These aggregates are among the pathological hallmarks of primary tauopathies such as frontotemporal dementia (FTD). Abnormal tau can also be observed in secondary tauopathies such as Alzheimer's disease (AD) and synucleinopathies such as Parkinson's disease (PD). On top of pathological findings, genetic data also links MAPT to these disorders. MAPT variations are a cause or risk factors for many tauopathies and synucleinopathies and are associated with certain clinical and pathological features in affected individuals. In addition to clinical, pathological, and genetic overlap, evidence also suggests that tau and alpha-synuclein may interact on the molecular level, and thus might collaborate in the neurodegenerative process. Understanding the role of MAPT variations in tauopathies and synucleinopathies is therefore essential to elucidate the role of tau in the pathogenesis and phenotype of those disorders, and ultimately to develop targeted therapies. In this review, we describe the role of MAPT genetic variations in tauopathies and synucleinopathies, several genotype-phenotype and pathological features, and discuss their implications for the classification and treatment of those disorders.
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Affiliation(s)
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA; Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-hospital), McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada; Department of Human Genetics, McGill University, Montréal, QC, Canada.
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Strickland SL, Reddy JS, Allen M, N'songo A, Burgess JD, Corda MM, Ballard T, Wang X, Carrasquillo MM, Biernacka JM, Jenkins GD, Mukherjee S, Boehme K, Crane P, Kauwe JS, Ertekin‐Taner N. MAPT haplotype-stratified GWAS reveals differential association for AD risk variants. Alzheimers Dement 2020; 16:983-1002. [PMID: 32400971 PMCID: PMC7983911 DOI: 10.1002/alz.12099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/26/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION MAPT H1 haplotype is implicated as a risk factor for neurodegenerative diseases including Alzheimer's disease (AD). METHODS Using Alzheimer's Disease Genetics Consortium (ADGC) genome-wide association study (GWAS) data (n = 18,841), we conducted a MAPT H1/H2 haplotype-stratified association to discover MAPT haplotype-specific AD risk loci. RESULTS We identified 11 loci-5 in H2-non-carriers and 6 in H2-carriers-although none of the MAPT haplotype-specific associations achieved genome-wide significance. The most significant H2 non-carrier-specific association was with a NECTIN2 intronic (P = 1.33E-07) variant, and that for H2 carriers was near NKX6-1 (P = 1.99E-06). The GABRG2 locus had the strongest epistasis with MAPT H1/H2 variant rs8070723 (P = 3.91E-06). Eight of the 12 genes at these loci had transcriptome-wide significant differential expression in AD versus control temporal cortex (q < 0.05). Six genes were members of the brain transcriptional co-expression network implicated in "synaptic transmission" (P = 9.85E-59), which is also enriched for neuronal genes (P = 1.0E-164), including MAPT. DISCUSSION This stratified GWAS identified loci that may confer AD risk in a MAPT haplotype-specific manner. This approach may preferentially enrich for neuronal genes implicated in synaptic transmission.
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Affiliation(s)
| | - Joseph S. Reddy
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | - Travis Ballard
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | - Xue Wang
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | | | | | - Paul Crane
- University of WashingtonSeattleWashingtonUSA
| | | | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
- Department of NeurologyMayo ClinicJacksonvilleFloridaUSA
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The puzzle of preserved cognition in the oldest old. Neurol Sci 2019; 41:441-447. [PMID: 31713754 DOI: 10.1007/s10072-019-04111-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
Abstract
Although epidemiological studies predict an exponential increase in the prevalence of dementia with age, recent studies have demonstrated that the oldest old are actually less frequently affected by dementia than the younger elderly. To explain this, I suggest a parallel between brain ageing and Alzheimer's disease (AD) and assume that theories concerning the brain's vulnerability to AD and its individual variability may also explain why some of the oldest old remain cognitively efficient. Some theories argue that AD is due to the continuing presence of the immature neurones vulnerable to amyloid beta protein (Aß) that are normally involved in brain development and then removed as a result of cell selection by the proteins associated with both brain development and AD. If a dysfunction in cell selection allows these immature neurones to survive, they degenerate early as a result of the neurotoxic action of Aß accumulation, which their mature counterparts can withstand. Consequently, age at the time of onset of AD and its clinical presentations depend on the number and location of such immature cells. I speculate that the same mechanism is responsible for the variability of normal brain ageing: the oldest old with well-preserved cognitive function are people genetically programmed for extreme ageing who have benefited from better cell selection during prenatal and neonatal life and therefore have fewer surviving neurones vulnerable to amyloid-promoted degeneration, whereas the process of early life cell selection was less successful in the oldest old who develop dementia.
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Talebi M, Delpak A, Khalaj-Kondori M, Sadigh-Eteghad S, Talebi M, Mehdizadeh E, Majdi A. ABCA7 and EphA1 Genes Polymorphisms in Late-Onset Alzheimer's Disease. J Mol Neurosci 2019; 70:167-173. [PMID: 31659653 DOI: 10.1007/s12031-019-01420-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023]
Abstract
Large-scale genome-wide studies have revealed the role of several genes and their respective single-nucleotide polymorphisms (SNPs) in the pathophysiology of late-onset Alzheimer's disease (LOAD). Here, the frequencies of ABCA7 SNPs rs3764650 and rs4147929 and EphA1 SNP rs11771145 were assessed and compared in LOAD patients and healthy subjects. In a case-control study, 110 patients with LOAD (case) and 88 healthy unrelated age- and gender-matched individuals (control), both from Azeri descent, were enrolled. DNA was extracted from blood samples using the salting out method, and the genotyping was performed by RFLP-PCR for rs3764650, rs4147929, and rs11771145 polymorphisms. Electrophoresis was carried out on agarose gel. Sequencing was utilized for confirmation of the results. No differences were found in the frequencies of ABCA7 SNP rs3764650 and EphA1 SNP rs11771145 between healthy subjects and LOAD patients. However, a significant difference was revealed in the frequencies of AA (p = 0.042, OR = 0.150; 95%CI = 0.005-1.410) and GG (p = 0.009, OR = 1.716; 95%CI = 0.918-3.218) genotypes of ABCA7 SNP rs4147929 between the mentioned groups. This study showed that ABCA7 SNP rs4147929 might be a predisposing factor for LOAD. However, such an association was not found between ABCA7 SNP rs3764650 as well as EphA1 SNP rs11771145 and LOAD. These results must be confirmed in other ethnic groups.
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Affiliation(s)
- Mahnaz Talebi
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Azra Delpak
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saeed Sadigh-Eteghad
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Malihe Talebi
- Health Center of East Azerbaijan Province, Tabriz, Iran
| | - Elham Mehdizadeh
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Majdi
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
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Giau VV, Bagyinszky E, Yang YS, Youn YC, An SSA, Kim SY. Genetic analyses of early-onset Alzheimer's disease using next generation sequencing. Sci Rep 2019; 9:8368. [PMID: 31182772 PMCID: PMC6557896 DOI: 10.1038/s41598-019-44848-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/23/2019] [Indexed: 12/24/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common type of neurodegenerative dementia, but the cause of AD remained poorly understood. Many mutations in the amyloid precursor protein (APP) and presenilin 1 and 2 (PSEN1 and PSEN2) have been reported as the pathogenic causes of early-onset AD (EOAD), which accounts for up to 5% of all AD cases. In this study, we screened familiar/de novo EOAD (n = 67) samples by next-generation sequencing (NGS) of a 50-gene panel, which included causative and possible pathogenic variants linked to neurodegenerative disorders. Remarkably, three missense mutations in PSEN1 (T119I, G209A, and G417A) and one known variant in PSEN2 (H169N) were discovered in 6% of the cases. Additionally, 67 missense mutations in susceptibility genes for late-onset AD were identified, which may be involved in cholesterol transport, inflammatory response, and β-amyloid modulation. We identified 70 additional novel and missense variants in other genes, such as MAPT, GRN, CSF1R, and PRNP, related to neurodegenerative diseases, which may represent overlapping clinical and neuropathological features with AD. Extensive genetic screening of Korean patients with EOAD identified multiple rare variants with potential roles in AD pathogenesis. This study suggests that individuals diagnosed with AD should be screened for other neurodegenerative disease-associated genes. Our findings expand the classic set of genes involved in neurodegenerative pathogenesis, which should be screened for in clinical trials. Main limitation of this study was the absence of functional assessment for possibly and probably pathogenic variants. Additional issues were that we could not perform studies on copy number variants, and we could not verify the segregation of mutations.
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Affiliation(s)
- Vo Van Giau
- Department of Bionano Technology, Gachon University, Seongnam, 13120, South Korea
| | - Eva Bagyinszky
- Department of Bionano Technology, Gachon University, Seongnam, 13120, South Korea
| | - Young Soon Yang
- Department of Neurology, Veterans Health Service Medical Center, Seoul, 05368, South Korea
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University Hospital, Seoul, 06973, South Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon University, Seongnam, 13120, South Korea.
| | - Sang Yun Kim
- Department of Neurology, Seoul National University College of Medicine & Neurocognitive Behavior Center, Seoul National University Bundang Hospital, Seongnam, 13620, South Korea.
