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Jiao B, Liu X, Zhou L, Wang MH, Zhou Y, Xiao T, Zhang W, Sun R, Waye MMY, Tang B, Shen L. Polygenic Analysis of Late-Onset Alzheimer's Disease from Mainland China. PLoS One 2015; 10:e0144898. [PMID: 26680604 PMCID: PMC4683047 DOI: 10.1371/journal.pone.0144898] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/24/2015] [Indexed: 01/14/2023] Open
Abstract
Recently, a number of single nucleotide polymorphisms (SNPs) were identified to be associated with late-onset Alzheimer disease (LOAD) through genome-wide association study data. Identification of SNP-SNP interaction played an important role in better understanding genetic basis of LOAD. In this study, fifty-eight SNPs were screened in a cohort of 229 LOAD cases and 318 controls from mainland China, and their interaction was evaluated by a series of analysis methods. Seven risk SNPs and six protective SNPs were identified to be associated with LOAD. Risk SNPs included rs9331888 (CLU), rs6691117 (CR1), rs4938933 (MS4A), rs9349407 (CD2AP), rs1160985 (TOMM40), rs4945261 (GAB2) and rs5984894 (PCDH11X); Protective SNPs consisted of rs744373 (BIN1), rs1562990 (MS4A), rs597668 (EXOC3L2), rs9271192 (HLA-DRB5/DRB1), rs157581 and rs11556505 (TOMM40). Among positive SNPs presented above, we found the interaction between rs4938933 (risk) and rs1562990 (protective) in MS4A weakened their each effect for LOAD; for three significant SNPs in TOMM40, their cumulative interaction induced the two protective SNPs effects lost and made the risk SNP effect aggravate for LOAD. Finally, we found rs6656401-rs3865444 (CR1-CD33) pairs were significantly associated with decreasing LOAD risk, while rs28834970-rs6656401 (PTK2B-CR1), and rs28834970-rs6656401 (PTK2B-CD33) were associated with increasing LOAD risk. In a word, our study indicates that SNP-SNP interaction existed in the same gene or cross different genes, which could weaken or aggravate their initial single effects for LOAD.
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Affiliation(s)
- Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyan Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lin Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Maggie Haitian Wang
- Division of Biostatistics, School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yafang Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Tingting Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Weiwei Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Rui Sun
- Division of Biostatistics, School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Mary Miu Yee Waye
- School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- State Key Laboratory of Medical Genetics, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- State Key Laboratory of Medical Genetics, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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The Impact of UNC5C Genetic Variations on Neuroimaging in Alzheimer’s Disease. Mol Neurobiol 2015; 53:6759-6767. [DOI: 10.1007/s12035-015-9589-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/29/2015] [Indexed: 12/11/2022]
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Sims R, Williams J. Defining the Genetic Architecture of Alzheimer's Disease: Where Next? NEURODEGENER DIS 2015; 16:6-11. [DOI: 10.1159/000440841] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/03/2015] [Indexed: 11/19/2022] Open
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Korvatska O, Leverenz JB, Jayadev S, McMillan P, Kurtz I, Guo X, Rumbaugh M, Matsushita M, Girirajan S, Dorschner MO, Kiianitsa K, Yu CE, Brkanac Z, Garden GA, Raskind WH, Bird TD. R47H Variant of TREM2 Associated With Alzheimer Disease in a Large Late-Onset Family: Clinical, Genetic, and Neuropathological Study. JAMA Neurol 2015; 72:920-7. [PMID: 26076170 DOI: 10.1001/jamaneurol.2015.0979] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
IMPORTANCE The R47H variant in the triggering receptor expressed on myeloid cells 2 gene (TREM2), a modulator of the immune response of microglia, is a strong genetic risk factor for Alzheimer disease (AD) and possibly other neurodegenerative disorders. OBJECTIVE To investigate a large family with late-onset AD (LOAD), in which R47H cosegregated with 75% of cases. DESIGN, SETTING, AND PARTICIPANTS This study includes genetic and pathologic studies of families with LOAD from 1985 to 2014. A total of 131 families with LOAD (751 individuals) were included from the University of Washington Alzheimer Disease Research Center. To identify LOAD genes/risk factors in the LOAD123 family with 21 affected members and 12 autopsies, we sequenced 4 exomes. Candidate variants were tested for cosegregation with the disease. TREM2 R47H was genotyped in an additional 130 families with LOAD. We performed clinical and neuropathological assessments of patients with and without R47H and evaluated the variant's effect on brain pathology, cellular morphology, and expression of microglial markers. MAIN OUTCOMES AND MEASURES We assessed the effect of TREM2 genotype on age at onset and disease duration. We compared Braak and Consortium to Establish a Registry for Alzheimer's Disease scores, presence of α-synuclein and TAR DNA-binding protein 43 aggregates, and additional vascular or Parkinson pathology in TREM2 R47H carriers vs noncarriers. Microglial activation was assessed by quantitative immunohistochemistry and