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Giau VV, Senanarong V, Bagyinszky E, An SSA, Kim S. Analysis of 50 Neurodegenerative Genes in Clinically Diagnosed Early-Onset Alzheimer's Disease. Int J Mol Sci 2019; 20:E1514. [PMID: 30917570 PMCID: PMC6471359 DOI: 10.3390/ijms20061514] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 01/22/2023] Open
Abstract
Alzheimer's disease (AD), Parkinson's disease (PD), frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), and prion diseases have a certain degree of clinical, pathological, and molecular overlapping. Previous studies revealed that many causative mutations in AD, PD, and FTD/ALS genes could be found in clinical familial and sporadic AD. To further elucidate the missing heritability in early-onset Alzheimer's disease (EOAD), we genetically characterized a Thai EOAD cohort by Next-Generation Sequencing (NGS) with a high depth of coverage, capturing variants in 50 previously recognized AD and other related disorders' genes. A novel mutation, APP p.V604M, and the known causative variant, PSEN1 p.E184G, were found in two of the familiar cases. Remarkably, among 61 missense variants were additionally discovered from 21 genes out of 50 genes, six potential mutations including MAPT P513A, LRRK2 p.R1628P, TREM2 p.L211P, and CSF1R (p.P54Q and pL536V) may be considered to be probably/possibly pathogenic and risk factors for other dementia leading to neuronal degeneration. All allele frequencies of the identified missense mutations were compared to 622 control individuals. Our study provides initial evidence that AD and other neurodegenerative diseases may represent shades of the same disease spectrum, and consideration should be given to offer exactly embracing genetic testing to patients diagnosed with EOAD. Our results need to be further confirmed with a larger cohort from this area.
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Affiliation(s)
- Vo Van Giau
- Department of Bionano Technology, Gachon University, Sungnam 13120, Korea.
| | | | - Eva Bagyinszky
- Department of Bionano Technology, Gachon University, Sungnam 13120, Korea.
| | - Seong Soo A An
- Department of Bionano Technology, Gachon University, Sungnam 13120, Korea.
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine and Neurocognitive Behavior Center, Seoul National University Bundang Hospital, Sungnam 13620, Korea.
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Misra A, Chakrabarti SS, Gambhir IS. New genetic players in late-onset Alzheimer's disease: Findings of genome-wide association studies. Indian J Med Res 2019; 148:135-144. [PMID: 30381536 PMCID: PMC6206761 DOI: 10.4103/ijmr.ijmr_473_17] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD) or sporadic AD is the most common form of AD. The precise pathogenetic changes that trigger the development of AD remain largely unknown. Large-scale genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms in multiple genes which are associated with AD; most notably, these are ABCA7, bridging integrator 1(B1N1), triggering receptor expressed on myeloid cells 2 (TREM2), CD33, clusterin (CLU), complement receptor 1 (CRI), ephrin type-A receptor 1 (EPHA1), membrane-spanning 4-domains, subfamily A (MS4A) and phosphatidylinositol binding clathrin assembly protein (PICALM) genes. The proteins coded by the candidate genes participate in a variety of cellular processes such as oxidative balance, protein metabolism, cholesterol metabolism and synaptic function. This review summarizes the major gene loci affecting LOAD identified by large GWASs. Tentative mechanisms have also been elaborated in various studies by which the proteins coded by these genes may exert a role in AD pathogenesis have also been elaborated. The review suggests that these may together affect LOAD pathogenesis in a complementary fashion.
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Affiliation(s)
- Anamika Misra
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | | | - Indrajeet Singh Gambhir
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Abstract
Within aging societies, the number of individuals suffering from Alzheimer disease (AD) is constistently increasing. This is paralleled by intense research aimed at improving treatment options and potentially even fostering effective prevention. The discussion on relevant outcomes of such interventions is ongoing. Here, different types of currently applied outcomes in the treatment of AD at the dementia stage, but also at the pre-dementia stages of mild cognitive impairment (MCI) and asymptomatic preclinical AD are discussed. Regulatory agencies require effects on the clinical measures of cognition and function. In novel disease-modifying therapy trials, biological markers are used as secondary and exploratory outcomes. Additional outcomes of great relevance for the individual patients are neuropsychiatric symptoms, quality of life, and goal attainment. In addition, costs and cost-benefit ratios are of interest for the reimbursement of interventions.
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Affiliation(s)
- Frank Jessen
- Department of Psychiatry, University of Cologne, Medical Faculty, Cologne, Germany
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12
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Nazarian A, Yashin AI, Kulminski AM. Genome-wide analysis of genetic predisposition to Alzheimer's disease and related sex disparities. ALZHEIMERS RESEARCH & THERAPY 2019; 11:5. [PMID: 30636644 PMCID: PMC6330399 DOI: 10.1186/s13195-018-0458-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common cause of dementia in the elderly and the sixth leading cause of death in the United States. AD is mainly considered a complex disorder with polygenic inheritance. Despite discovering many susceptibility loci, a major proportion of AD genetic variance remains to be explained. METHODS We investigated the genetic architecture of AD in four publicly available independent datasets through genome-wide association, transcriptome-wide association, and gene-based and pathway-based analyses. To explore differences in the genetic basis of AD between males and females, analyses were performed on three samples in each dataset: males and females combined, only males, or only females. RESULTS Our genome-wide association analyses corroborated the associations of several previously detected AD loci and revealed novel significant associations of 35 single-nucleotide polymorphisms (SNPs) outside the chromosome 19q13 region at the suggestive significance level of p < 5E-06. These SNPs were mapped to 21 genes in 19 chromosomal regions. Of these, 17 genes were not associated with AD at genome-wide or suggestive levels of associations by previous genome-wide association studies. Also, the chromosomal regions corresponding to 8 genes did not contain any previously detected AD-associated SNPs with p < 5E-06. Our transcriptome-wide association and gene-based analyses revealed that 26 genes located in 20 chromosomal regions outside chromosome 19q13 had evidence of potential associations with AD at a false discovery rate of 0.05. Of these, 13 genes/regions did not contain any previously AD-associated SNPs at genome-wide or suggestive levels of associations. Most of the newly detected AD-associated SNPs and genes were sex specific, indicating sex disparities in the genetic basis of AD. Also, 7 of 26 pathways that showed evidence of associations with AD in our pathway-bases analyses were significant only in females. CONCLUSIONS Our findings, particularly the newly discovered sex-specific genetic contributors, provide novel insight into the genetic architecture of AD and can advance our understanding of its pathogenesis.
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Affiliation(s)
- Alireza Nazarian
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA.
| | - Anatoliy I Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA.
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Skrobot OA, McKnight AJ, Passmore PA, Seripa D, Mecocci P, Panza F, Kalaria R, Wilcock G, Munafò M, Erkinjuntti T, Karhunen P, Pessi T, Martiskainen M, Love S, Kehoe PG. A Validation Study of Vascular Cognitive Impairment Genetics Meta-Analysis Findings in an Independent Collaborative Cohort. J Alzheimers Dis 2018; 53:981-9. [PMID: 27314523 DOI: 10.3233/jad-150862] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Vascular cognitive impairment (VCI), including its severe form, vascular dementia (VaD), is the second most common form of dementia. The genetic etiology of sporadic VCI remains largely unknown. We previously conducted a systematic review and meta-analysis of all published genetic association studies of sporadic VCI prior to 6 July 2012, which demonstrated that APOE (ɛ4, ɛ2) and MTHFR (rs1801133) variants were associated with susceptibility for VCI. De novo genotyping was conducted in a new independent relatively large collaborative European cohort of VaD (nmax = 549) and elderly non-demented samples (nmax = 552). Where available, genotype data derived from Illumina's 610-quad array for 1210 GERAD1 control samples were also included in analyses of genes examined. Associations were tested using the Cochran-Armitage trend test: MTHFR rs1801133 (OR = 1.36, 95% CI 1.16-1.58, p = <0.0001), APOE rs7412 (OR = 0.62, 95% CI 0.42-0.90, p = 0.01), and APOE rs429358 (OR = 1.59, 95% CI 1.17-2.16, p = 0.003). Association was also observed with APOE epsilon alleles; ɛ4 (OR = 1.85, 95% CI 1.35-2.52, p = <0.0001) and ɛ2 (OR = 0.67, 95% CI 0.46-0.98, p = 0.03). Logistic regression and Bonferroni correction in a subgroup of the cohort adjusted for gender, age, and population maintained the association of APOE rs429358 and ɛ4 allele.
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Affiliation(s)
- Olivia Anna Skrobot
- Dementia Research Group, University of Bristol, Level 1, Learning & Research, Southmead Hospital, Bristol, UK
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Belfast, UK
| | - Peter Anthony Passmore
- Institute of Clinical Sciences, Block B, Queens University Belfast, Royal Victoria Hospital, Belfast, UK
| | - Davide Seripa
- Geriatric Unit & Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences, I.R.C.C.S. "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, University of Perugia, Ospedale S.M. della Misericordia, Perugia, Italy
| | - Francesco Panza
- Geriatric Unit & Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences, I.R.C.C.S. "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy.,Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Policlinico, Bari, Italy
| | - Rajesh Kalaria
- Institute of Neuroscience, NIHR Biomedical Research Building, Campus for Ageing & Vitality Newcastle upon Tyne, UK
| | - Gordon Wilcock
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Headington, Oxford, UK
| | - Marcus Munafò
- MRC Integrative Epidemiology Unit, UK Centre for Tobacco and Alcohol Studies, School of Experimental Psychology, University of Bristol, Bristol, UK
| | - Timo Erkinjuntti
- Department of Neurology and Memory Research Unit, Helsinki University Central Hospital, HUS, Finland
| | - Pekka Karhunen
- School of Medicine, University of Tampere, Finland.,Fimlab Laboratories Ltd, Tampere University Hospital region, Finland
| | - Tanja Pessi
- School of Medicine, University of Tampere, Finland.,Fimlab Laboratories Ltd, Tampere University Hospital region, Finland
| | - Mika Martiskainen
- School of Medicine, University of Tampere, Finland.,Fimlab Laboratories Ltd, Tampere University Hospital region, Finland
| | - Seth Love
- Dementia Research Group, University of Bristol, Level 1, Learning & Research, Southmead Hospital, Bristol, UK
| | | | - Patrick Gavin Kehoe
- Dementia Research Group, University of Bristol, Level 1, Learning & Research, Southmead Hospital, Bristol, UK
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14
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Tang M, Reitz C. Genetics of Alzheimer's disease: an update. FUTURE NEUROLOGY 2017. [DOI: 10.2217/fnl-2017-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is clear that late-onset Alzheimer's disease (AD), the most common form of dementia in western societies, has a significant genetic component. The recent technological advances in high-throughput genome technologies have enabled the identification of more than 20 novel susceptibility loci. These findings have significantly advanced the understanding of the molecular mechanisms potentially underlying AD etiology, and have therefore provided valuable information for the development of targets for genetic testing, prevention and treatment. This article reviews these recent findings in AD genomics and discusses their implications for understanding the molecular underpinnings of the disease.
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Affiliation(s)
- Min Tang
- The Gertrude H Sergievsky Center, Columbia University, 630 West 168th Street, NY 10032, USA
| | - Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, 630 West 168th Street, NY 10032, USA
- The Gertrude H Sergievsky Center, Columbia University, 630 West 168th Street, NY 10032, USA
- The Department of Neurology, Columbia University, NY 10032, USA
- The Department of Epidemiology, Columbia University, NY 10032, USA
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15
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Fernández MV, Kim JH, Budde JP, Black K, Medvedeva A, Saef B, Deming Y, Del-Aguila J, Ibañez L, Dube U, Harari O, Norton J, Chasse R, Morris JC, Goate A, Cruchaga C. Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. PLoS Genet 2017; 13:e1007045. [PMID: 29091718 PMCID: PMC5683650 DOI: 10.1371/journal.pgen.1007045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/13/2017] [Accepted: 09/27/2017] [Indexed: 12/12/2022] Open
Abstract
Alzheimer disease (AD), Frontotemporal lobar degeneration (FTD), Amyotrophic lateral sclerosis (ALS) and Parkinson disease (PD) have a certain degree of clinical, pathological and molecular overlap. Previous studies indicate that causative mutations in AD and FTD/ALS genes can be found in clinical familial AD. We examined the presence of causative and low frequency coding variants in the AD, FTD, ALS and PD Mendelian genes, in over 450 families with clinical history of AD and over 11,710 sporadic cases and cognitive normal participants from North America. Known pathogenic mutations were found in 1.05% of the sporadic cases, in 0.69% of the cognitively normal participants and in 4.22% of the families. A trend towards enrichment, albeit non-significant, was observed for most AD, FTD and PD genes. Only PSEN1 and PINK1 showed consistent association with AD cases when we used ExAC as the control population. These results suggest that current study designs may contain heterogeneity and contamination of the control population, and that current statistical methods for the discovery of novel genes with real pathogenic variants in complex late onset diseases may be inadequate or underpowered to identify genes carrying pathogenic mutations.
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Affiliation(s)
- Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jong Hun Kim
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Neurology, Dementia Center, Ilsan hospital, National Health Insurance Service, Goyang, South Korea
| | - John P. Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alexandra Medvedeva
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Ben Saef
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jorge Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Laura Ibañez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Medical Scientist Training Program, Division of Biology and Biomedical sciences, School of Medicine, Washington University in Saint Louis, St. Louis, MO, United States of America
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Rachel Chasse
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alison Goate
- Ronald M. Loeb Center for Alzheimer’s disease, Dept of Neuroscience, Icahn School of Medicine at Mount Sinai, ICAHN 10–52, New York, NY, United States of America
| | | | | | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States of America
- * E-mail:
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16
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Xie B, Liu Z, Liu W, Jiang L, Zhang R, Cui D, Zhang Q, Xu S. DNA Methylation and Tag SNPs of the BDNF Gene in Conversion of Amnestic Mild Cognitive Impairment into Alzheimer’s Disease: A Cross-Sectional Cohort Study. J Alzheimers Dis 2017; 58:263-274. [PMID: 28387675 DOI: 10.3233/jad-170007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bing Xie
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Zanchao Liu
- Department of Endocrinology, The Second Hospital of Shijiazhuang City, Shijiazhuang, P. R. China
- Department of Endocrinology, The 306th hospital of PLA, Beijing, P. R. China
| | - Wenxuan Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, P. R. China
| | - Lei Jiang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Rui Zhang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Dongsheng Cui
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Qingfu Zhang
- Department of Burns and Plastic Surgery, The First Hospital of Hebei Medical University, Shijiazhuang, P. R. China
- Burn Engineering Center of Hebei Province, Shijiazhuang, P. R. China
| | - Shunjiang Xu
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P. R. China
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17
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Tosto G, Reitz C. Genomics of Alzheimer's disease: Value of high-throughput genomic technologies to dissect its etiology. Mol Cell Probes 2016; 30:397-403. [PMID: 27618776 DOI: 10.1016/j.mcp.2016.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 12/31/2022]
Abstract
Late-onset Alzheimer's disease (AD), the most common neurodegenerative disorder in western countries, is clinically defined by progressive worsening in cognitive functions along with function and behavioral impairment. This ultimately results in complete incapacity and death. AD is a clinically and pathologically heterogeneous disease, and this is reflected by the numerous genetic findings that point to several diverse molecular mechanisms and pathways. Linkage, genome-wide association and next-generation sequencing studies have led to the identification of more than 20 novel susceptibility loci for AD. While these observations have significantly increased the knowledge of pathogenic mechanisms and potential therapeutic targets, a large part of the genetic component underlying AD is still unexplained. This review will summarize and discuss the major genetic findings and their potential impact on AD diagnosis and prediction of prognosis.
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Affiliation(s)
- Giuseppe Tosto
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA; The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA; The Department of Neurology, Columbia University, New York, NY, USA
| | - Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA; The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA; The Department of Neurology, Columbia University, New York, NY, USA; The Dept. of Epidemiology, Columbia University, New York, NY, USA.
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18
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Nho K, Horgusluoglu E, Kim S, Risacher SL, Kim D, Foroud T, Aisen PS, Petersen RC, Jack CR, Shaw LM, Trojanowski JQ, Weiner MW, Green RC, Toga AW, Saykin AJ. Integration of bioinformatics and imaging informatics for identifying rare PSEN1 variants in Alzheimer's disease. BMC Med Genomics 2016; 9 Suppl 1:30. [PMID: 27535542 PMCID: PMC4989889 DOI: 10.1186/s12920-016-0190-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Pathogenic mutations in PSEN1 are known to cause familial early-onset Alzheimer’s disease (EOAD) but common variants in PSEN1 have not been found to strongly influence late-onset AD (LOAD). The association of rare variants in PSEN1 with LOAD-related endophenotypes has received little attention. In this study, we performed a rare variant association analysis of PSEN1 with quantitative biomarkers of LOAD using whole genome sequencing (WGS) by integrating bioinformatics and imaging informatics. Methods A WGS data set (N = 815) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort was used in this analysis. 757 non-Hispanic Caucasian participants underwent WGS from a blood sample and high resolution T1-weighted structural MRI at baseline. An automated MRI analysis technique (FreeSurfer) was used to measure cortical thickness and volume of neuroanatomical structures. We assessed imaging and cerebrospinal fluid (CSF) biomarkers as LOAD-related quantitative endophenotypes. Single variant analyses were performed using PLINK and gene-based analyses of rare variants were performed using the optimal Sequence Kernel Association Test (SKAT-O). Results A total of 839 rare variants (MAF < 1/√(2 N) = 0.0257) were found within a region of ±10 kb from PSEN1. Among them, six exonic (three non-synonymous) variants were observed. A single variant association analysis showed that the PSEN1 p. E318G variant increases the risk of LOAD only in participants carrying APOE ε4 allele where individuals carrying the minor allele of this PSEN1 risk variant have lower CSF Aβ1–42 and higher CSF tau. A gene-based analysis resulted in a significant association of rare but not common (MAF ≥ 0.0257) PSEN1 variants with bilateral entorhinal cortical thickness. Conclusions This is the first study to show that PSEN1 rare variants collectively show a significant association with the brain atrophy in regions preferentially affected by LOAD, providing further support for a role of PSEN1 in LOAD. The PSEN1 p. E318G variant increases the risk of LOAD only in APOE ε4 carriers. Integrating bioinformatics with imaging informatics for identification of rare variants could help explain the missing heritability in LOAD.
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Affiliation(s)
- Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA. .,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA. .,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Emrin Horgusluoglu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shannon L Risacher
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dokyoon Kim
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Tatiana Foroud
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Paul S Aisen
- Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Clifford R Jack
- Department of Radiology, Mayo Clinic Minnesota, Rochester, MN, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Michael W Weiner
- Departments of Radiology, Medicine, and Psychiatry, University of California-San Francisco, San Francisco, CA, USA.,Department of Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arthur W Toga
- The Institute for Neuroimaging and Informatics and Laboratory of Neuro Imaging, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA. .,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA. .,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA.