morphometry. RESULTS Twelve of 16 patients with AD in the LOAD123 family carried R47H. Eleven patients with dementia had apolipoprotein E 4 (ApoE4) and R47H genotypes. We also found a rare missense variant, D353N, in a nominated AD risk gene, unc-5 homolog C (UNC5C), in 5 affected individuals in the LOAD123 family. R47H carriers demonstrated a shortened disease duration (mean [SD], 6.7 [2.8] vs 11.1 [6.6] years; 2-tailed t test; P = .04) and more frequent α-synucleinopathy. The panmicroglial marker ionized calcium-binding adapter molecule 1 was decreased in all AD cases and the decrease was most pronounced in R47H carriers (mean [SD], in the hilus: 0.114 [0.13] for R47H_AD vs 0.574 [0.26] for control individuals; 2-tailed t test; P = .005 and vs 0.465 [0.32] for AD; P = .02; in frontal cortex gray matter: 0.006 [0.004] for R47H_AD vs 0.016 [0.01] for AD; P = .04 and vs 0.033 [0.013] for control individuals; P < .001). Major histocompatibility complex class II, a marker of microglial activation, was increased in all patients with AD (AD: 2.5, R47H_AD: 2.7, and control: 1.0; P < .01). CONCLUSIONS AND RELEVANCE Our results demonstrate a complex genetic landscape of LOAD, even in a single pedigree with an apparent autosomal dominant pattern of inheritance. ApoE4, TREM2 R47H, and rare variants in other genes, such as UNC5C D353N, are likely responsible for the notable occurrence of AD in this family. Our findings support the role of the TREM2 receptor in microglial clearance of aggregation-prone proteins that is compromised in R47H carriers and may accelerate the course of disease.
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Affiliation(s)
- Olena Korvatska
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle
| | - James B Leverenz
- Lou Ruvo Center for Brain Health, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle
| | - Pamela McMillan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle4Mental Illness Research, Education, and Clinical Center, Department of Veteran Affairs, Seattle, Washington
| | - Irina Kurtz
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle
| | - Xindi Guo
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle
| | - Malia Rumbaugh
- Department of Neurology, University of Washington, Seattle
| | - Mark Matsushita
- Department of Medicine (Medical Genetics), University of Washington, Seattle
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College7Department of Anthropology, Pennsylvania State University, State College
| | - Michael O Dorschner
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle8Department of Pathology, University of Washington, Seattle
| | - Kostantin Kiianitsa
- Department of Medicine (Medical Genetics), University of Washington, Seattle
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington10Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle
| | - Gwenn A Garden
- Department of Neurology, University of Washington, Seattle8Department of Pathology, University of Washington, Seattle
| | - Wendy H Raskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle4Mental Illness Research, Education, and Clinical Center, Department of Veteran Affairs, Seattle, Washington5Department of Medicine (Medical Genetics), University of Washin
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle5Department of Medicine (Medical Genetics), University of Washington, Seattle9Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington
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105
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Talwar P, Sinha J, Grover S, Rawat C, Kushwaha S, Agarwal R, Taneja V, Kukreti R. Dissecting Complex and Multifactorial Nature of Alzheimer's Disease Pathogenesis: a Clinical, Genomic, and Systems Biology Perspective. Mol Neurobiol 2015; 53:4833-64. [PMID: 26351077 DOI: 10.1007/s12035-015-9390-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/11/2015] [Indexed: 01/14/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by loss of memory and other cognitive functions. AD can be classified into familial AD (FAD) and sporadic AD (SAD) based on heritability and into early onset AD (EOAD) and late onset AD (LOAD) based on age of onset. LOAD cases are more prevalent with genetically complex architecture. In spite of significant research focused on understanding the etiological mechanisms, search for diagnostic biomarker(s) and disease-modifying therapy is still on. In this article, we aim to comprehensively review AD literature on established etiological mechanisms including role of beta-amyloid and apolipoprotein E (APOE) along with promising newer etiological factors such as epigenetic modifications that have been associated with AD suggesting its multifactorial nature. As genomic studies have recently played a significant role in elucidating AD pathophysiology, a systematic review of findings from genome-wide linkage (GWL), genome-wide association (GWA), genome-wide expression (GWE), and epigenome-wide association studies (EWAS) was conducted. The availability of multi-dimensional genomic data has further coincided with the advent of computational and network biology approaches in recent years. Our review highlights the importance of integrative approaches involving genomics and systems biology perspective in elucidating AD pathophysiology. The promising newer approaches may provide reliable means of early and more specific diagnosis and help identify therapeutic interventions for LOAD.