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19
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Suzuki A, Shibata N, Kasanuki K, Nagata T, Shinagawa S, Kobayashi N, Ohnuma T, Takeshita Y, Kawai E, Takayama T, Nishioka K, Motoi Y, Hattori N, Nakayama K, Yamada H, Arai H. Genetic Association between Presenilin 2 Polymorphisms and Alzheimer's Disease and Dementia of Lewy Body Type in a Japanese Population. Dement Geriatr Cogn Dis Extra 2016; 6:90-7. [PMID: 27065294 PMCID: PMC4821141 DOI: 10.1159/000444080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background/Aims Mutations in the presenilin 2 (PSEN2) gene cause familial Alzheimer's disease (AD). Common polymorphisms affect gene activity and increase the risk of AD. Nonsynonymous polymorphisms in the PSEN2 gene showed Lewy body dementia (LBD) phenotypes clinically. Therefore, we aimed to investigate whether PSEN2 gene polymorphisms were associated with AD or LBD. Methods Seven single nucleotide polymorphisms (SNPs) of the gene were analyzed using a case-control study design comprising 288 AD patients, 76 LBD patients, and 105 age-matched controls. Results Linkage disequilibrium (LD) examination showed strong LD from rs1295645 to rs8383 on the gene in our cases from Japan. There were no associations between the SNPs studied here and AD onset, and haplotypic analyses did not detect genetic associations between AD and the PSEN2 gene. Although the number of the cases was small, the SNPs studied did not modify the risk of developing LBD in a Japanese population. Conclusion The common SNPs of the PSEN2 gene did not affect the risk of AD or LBD in a Japanese population. Because genetic variability of the PSEN2 gene is associated with behavioral and psychological symptoms of dementia (BPSD) in AD and LBD, further detailed analyses considering BPSD of both diseases would be required.
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Affiliation(s)
- Ayako Suzuki
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Nobuto Shibata
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Koji Kasanuki
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Tomoyuki Nagata
- Department of Psychiatry, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan; Division of Molecular Genetics, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Shunichiro Shinagawa
- Department of Psychiatry, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Nobuyuki Kobayashi
- Department of Psychiatry, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Tohru Ohnuma
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Yoshihide Takeshita
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Eri Kawai
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Toshiki Takayama
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Kenya Nishioka
- Departments of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Yumiko Motoi
- Departments of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Nobutaka Hattori
- Departments of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Kazuhiko Nakayama
- Department of Psychiatry, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Hisashi Yamada
- Division of Molecular Genetics, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Heii Arai
- Departments of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
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20
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Abstract
Late-onset Alzheimer's disease (AD), a highly prevalent neurodegenerative disorder characterized by progressive deterioration in cognition, function and behavior terminating in incapacity and death, is a clinically and pathologically heterogeneous disease with a substantial heritable component. During the past 5 years, the technological developments in next-generation high-throughput genome technologies have led to the identification of more than 20 novel susceptibility loci for AD, and have implicated specific pathways in the disease, in particular intracellular trafficking/endocytosis, inflammation and immune response and lipid metabolism. These observations have significantly advanced our understanding of underlying pathogenic mechanisms and potential therapeutic targets. This review article summarizes these recent advances in AD genomics and discusses the value of identified susceptibility loci for diagnosis and prognosis of AD.
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21
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Desikan RS, Schork AJ, Wang Y, Witoelar A, Sharma M, McEvoy LK, Holland D, Brewer JB, Chen CH, Thompson WK, Harold D, Williams J, Owen MJ, O’Donovan MC, Pericak-Vance MA, Mayeux R, Haines JL, Farrer LA, Schellenberg GD, Heutink P, Singleton AB, Brice A, Wood NW, Hardy J, Martinez M, Choi SH, DeStefano A, Ikram MA, Bis JC, Smith A, Fitzpatrick AL, Launer L, van Duijn C, Seshadri S, Ulstein ID, Aarsland D, Fladby T, Djurovic S, Hyman BT, Snaedal J, Stefansson H, Stefansson K, Gasser T, Andreassen OA, Dale AM. Genetic overlap between Alzheimer's disease and Parkinson's disease at the MAPT locus. Mol Psychiatry 2015; 20:1588-95. [PMID: 25687773 PMCID: PMC4539304 DOI: 10.1038/mp.2015.6] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/29/2014] [Accepted: 01/08/2015] [Indexed: 12/18/2022]
Abstract
We investigated the genetic overlap between Alzheimer's disease (AD) and Parkinson's disease (PD). Using summary statistics (P-values) from large recent genome-wide association studies (GWAS) (total n=89 904 individuals), we sought to identify single nucleotide polymorphisms (SNPs) associating with both AD and PD. We found and replicated association of both AD and PD with the A allele of rs393152 within the extended MAPT region on chromosome 17 (meta analysis P-value across five independent AD cohorts=1.65 × 10(-7)). In independent datasets, we found a dose-dependent effect of the A allele of rs393152 on intra-cerebral MAPT transcript levels and volume loss within the entorhinal cortex and hippocampus. Our findings identify the tau-associated MAPT locus as a site of genetic overlap between AD and PD, and extending prior work, we show that the MAPT region increases risk of Alzheimer's neurodegeneration.
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Affiliation(s)
- Rahul S. Desikan
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA,Correspondence should be addressed to: Drs. Rahul S. Desikan and Anders M. Dale, Department of Radiology, University of California, San Diego, 8950 Villa La Jolla Drive, Suite C101, La Jolla, CA, USA 92037-0841, , , Phone: (858)-822-6671, Fax: (858)-534-1078, Dr. Ole A. Andreassen: KG Jebsen Centre for Psychosis Research, Building 49, Oslo University Hospital, Ullevål, Kirkeveien 166, PO Box 4956 Nydalen, 0424 Oslo, Norway, , Ph: +47 23 02 73 50 (22 11 78 43 dir), Fax: +47 23 02 73 33
| | - Andrew J. Schork
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Yunpeng Wang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA,NORMENT; Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Aree Witoelar
- NORMENT; Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Manu Sharma
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research University of Tubingen, Germany,Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Germany
| | - Linda K. McEvoy
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
| | - Dominic Holland
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - James B. Brewer
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA,Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Chi-Hua Chen
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA,Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Wesley K. Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Denise Harold
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Wales
| | - Julie Williams
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Wales
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Wales
| | - Michael C. O’Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Wales
| | | | - Richard Mayeux
- Department of Neurology, Taub Institute on Alzheimer's Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
| | - Jonathan L. Haines
- Department of Molecular Physiology and Biophysics, Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Biostatistics, and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Paul-Ehrlich-Straße 15, 72076 Tübingen, Germany
| | | | - Alexis Brice
- Sorbonne Université, UPMC Univ Paris 06, UM 75, ICM; Inserm, U 1127, ICM; Cnrs, UMR 7225, ICM; ICM, Paris, F-75013 Paris, France
| | - Nicolas W. Wood
- UCL Genetics Institute; and Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Seung Hoi Choi
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Anita DeStefano
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA,The National Heart Lung and Blood Institute’s Framingham Heart Study, Framingham, MA
| | - M. Arfan Ikram
- Deparment of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Joshua C. Bis
- Deparment of Internal Medicine, University of Washington, Seattle, WA, USA
| | | | | | - Lenore Launer
- Laboratory of Epidemiology, Demography and Biometry, Intramural Research Program, National Institute on Aging, Washington, DC, USA
| | - Cornelia van Duijn
- Deparment of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA,The National Heart Lung and Blood Institute’s Framingham Heart Study, Framingham, MA
| | - Ingun Dina Ulstein
- Norwegian Centre for Dementia Research, Department of Old Age Psychiatry, Oslo University Hospital, Oslo, Norway
| | - Dag Aarsland
- Alzheimer’s Disease Research Centre, Department of Neurobiology, Care Sciences and Society, Karolinska Institute, Stockholm, Sweden; Centre for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway; Department of Geriatric Psychiatry, Akershus University Hospital, Oslo, Norway
| | - Tormod Fladby
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Neurology, Akershus University Hospital, Norway
| | - Srdjan Djurovic
- NORMENT; Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bradley T. Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Jon Snaedal
- Department of Geriatric Medicine, University Hospital Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Thomas Gasser
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research University of Tubingen, Germany
| | - Ole A. Andreassen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA,NORMENT; Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Correspondence should be addressed to: Drs. Rahul S. Desikan and Anders M. Dale, Department of Radiology, University of California, San Diego, 8950 Villa La Jolla Drive, Suite C101, La Jolla, CA, USA 92037-0841, , , Phone: (858)-822-6671, Fax: (858)-534-1078, Dr. Ole A. Andreassen: KG Jebsen Centre for Psychosis Research, Building 49, Oslo University Hospital, Ullevål, Kirkeveien 166, PO Box 4956 Nydalen, 0424 Oslo, Norway, , Ph: +47 23 02 73 50 (22 11 78 43 dir), Fax: +47 23 02 73 33
| | - Anders M. Dale
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA,Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA,Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA,Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA,Correspondence should be addressed to: Drs. Rahul S. Desikan and Anders M. Dale, Department of Radiology, University of California, San Diego, 8950 Villa La Jolla Drive, Suite C101, La Jolla, CA, USA 92037-0841, , , Phone: (858)-822-6671, Fax: (858)-534-1078, Dr. Ole A. Andreassen: KG Jebsen Centre for Psychosis Research, Building 49, Oslo University Hospital, Ullevål, Kirkeveien 166, PO Box 4956 Nydalen, 0424 Oslo, Norway, , Ph: +47 23 02 73 50 (22 11 78 43 dir), Fax: +47 23 02 73 33
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22
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Abstract
Alzheimer's disease (AD) represents the main form of dementia, and is a major public health problem. Despite intensive research efforts, current treatments have only marginal symptomatic benefits and there are no effective disease-modifying or preventive interventions. AD has a strong genetic component, so much research in AD has focused on identifying genetic causes and risk factors. This chapter will cover genetic discoveries in AD and their consequences in terms of improved knowledge regarding the disease and the identification of biomarkers and drug targets. First, we will discuss the study of the rare early-onset, autosomal dominant forms of AD that led to the discovery of mutations in three major genes, APP, PSEN1, and PSEN2. These discoveries have shaped our current understanding of the pathophysiology and natural history of AD as well as the development of therapeutic targets and the design of clinical trials. Then, we will explore linkage analysis and candidate gene approaches, which identified variants in Apolipoprotein E (APOE) as the major genetic risk factor for late-onset, "sporadic" forms of AD (LOAD), but failed to robustly identify other genetic risk factors, with the exception of variants in SORL1. The main focus of this chapter will be on recent genome-wide association studies that have successfully identified common genetic variations at over 20 loci associated with LOAD outside of the APOE locus. These loci are in or near-novel AD genes including BIN1, CR1, CLU, phosphatidylinositol-binding clathrin assembly protein (PICALM), CD33, EPHA1, MS4A4/MS4A6, ABCA7, CD2AP, SORL1, HLA-DRB5/DRB1, PTK2B, SLC24A4-RIN3, INPP5D, MEF2C, NME8, ZCWPW1, CELF1, FERMT2, CASS4, and TRIP4 and each has small effects on risk of AD (relative risks of 1.1-1.3). Finally, we will touch upon the ongoing effort to identify less frequent and rare variants through whole exome and whole genome sequencing. This effort has identified two novel genes, TREM2 and PLD3, and shown a role for APP in LOAD. The identification of these recently identified genes has implicated previously unsuspected biological pathways in the pathophysiology of AD.
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Affiliation(s)
- Vincent Chouraki
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Framingham Heart Study, Framingham, MA, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Framingham Heart Study, Framingham, MA, USA
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23
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Gan-Or Z, Dion PA, Rouleau GA. Genetic perspective on the role of the autophagy-lysosome pathway in Parkinson disease. Autophagy 2015; 11:1443-57. [PMID: 26207393 PMCID: PMC4590678 DOI: 10.1080/15548627.2015.1067364] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/10/2015] [Accepted: 06/24/2015] [Indexed: 02/09/2023] Open
Abstract
Parkinson disease (PD), once considered as a prototype of a sporadic disease, is now known to be considerably affected by various genetic factors, which interact with environmental factors and the normal process of aging, leading to PD. Large studies determined that the hereditary component of PD is at least 27%, and in some populations, single genetic factors are responsible for more than 33% of PD patients. Interestingly, many of these genetic factors, such as LRRK2, GBA, SMPD1, SNCA, PARK2, PINK1, PARK7, SCARB2, and others, are involved in the autophagy-lysosome pathway (ALP). Some of these genes encode lysosomal enzymes, whereas others correspond to proteins that are involved in transport to the lysosome, mitophagy, or other autophagic-related functions. Is it possible that all these factors converge into a single pathway that causes PD? In this review, we will discuss these genetic findings and the role of the ALP in the pathogenesis of PD and will try to answer this question. We will suggest a novel hypothesis for the pathogenic mechanism of PD that involves the lysosome and the different autophagy pathways.
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Affiliation(s)
- Ziv Gan-Or
- The Department of Human Genetics; McGill University; Montreal, QC Canada
- Montreal Neurological Institute; McGill University; Montreal, QC Canada
| | - Patrick A Dion
- The Department of Human Genetics; McGill University; Montreal, QC Canada
- Montreal Neurological Institute; McGill University; Montreal, QC Canada
- The Department of Neurology & Neurosurgery; McGill University; Montreal, QC Canada
| | - Guy A Rouleau
- The Department of Human Genetics; McGill University; Montreal, QC Canada
- Montreal Neurological Institute; McGill University; Montreal, QC Canada
- The Department of Neurology & Neurosurgery; McGill University; Montreal, QC Canada
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24
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Abstract
Loss of memory is among the first symptoms reported by patients suffering from Alzheimer's disease (AD) and by their caretakers. Working memory and long-term declarative memory are affected early during the course of the disease. The individual pattern of impaired memory functions correlates with parameters of structural or functional brain integrity. AD pathology interferes with the formation of memories from the molecular level to the framework of neural networks. The investigation of AD memory loss helps to identify the involved neural structures, such as the default mode network, the influence of epigenetic and genetic factors, such as ApoE4 status, and evolutionary aspects of human cognition. Clinically, the analysis of memory assists the definition of AD subtypes, disease grading, and prognostic predictions. Despite new AD criteria that allow the earlier diagnosis of the disease by inclusion of biomarkers derived from cerebrospinal fluid or hippocampal volume analysis, neuropsychological testing remains at the core of AD diagnosis.
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Affiliation(s)
- Holger Jahn
- University Hospital Hamburg-Eppendorf, Dept of Psychiatry and Psychotherapy, Hamburg, Germany
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25
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Khabirova E, Moloney A, Marciniak SJ, Williams J, Lomas DA, Oliver SG, Favrin G, Sattelle DB, Crowther DC. The TRiC/CCT chaperone is implicated in Alzheimer's disease based on patient GWAS and an RNAi screen in Aβ-expressing Caenorhabditis elegans. PLoS One 2014; 9:e102985. [PMID: 25080104 PMCID: PMC4117641 DOI: 10.1371/journal.pone.0102985] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/25/2014] [Indexed: 01/02/2023] Open
Abstract
The human Aβ peptide causes progressive paralysis when expressed in the muscles of the nematode worm, C. elegans. We have exploited this model of Aβ toxicity by carrying out an RNAi screen to identify genes whose reduced expression modifies the severity of this locomotor phenotype. Our initial finding was that none of the human orthologues of these worm genes is identical with the genome-wide significant GWAS genes reported to date (the “white zone”); moreover there was no identity between worm screen hits and the longer list of GWAS genes which included those with borderline levels of significance (the “grey zone”). This indicates that Aβ toxicity should not be considered as equivalent to sporadic AD. To increase the sensitivity of our analysis, we then considered the physical interactors (+1 interactome) of the products of the genes in both the worm and the white+grey zone lists. When we consider these worm and GWAS gene lists we find that 4 of the 60 worm genes have a +1 interactome overlap that is larger than expected by chance. Two of these genes form a chaperonin complex, the third is closely associated with this complex and the fourth gene codes for actin, the major substrate of the same chaperonin.
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Affiliation(s)
- Eleonora Khabirova
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Aileen Moloney
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Stefan J. Marciniak
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Julie Williams
- Department of Psychiatry and Neurology, MRC Centre for Neuropsychiatric Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David A. Lomas
- Department of Medicine, University College London, London, United Kingdom
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (SGO); (DCC)
| | - Giorgio Favrin
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - David B. Sattelle
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- The Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Damian C. Crowther
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (SGO); (DCC)
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26
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Allen M, Kachadoorian M, Quicksall Z, Zou F, Chai HS, Younkin C, Crook JE, Pankratz VS, Carrasquillo MM, Krishnan S, Nguyen T, Ma L, Malphrus K, Lincoln S, Bisceglio G, Kolbert CP, Jen J, Mukherjee S, Kauwe JK, Crane PK, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD, Parisi JE, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. Association of MAPT haplotypes with Alzheimer's disease risk and MAPT brain gene expression levels. ALZHEIMERS RESEARCH & THERAPY 2014; 6:39. [PMID: 25324900 PMCID: PMC4198935 DOI: 10.1186/alzrt268] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/28/2014] [Indexed: 01/01/2023]
Abstract
Introduction MAPT encodes for tau, the predominant component of neurofibrillary tangles that are neuropathological hallmarks of Alzheimer’s disease (AD). Genetic association of MAPT variants with late-onset AD (LOAD) risk has been inconsistent, although insufficient power and incomplete assessment of MAPT haplotypes may account for this. Methods We examined the association of MAPT haplotypes with LOAD risk in more than 20,000 subjects (n-cases = 9,814, n-controls = 11,550) from Mayo Clinic (n-cases = 2,052, n-controls = 3,406) and the Alzheimer’s Disease Genetics Consortium (ADGC, n-cases = 7,762, n-controls = 8,144). We also assessed associations with brain MAPT gene expression levels measured in the cerebellum (n = 197) and temporal cortex (n = 202) of LOAD subjects. Six single nucleotide polymorphisms (SNPs) which tag MAPT haplotypes with frequencies greater than 1% were evaluated. Results H2-haplotype tagging rs8070723-G allele associated with reduced risk of LOAD (odds ratio, OR = 0.90, 95% confidence interval, CI = 0.85-0.95, p = 5.2E-05) with consistent results in the Mayo (OR = 0.81, p = 7.0E-04) and ADGC (OR = 0.89, p = 1.26E-04) cohorts. rs3785883-A allele was also nominally significantly associated with LOAD risk (OR = 1.06, 95% CI = 1.01-1.13, p = 0.034). Haplotype analysis revealed significant global association with LOAD risk in the combined cohort (p = 0.033), with significant association of the H2 haplotype with reduced risk of LOAD as expected (p = 1.53E-04) and suggestive association with additional haplotypes. MAPT SNPs and haplotypes also associated with brain MAPT levels in the cerebellum and temporal cortex of AD subjects with the strongest associations observed for the H2 haplotype and reduced brain MAPT levels (β = -0.16 to -0.20, p = 1.0E-03 to 3.0E-03). Conclusions These results confirm the previously reported MAPT H2 associations with LOAD risk in two large series, that this haplotype has the strongest effect on brain MAPT expression amongst those tested and identify additional haplotypes with suggestive associations, which require replication in independent series. These biologically congruent results provide compelling evidence to screen the MAPT region for regulatory variants which confer LOAD risk by influencing its brain gene expression.