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Affiliation(s)
- Puneet Talwar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India.,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Juhi Sinha
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Sandeep Grover
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India.,Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Chitra Rawat
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India.,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Suman Kushwaha
- Institute of Human Behaviour and Allied Sciences (IHBAS), Delhi, India
| | - Rachna Agarwal
- Institute of Human Behaviour and Allied Sciences (IHBAS), Delhi, India
| | - Vibha Taneja
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Ritushree Kukreti
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India. .,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India.
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106
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Del-Aguila JL, Koboldt DC, Black K, Chasse R, Norton J, Wilson RK, Cruchaga C. Alzheimer's disease: rare variants with large effect sizes. Curr Opin Genet Dev 2015; 33:49-55. [PMID: 26311074 DOI: 10.1016/j.gde.2015.07.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/27/2022]
Abstract
Recent advances in sequencing technology and novel genotyping arrays (focused on low-frequency and coding variants) have made it possible to identify novel coding variants with large effect sizes and also novel genes (TREM2, PLD3, UNC5C, and AKAP9) associated with Alzheimer's disease (AD) risk. The major advantages of these studies over the classic genome-wide association studies (GWAS) include the identification of the functional variant and the gene-driven association. In addition to the large effect size, these studies make it possible to model these variants and genes using cell and animal systems. On the other hand, the underlying population-variability of these very low allele frequency variants poses a great challenge to replicating results. Studies that include very large datasets (>10,000 cases and controls) and combine sequencing and genotyping approaches will lead to the identification of novel genes for Alzheimer's disease.
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Affiliation(s)
- Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Rachel Chasse
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA.
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107
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Farrer LA. Expanding the genomic roadmap of Alzheimer's disease. Lancet Neurol 2015; 14:783-785. [PMID: 26141618 DOI: 10.1016/s1474-4422(15)00146-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Lindsay A Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA 02118, USA.
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108
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Moon SW, Dinov ID, Kim J, Zamanyan A, Hobel S, Thompson PM, Toga AW. Structural Neuroimaging Genetics Interactions in Alzheimer's Disease. J Alzheimers Dis 2015; 48:1051-63. [PMID: 26444770 PMCID: PMC4730943 DOI: 10.3233/jad-150335] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This article investigates late-onset cognitive impairment using neuroimaging and genetics biomarkers for Alzheimer's Disease Neuroimaging Initiative (ADNI) participants. Eight-hundred and eight ADNI subjects were identified and divided into three groups: 200 subjects with Alzheimer's disease (AD), 383 subjects with mild cognitive impairment (MCI), and 225 asymptomatic normal controls (NC). Their structural magnetic resonance imaging (MRI) data were parcellated using BrainParser, and the 80 most important neuroimaging biomarkers were extracted using the global shape analysis Pipeline workflow. Using Plink via the Pipeline environment, we obtained 80 SNPs highly-associated with the imaging biomarkers. In the AD cohort, rs2137962 was significantly associated bilaterally with changes in the hippocampi and the parahippocampal gyri, and rs1498853, rs288503, and rs288496 were associated with the left and right hippocampi, the right parahippocampal gyrus, and the left inferior temporal gyrus. In the MCI cohort, rs17028008 and rs17027976 were significantly associated with the right caudate and right fusiform gyrus, rs2075650 (TOMM40) was associated with the right caudate, and rs1334496 and rs4829605 were significantly associated with the right inferior temporal gyrus. In the NC cohort, Chromosome 15 [rs734854 (STOML1), rs11072463 (PML), rs4886844 (PML), and rs1052242 (PML)] was significantly associated with both hippocampi and both insular cortices, and rs4899412 (RGS6) was significantly associated with the caudate. We observed significant correlations between genetic and neuroimaging phenotypes in the 808 ADNI subjects. These results suggest that differences between AD, MCI, and NC cohorts may be examined by using powerful joint models of morphometric, imaging and genotypic data.
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Affiliation(s)
- Seok Woo Moon
- Department of Psychiatry, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Ivo D. Dinov
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
- University of Michigan, School of Nursing, Ann Arbor, Michigan, United States of America
| | - Jaebum Kim
- Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Alen Zamanyan
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
| | - Sam Hobel
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
| | - Paul M. Thompson
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
| | - Arthur W. Toga
- Laboratory of Neuro Imaging, Institute for Neuroimaging and Informatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States of America
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