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Affiliation(s)
- Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | | | - Zachary Quicksall
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Fanggeng Zou
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - High Seng Chai
- Department of Health Sciences Research, Mayo Clinic Minnesota, Rochester, MN 55905, USA
| | - Curtis Younkin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - V Shane Pankratz
- Department of Health Sciences Research, Mayo Clinic Minnesota, Rochester, MN 55905, USA
| | | | - Siddharth Krishnan
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Li Ma
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Kimberly Malphrus
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Sarah Lincoln
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Gina Bisceglio
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | | | - Jin Jen
- Medical Genome Facility, Mayo Clinic Minnesota, Rochester, MN 55905, USA
| | | | - John K Kauwe
- Departments of Biology, Neuroscience, Brigham Young University, Provo, UT 84602, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle 98104, WA, USA
| | - Jonathan L Haines
- Department of Molecular Physiology and Biophysics, and the Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA ; Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Richard Mayeux
- Gertrude H. Sergievsky Center, Department of Neurology, and Taub Institute on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Lindsay A Farrer
- Departments of Biostatistics, Medicine (Genetics Program), Ophthalmology, Neurology, and Epidemiology, Boston University, Boston, MA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Joseph E Parisi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ronald C Petersen
- Department of Neurology, Mayo Clinic Minnesota, Rochester, MN 55905, USA
| | - Neill R Graff-Radford
- Department of Neurology, Mayo Clinic Florida, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Steven G Younkin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA ; Department of Neurology, Mayo Clinic Florida, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224, USA
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27
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Wang J, Bi W, Cheng A, Freire D, Vempati P, Zhao W, Gong B, Janle EM, Chen TY, Ferruzzi MG, Schmeidler J, Ho L, Pasinetti GM. Targeting multiple pathogenic mechanisms with polyphenols for the treatment of Alzheimer's disease-experimental approach and therapeutic implications. Front Aging Neurosci 2014; 6:42. [PMID: 24672477 PMCID: PMC3954102 DOI: 10.3389/fnagi.2014.00042] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/26/2014] [Indexed: 01/13/2023] Open
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease of aging and currently has no cure. Its onset and progression are influenced by multiple factors. There is growing consensus that successful treatment will rely on simultaneously targeting multiple pathological features of AD. Polyphenol compounds have many proven health benefits. In this study, we tested the hypothesis that combining three polyphenolic preparations (grape seed extract, resveratrol, and Concord grape juice extract), with different polyphenolic compositions and partially redundant bioactivities, may simultaneously and synergistically mitigate amyloid-β (Aβ) mediated neuropathology and cognitive impairments in a mouse model of AD. We found that administration of the polyphenols in combination did not alter the profile of bioactive polyphenol metabolites in the brain. We also found that combination treatment resulted in better protection against cognitive impairments compared to individual treatments, in J20 AD mice. Electrophysiological examination showed that acute treatment with select brain penetrating polyphenol metabolites, derived from these polyphenols, improved oligomeric Aβ (oAβ)-induced long term potentiation (LTP) deficits in hippocampal slices. Moreover, we found greatly reduced total amyloid content in the brain following combination treatment. Our studies provided experimental evidence that application of polyphenols targeting multiple disease-mechanisms may yield a greater likelihood of therapeutic efficacy.
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Affiliation(s)
- Jun Wang
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA ; Geriatric Research, Education and Clinical Center, James J. Peters Veterans Affairs Medical Center Bronx, NY, USA
| | - Weina Bi
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Alice Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Daniel Freire
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Prashant Vempati
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Wei Zhao
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Bing Gong
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Elsa M Janle
- Departments of Food Science and Foods and Nutrition, Purdue University West Lafayette, IN, USA
| | - Tzu-Ying Chen
- Departments of Food Science and Foods and Nutrition, Purdue University West Lafayette, IN, USA
| | - Mario G Ferruzzi
- Departments of Food Science and Foods and Nutrition, Purdue University West Lafayette, IN, USA
| | - James Schmeidler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Lap Ho
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Giulio M Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai New York, NY, USA ; Geriatric Research, Education and Clinical Center, James J. Peters Veterans Affairs Medical Center Bronx, NY, USA
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28
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Roses AD, Saunders AM, Lutz MW, Zhang N, Hariri AR, Asin KE, Crenshaw DG, Budur K, Burns DK, Brannan SK. New applications of disease genetics and pharmacogenetics to drug development. Curr Opin Pharmacol 2014; 14:81-9. [PMID: 24565016 DOI: 10.1016/j.coph.2013.12.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 11/28/2022]
Abstract
TOMMORROW is a Phase III delay of onset clinical trial to determine whether low doses of pioglitazone, a molecule that induces mitochondrial doubling, delays the onset of MCI-AD in normal subjects treated with low dose compared to placebo. BOLD imaging studies in rodents and man were used to find the dose that increases oxygen consumption at central regions of the brain in higher proportion than activation of large corticol regions. The trial is made practical by the use of a pharmacogenetic algorithm based on TOMM40 and APOE genotypes and age to identify normal subjects at high risk of MCI-AD between the ages of 65-83 years within a five year follow-up period.
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Affiliation(s)
- Allen D Roses
- Zinfandel Pharmaceuticals, Inc., Durham, NC, United States; Duke University Medical Center, Department of Neurology, Durham, NC, United States.
| | - Ann M Saunders
- Duke University Medical Center, Department of Neurology, Durham, NC, United States
| | - Michael W Lutz
- Duke University Medical Center, Department of Neurology, Durham, NC, United States
| | - Nanyin Zhang
- Pennsylvania State University, Department of Biomedical Engineering, State College, PA, United States
| | - Ahmad R Hariri
- Duke University Medical Center, Department of Neurology, Durham, NC, United States
| | - Karen E Asin
- Takeda Pharmaceuticals, Deerfield, IL, United States
| | | | - Kumar Budur
- Takeda Pharmaceuticals, Deerfield, IL, United States
| | - Daniel K Burns
- Zinfandel Pharmaceuticals, Inc., Durham, NC, United States
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29
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Boudreau RL, Jiang P, Gilmore BL, Spengler RM, Tirabassi R, Nelson JA, Ross CA, Xing Y, Davidson BL. Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron 2014; 81:294-305. [PMID: 24389009 DOI: 10.1016/j.neuron.2013.10.062] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2013] [Indexed: 12/15/2022]
Abstract
The orchestration of brain function requires complex gene regulatory networks that are modulated, in part, by microRNAs (miRNAs). These noncoding RNAs associate with argonaute (Ago) proteins in order to direct posttranscriptional gene suppression via base pairing with target transcripts. In order to better understand how miRNAs contribute to human-specialized brain processes and neurological phenotypes, identifying their targets is of paramount importance. Here, we address the latter by profiling Ago2:RNA interactions using HITS-CLIP to generate a transcriptome-wide map of miRNA binding sites in human brain. We uncovered ∼ 7,000 stringent Ago2 binding sites that are highly enriched for conserved sequences corresponding to abundant brain miRNAs. This interactome points to functional miRNA:target pairs across >3,000 genes and represents a valuable resource for accelerating our understanding of miRNA functions in brain. We demonstrate the utility of this map for exploring clinically relevant miRNA binding sites that may facilitate the translation of genetic studies of complex neuropsychiatric diseases into therapeutics.
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Affiliation(s)
- Ryan L Boudreau
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Peng Jiang
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Brian L Gilmore
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Ryan M Spengler
- Program in Molecular and Cellular Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Rebecca Tirabassi
- Vaccine and Gene Therapy Institute, Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | - Jay A Nelson
- Vaccine and Gene Therapy Institute, Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | - Christopher A Ross
- Division of Neurobiology; Departments of Psychiatry, Neurology Neuroscience, and Pharmacology; and Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yi Xing
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Beverly L Davidson
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Neurology, University of Iowa, Iowa City, IA 52242, USA; Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Program in Molecular and Cellular Biology, University of Iowa, Iowa City, IA 52242, USA.
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Combarros O. Genetic Risk Factors for Alzheimer’s Disease. NEURODEGENER DIS 2014. [DOI: 10.1007/978-1-4471-6380-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Mohamed NV, Herrou T, Plouffe V, Piperno N, Leclerc N. Spreading of tau pathology in Alzheimer's disease by cell-to-cell transmission. Eur J Neurosci 2013; 37:1939-48. [PMID: 23773063 DOI: 10.1111/ejn.12229] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 11/28/2022]
Abstract
It is well documented that neurofibrillary tangles composed of aggregated tau protein propagate in a predictable pattern in Alzheimer's disease (AD). The mechanisms underlying the propagation of tau pathology are still poorly understood. Recent studies have provided solid data demonstrating that in several neurodegenerative diseases including AD, the spreading of misfolded protein aggregates in the brain would result from prion-like cell-to-cell transmission. Consistent with this new concept, recent studies have reported that human tau can be released in the extracellular space by an active process of secretion, and can be endocytosed both in vitro and in vivo. Most importantly, it was reported that the spreading of tau pathology was observed along synaptically connected circuits in a transgenic mouse model where human tau overexpression was restricted in the entorhinal cortex. This indicates that secretion of tau by presynaptic neurons and its uptake by postsynaptic neurons could be the sequential events leading to the propagation of tau pathology in the brain.
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Affiliation(s)
- Nguyen-Vi Mohamed
- Département de pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada
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Familial Alzheimer's disease coding mutations reduce Presenilin-1 expression in a novel genomic locus reporter model. Neurobiol Aging 2013; 35:443.e5-443.e16. [PMID: 24011544 DOI: 10.1016/j.neurobiolaging.2013.07.026] [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: 06/18/2013] [Revised: 07/28/2013] [Accepted: 07/31/2013] [Indexed: 01/13/2023]
Abstract
We have generated a physiologically relevant bacterial artificial chromosome (BAC)-based genomic DNA expression model to study PS1 gene expression and function. The PS1-WT-BAC construct restored γ-secretase function, whereas the mutant PS1 BACs demonstrated partial to complete loss of enzymatic activity when stably expressed in a PS double knock-out clonal cell line. We then engineered WT and mutant human PS1-BAC-Luciferase whole genomic locus reporter transgenes, which we transiently transduced in mouse and human non-neuronal and neuronal-like cells, respectively. PS1 ΔE9 and C410Y FAD were found to lower PS1 gene expression in both cell lines, whereas PS1-M146V showed a neuron-specific effect. The nonclinical γ-secretase inactive PS1-D257A mutation did not alter gene expression in either cell line. This is the first time that pathogenic coding mutations in the PS1 gene have been shown to lower PS1 gene expression. These findings may represent a pathologic mechanism for PS1 FAD mutations independent of their effects on γ-secretase activity and demonstrate how dominant PS1 mutations may exert their pathogenic effects by a loss-of-function mechanism.
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Benitez BA, Karch CM, Cai Y, Jin SC, Cooper B, Carrell D, Bertelsen S, Chibnik L, Schneider JA, Bennett DA, Fagan AM, Holtzman D, Morris JC, Goate AM, Cruchaga C. The PSEN1, p.E318G variant increases the risk of Alzheimer's disease in APOE-ε4 carriers. PLoS Genet 2013; 9:e1003685. [PMID: 23990795 PMCID: PMC3750021 DOI: 10.1371/journal.pgen.1003685] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/14/2013] [Indexed: 01/18/2023] Open
Abstract
The primary constituents of plaques (Aβ42/Aβ40) and neurofibrillary tangles (tau and phosphorylated forms of tau [ptau]) are the current leading diagnostic and prognostic cerebrospinal fluid (CSF) biomarkers for AD. In this study, we performed deep sequencing of APP, PSEN1, PSEN2, GRN, APOE and MAPT genes in individuals with extreme CSF Aβ42, tau, or ptau levels. One known pathogenic mutation (PSEN1 p.A426P), four high-risk variants for AD (APOE p.L46P, MAPT p.A152T, PSEN2 p.R62H and p.R71W) and nine novel variants were identified. Surprisingly, a coding variant in PSEN1, p.E318G (rs17125721-G) exhibited a significant association with high CSF tau (p = 9.2 × 10(-4)) and ptau (p = 1.8 × 10(-3)) levels. The association of the p.E318G variant with Aβ deposition was observed in APOE-ε4 allele carriers. Furthermore, we found that in a large case-control series (n = 5,161) individuals who are APOE-ε4 carriers and carry the p.E318G variant are at a risk of developing AD (OR = 10.7, 95% CI = 4.7-24.6) that is similar to APOE-ε4 homozygous (OR = 9.9, 95% CI = 7.2.9-13.6), and double the risk for APOE-ε4 carriers that do not carry p.E318G (OR = 3.9, 95% CI = 3.4-4.4). The p.E318G variant is present in 5.3% (n = 30) of the families from a large clinical series of LOAD families (n = 565) and exhibited a higher frequency in familial LOAD (MAF = 2.5%) than in sporadic LOAD (MAF = 1.6%) (p = 0.02). Additionally, we found that in the presence of at least one APOE-ε4 allele, p.E318G is associated with more Aβ plaques and faster cognitive decline. We demonstrate that the effect of PSEN1, p.E318G on AD susceptibility is largely dependent on an interaction with APOE-ε4 and mediated by an increased burden of Aβ deposition.
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Affiliation(s)
- Bruno A. Benitez
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Celeste M. Karch
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Yefei Cai
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Sheng Chih Jin
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Breanna Cooper
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - David Carrell
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Sarah Bertelsen
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Lori Chibnik
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard University and M.I.T., Cambridge, Massachusetts, United States of America
| | - Julie A. Schneider
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - David A. Bennett
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | | | | | - Anne M. Fagan
- Department of Neurology, School of Medicine, Washington University, St. Louis, Missouri, United States of America
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University St. Louis, Missouri, United States of America
| | - David Holtzman
- Department of Neurology, School of Medicine, Washington University, St. Louis, Missouri, United States of America
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University St. Louis, Missouri, United States of America
| | - John C. Morris
- Department of Neurology, School of Medicine, Washington University, St. Louis, Missouri, United States of America
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University St. Louis, Missouri, United States of America
| | - Alison M. Goate
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
- Department of Neurology, School of Medicine, Washington University, St. Louis, Missouri, United States of America
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University St. Louis, Missouri, United States of America
- Department of Genetics, School of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Carlos Cruchaga
- Department of Psychiatry, School of Medicine, Washington University, St. Louis, Missouri, United States of America
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University St. Louis, Missouri, United States of America
- * E-mail:
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Leidinger P, Backes C, Deutscher S, Schmitt K, Mueller SC, Frese K, Haas J, Ruprecht K, Paul F, Stähler C, Lang CJG, Meder B, Bartfai T, Meese E, Keller A. A blood based 12-miRNA signature of Alzheimer disease patients. Genome Biol 2013; 14:R78. [PMID: 23895045 PMCID: PMC4053778 DOI: 10.1186/gb-2013-14-7-r78] [Citation(s) in RCA: 351] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 07/29/2013] [Indexed: 01/06/2023] Open
Abstract
Background Alzheimer disease (AD) is the most common form of dementia but the identification of reliable, early and non-invasive biomarkers remains a major challenge. We present a novel miRNA-based signature for detecting AD from blood samples. Results We apply next-generation sequencing to miRNAs from blood samples of 48 AD patients and 22 unaffected controls, yielding a total of 140 unique mature miRNAs with significantly changed expression levels. Of these, 82 have higher and 58 have lower abundance in AD patient samples. We selected a panel of 12 miRNAs for an RT-qPCR analysis on a larger cohort of 202 samples, comprising not only AD patients and healthy controls but also patients with other CNS illnesses. These included mild cognitive impairment, which is assumed to represent a transitional period before the development of AD, as well as multiple sclerosis, Parkinson disease, major depression, bipolar disorder and schizophrenia. miRNA target enrichment analysis of the selected 12 miRNAs indicates an involvement of miRNAs in nervous system development, neuron projection, neuron projection development and neuron projection morphogenesis. Using this 12-miRNA signature, we differentiate between AD and controls with an accuracy of 93%, a specificity of 95% and a sensitivity of 92%. The differentiation of AD from other neurological diseases is possible with accuracies between 74% and 78%. The differentiation of the other CNS disorders from controls yields even higher accuracies. Conclusions The data indicate that deregulated miRNAs in blood might be used as biomarkers in the diagnosis of AD or other neurological diseases.
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Abstract
PURPOSE OF REVIEW This article discusses the current status of knowledge regarding the genetic basis of Alzheimer disease (AD) with a focus on clinically relevant aspects. RECENT FINDINGS The genetic architecture of AD is complex, as it includes multiple susceptibility genes and likely nongenetic factors. Rare but highly penetrant autosomal dominant mutations explain a small minority of the cases but have allowed tremendous advances in understanding disease pathogenesis. The identification of a strong genetic risk factor, APOE, reshaped the field and introduced the notion of genetic risk for AD. More recently, large-scale genome-wide association studies are adding to the picture a number of common variants with very small effect sizes. Large-scale resequencing studies are expected to identify additional risk factors, including rare susceptibility variants and structural variation. SUMMARY Genetic assessment is currently of limited utility in clinical practice because of the low frequency (Mendelian mutations) or small effect size (common risk factors) of the currently known susceptibility genes. However, genetic studies are identifying with confidence a number of novel risk genes, and this will further our understanding of disease biology and possibly the identification of therapeutic targets.
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Affiliation(s)
- John M Ringman
- Easton Center for Alzheimer’s Disease Research at UCLA, 10911 Weyburn Ave, #200, Los Angeles, CA 90095-7226, USA.
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Elias-Sonnenschein LS, Bertram L, Visser PJ. Relationship between genetic risk factors and markers for Alzheimer's disease pathology. Biomark Med 2013; 6:477-95. [PMID: 22917148 DOI: 10.2217/bmm.12.56] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by neuritic plaques (main constituent: β-amyloid [Aβ]) and neurofibrillary tangles (hyperphosphorylated tau protein) in the brain. Abnormalities in Aβ and tau can be measured upon neuropathological examination, in cerebrospinal fluid or by PET. Etiologically, a growing body of evidence suggests that susceptibility to AD is genetically controlled. However, the precise nature of the underlying risk genes and their relation to AD biomarkers remains largely elusive. To this end, we performed a qualitative review of 17 studies (covering 47 polymorphisms in 26 genes) and investigated the potential relation between the most compelling AD risk genes and markers for Aβ and tau in cerebrospinal fluid, PET imaging and neuropathological examination. Of all covered genes, only APOE and PICALM showed consistent effects on Aβ but not on tau, while no obvious effects were observed for CLU, CR1, ACE, SORL and MAPT.
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Affiliation(s)
- Lyzel S Elias-Sonnenschein
- School for Mental Health & Neuroscience, Alzheimer Centrum Limburg, Department of Psychiatry & Neuropsychology, Maastricht University, Maastricht, The Netherlands.
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Abstract
Six tau isoforms differing in their affinity for microtubules are produced by alternative splicing from the MAPT (microtubule-associated protein tau) gene in adult human brain. Several MAPT mutations causing the familial tauopathy, FTDP-17 (frontotemporal dementia with parkinsonism linked to chromosome 17), affect alternative splicing of exon 10, encoding a microtubule-binding motif. Advanced RNA analysis methods have suggested that levels of exon 10-containing MAPT mRNA are elevated in Alzheimer's disease. Furthermore, the MAPT H1 haplotype, associated with Alzheimer's disease, promotes exon 10 inclusion in MAPT mRNA. Thus an accurate regulation of tau alternative splicing is critical for the maintenance of neuronal viability, and its alteration might be a contributing factor to Alzheimer's disease. Tau alternative splicing could represent a target for therapeutic intervention to delay the progression of pathology in familial as well as sporadic tauopathies.
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Abstract
Despite tremendous investments in understanding the complex molecular mechanisms underlying Alzheimer disease (AD), recent clinical trials have failed to show efficacy. A potential problem underlying these failures is the assumption that the molecular mechanism mediating the genetically determined form of the disease is identical to the one resulting in late-onset AD. Here, we integrate experimental evidence outside the 'spotlight' of the genetic drivers of amyloid-β (Aβ) generation published during the past two decades, and present a mechanistic explanation for the pathophysiological changes that characterize late-onset AD. We propose that chronic inflammatory conditions cause dysregulation of mechanisms to clear misfolded or damaged neuronal proteins that accumulate with age, and concomitantly lead to tau-associated impairments of axonal integrity and transport. Such changes have several neuropathological consequences: focal accumulation of mitochondria, resulting in metabolic impairments; induction of axonal swelling and leakage, followed by destabilization of synaptic contacts; deposition of amyloid precursor protein in swollen neurites, and generation of aggregation-prone peptides; further tau hyperphosphorylation, ultimately resulting in neurofibrillary tangle formation and neuronal death. The proposed sequence of events provides a link between Aβ and tau-related neuropathology, and underscores the concept that degenerating neurites represent a cause rather than a consequence of Aβ accumulation in late-onset AD.
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Mullane K, Williams M. Alzheimer's therapeutics: continued clinical failures question the validity of the amyloid hypothesis-but what lies beyond? Biochem Pharmacol 2012. [PMID: 23178653 DOI: 10.1016/j.bcp.2012.11.014] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The worldwide incidence of Alzheimer's disease (AD) is increasing with estimates that 115 million individuals will have AD by 2050, creating an unsustainable healthcare challenge due to a lack of effective treatment options highlighted by multiple clinical failures of agents designed to reduce the brain amyloid burden considered synonymous with the disease. The amyloid hypothesis that has been the overarching focus of AD research efforts for more than two decades has been questioned in terms of its causality but has not been unequivocally disproven despite multiple clinical failures, This is due to issues related to the quality of compounds advanced to late stage clinical trials and the lack of validated biomarkers that allow the recruitment of AD patients into trials before they are at a sufficiently advanced stage in the disease where therapeutic intervention is deemed futile. Pursuit of a linear, reductionistic amyloidocentric approach to AD research, which some have compared to a religious faith, has resulted in other, equally plausible but as yet unvalidated AD hypotheses being underfunded leading to a disastrous roadblock in the search for urgently needed AD therapeutics. Genetic evidence supporting amyloid causality in AD is reviewed in the context of the clinical failures, and progress in tau-based and alternative approaches to AD, where an evolving modus operandi in biomedical research fosters excessive optimism and a preoccupation with unproven, and often ephemeral, biomarker/genome-based approaches that override transparency, objectivity and data-driven decision making, resulting in low probability environments where data are subordinate to self propagating hypotheses.
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Wijsman EM. The role of large pedigrees in an era of high-throughput sequencing. Hum Genet 2012; 131:1555-63. [PMID: 22714655 PMCID: PMC3638020 DOI: 10.1007/s00439-012-1190-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/07/2012] [Indexed: 12/13/2022]
Abstract
Rare variation is the current frontier in human genetics. The large pedigree design is practical, efficient, and well-suited for investigating rare variation. In large pedigrees, specific rare variants that co-segregate with a trait will occur in sufficient numbers so that effects can be measured, and evidence for association can be evaluated, by making use of methods that fully use the pedigree information. Evidence from linkage analysis can focus investigation, both reducing the multiple testing burden and expanding the variants that can be evaluated and followed up, as recent studies have shown. The large pedigree design requires only a small fraction of the sample size needed to identify rare variants of interest in population-based designs, and many highly suitable, well-understood, and available statistical and computational tools already exist. Samples consisting of large pedigrees with existing rich phenotype and genome scan data should be prime candidates for high-throughput sequencing in the search of the determinants of complex traits.
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Affiliation(s)
- Ellen M Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA 98195-7720, USA.
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The role of MAPT sequence variation in mechanisms of disease susceptibility. Biochem Soc Trans 2012; 40:687-92. [DOI: 10.1042/bst20120063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The microtubule-associated protein tau (MAPT or tau) is of great interest in the field of neurodegeneration as there is a well-established genetic link between the MAPT gene locus and tauopathies, a diverse group of neurodegenerative dementias and movement disorders. The genomic architecture in the region spanning the MAPT locus contains a ~1.8 Mb block of linkage disequilibrium characterized by two major haplotypes: H1 and H2. Recent studies have established strong genetic association between the MAPT locus and neurodegenerative disease and uncovered haplotype-specific differences in expression and alternative splicing of MAPT transcripts. Integrating genetic association data and gene expression data to understand how non-coding genetic variation at a gene locus affects gene expression and leads to susceptibility to disease is a high priority in disease genetics, and the MAPT locus provides an excellent paradigm for this. In the absence of protein-coding changes caused by haplotype sequence variation, altered levels of protein expression or altered ratios of isoform expression are excellent candidate mechanisms to link the MAPT genetic disease association with biological function. The use of novel transgenic and endogenous genetic models are required to understand the role of MAPT sequence variation in mechanisms of disease susceptibility.
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Trabzuni D, Wray S, Vandrovcova J, Ramasamy A, Walker R, Smith C, Luk C, Gibbs JR, Dillman A, Hernandez DG, Arepalli S, Singleton AB, Cookson MR, Pittman AM, de Silva R, Weale ME, Hardy J, Ryten M. MAPT expression and splicing is differentially regulated by brain region: relation to genotype and implication for tauopathies. Hum Mol Genet 2012; 21:4094-103. [PMID: 22723018 PMCID: PMC3428157 DOI: 10.1093/hmg/dds238] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The MAPT (microtubule-associated protein tau) locus is one of the most remarkable in neurogenetics due not only to its involvement in multiple neurodegenerative disorders, including progressive supranuclear palsy, corticobasal degeneration, Parksinson's disease and possibly Alzheimer's disease, but also due its genetic evolution and complex alternative splicing features which are, to some extent, linked and so all the more intriguing. Therefore, obtaining robust information regarding the expression, splicing and genetic regulation of this gene within the human brain is of immense importance. In this study, we used 2011 brain samples originating from 439 individuals to provide the most reliable and coherent information on the regional expression, splicing and regulation of MAPT available to date. We found significant regional variation in mRNA expression and splicing of MAPT within the human brain. Furthermore, at the gene level, the regional distribution of mRNA expression and total tau protein expression levels were largely in agreement, appearing to be highly correlated. Finally and most importantly, we show that while the reported H1/H2 association with gene level expression is likely to be due to a technical artefact, this polymorphism is associated with the expression of exon 3-containing isoforms in human brain. These findings would suggest that contrary to the prevailing view, genetic risk factors for neurodegenerative diseases at the MAPT locus are likely to operate by changing mRNA splicing in different brain regions, as opposed to the overall expression of the MAPT gene.
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Affiliation(s)
- Daniah Trabzuni
- Reta Lila Weston Institute and Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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Cruchaga C, Haller G, Chakraverty S, Mayo K, Vallania FLM, Mitra RD, Faber K, Williamson J, Bird T, Diaz-Arrastia R, Foroud TM, Boeve BF, Graff-Radford NR, St Jean P, Lawson M, Ehm MG, Mayeux R, Goate AM. Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families. PLoS One 2012; 7:e31039. [PMID: 22312439 PMCID: PMC3270040 DOI: 10.1371/journal.pone.0031039] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 12/30/2011] [Indexed: 12/15/2022] Open
Abstract
Pathogenic mutations in APP, PSEN1, PSEN2, MAPT and GRN have previously been linked to familial early onset forms of dementia. Mutation screening in these genes has been performed in either very small series or in single families with late onset AD (LOAD). Similarly, studies in single families have reported mutations in MAPT and GRN associated with clinical AD but no systematic screen of a large dataset has been performed to determine how frequently this occurs. We report sequence data for 439 probands from late-onset AD families with a history of four or more affected individuals. Sixty sequenced individuals (13.7%) carried a novel or pathogenic mutation. Eight pathogenic variants, (one each in APP and MAPT, two in PSEN1 and four in GRN) three of which are novel, were found in 14 samples. Thirteen additional variants, present in 23 families, did not segregate with disease, but the frequency of these variants is higher in AD cases than controls, indicating that these variants may also modify risk for disease. The frequency of rare variants in these genes in this series is significantly higher than in the 1,000 genome project (p = 5.09 × 10⁻⁵; OR = 2.21; 95%CI = 1.49-3.28) or an unselected population of 12,481 samples (p = 6.82 × 10⁻⁵; OR = 2.19; 95%CI = 1.347-3.26). Rare coding variants in APP, PSEN1 and PSEN2, increase risk for or cause late onset AD. The presence of variants in these genes in LOAD and early-onset AD demonstrates that factors other than the mutation can impact the age at onset and penetrance of at least some variants associated with AD. MAPT and GRN mutations can be found in clinical series of AD most likely due to misdiagnosis. This study clearly demonstrates that rare variants in these genes could explain an important proportion of genetic heritability of AD, which is not detected by GWAS.
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Affiliation(s)
- Carlos Cruchaga
- Department of Psychiatry and Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University, St. Louis, Missouri, United States of America.
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