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Peng Q, Gilder DA, Bernert RA, Karriker-Jaffe KJ, Ehlers CL. Genetic factors associated with suicidal behaviors and alcohol use disorders in an American Indian population. Mol Psychiatry 2024; 29:902-913. [PMID: 38177348 PMCID: PMC11176067 DOI: 10.1038/s41380-023-02379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
American Indians (AI) demonstrate the highest rates of both suicidal behaviors (SB) and alcohol use disorders (AUD) among all ethnic groups in the US. Rates of suicide and AUD vary substantially between tribal groups and across different geographical regions, underscoring a need to delineate more specific risk and resilience factors. Using data from over 740 AI living within eight contiguous reservations, we assessed genetic risk factors for SB by investigating: (1) possible genetic overlap with AUD, and (2) impacts of rare and low-frequency genomic variants. Suicidal behaviors included lifetime history of suicidal thoughts and acts, including verified suicide deaths, scored using a ranking variable for the SB phenotype (range 0-4). We identified five loci significantly associated with SB and AUD, two of which are intergenic and three intronic on genes AACSP1, ANK1, and FBXO11. Nonsynonymous rare and low-frequency mutations in four genes including SERPINF1 (PEDF), ZNF30, CD34, and SLC5A9, and non-intronic rare and low-frequency mutations in genes OPRD1, HSD17B3 and one lincRNA were significantly associated with SB. One identified pathway related to hypoxia-inducible factor (HIF) regulation, whose 83 nonsynonymous rare and low-frequency variants on 10 genes were significantly linked to SB as well. Four additional genes, and two pathways related to vasopressin-regulated water metabolism and cellular hexose transport, also were strongly associated with SB. This study represents the first investigation of genetic factors for SB in an American Indian population that has high risk for suicide. Our study suggests that bivariate association analysis between comorbid disorders can increase statistical power; and rare and low-frequency variant analysis in a high-risk population enabled by whole-genome sequencing has the potential to identify novel genetic factors. Although such findings may be population specific, rare functional mutations relating to PEDF and HIF regulation align with past reports and suggest a biological mechanism for suicide risk and a potential therapeutic target for intervention.
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Affiliation(s)
- Qian Peng
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA.
| | - David A Gilder
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebecca A Bernert
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | | | - Cindy L Ehlers
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
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2
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Gilder D, Bernert R, Karriker-Jaffe K, Ehlers C, Peng Q. Genetic Factors Associated with Suicidal Behaviors and Alcohol Use Disorders in an American Indian Population. RESEARCH SQUARE 2023:rs.3.rs-2950284. [PMID: 37398076 PMCID: PMC10312956 DOI: 10.21203/rs.3.rs-2950284/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
American Indians (AI) demonstrate the highest rates of both suicidal behaviors (SB) and alcohol use disorders (AUD) among all ethnic groups in the US. Rates of suicide and AUD vary substantially between tribal groups and across different geographical regions, underscoring a need to delineate more specific risk and resilience factors. Using data from over 740 AI living within eight contiguous reservations, we assessed genetic risk factors for SB by investigating: (1) possible genetic overlap with AUD, and (2) impacts of rare and low frequency genomic variants. Suicidal behaviors included lifetime history of suicidal thoughts and acts, including verified suicide deaths, scored using a ranking variable for the SB phenotype (range 0-4). We identified five loci significantly associated with SB and AUD, two of which are intergenic and three intronic on genes AACSP1, ANK1, and FBXO11. Nonsynonymous rare mutations in four genes including SERPINF1 (PEDF), ZNF30, CD34, and SLC5A9, and non-intronic rare mutations in genes OPRD1, HSD17B3 and one lincRNA were significantly associated with SB. One identified pathway related to hypoxia-inducible factor (HIF) regulation, whose 83 nonsynonymous rare variants on 10 genes were significantly linked to SB as well. Four additional genes, and two pathways related to vasopressin-regulated water metabolism and cellular hexose transport, also were strongly associated with SB. This study represents the first investigation of genetic factors for SB in an American Indian population that has high risk for suicide. Our study suggests that bivariate association analysis between comorbid disorders can increase statistical power; and rare variant analysis in a high-risk population enabled by whole-genome sequencing has the potential to identify novel genetic factors. Although such findings may be population specific, rare functional mutations relating to PEDF and HIF regulation align with past reports and suggest a biological mechanism for suicide risk and a potential therapeutic target for intervention.
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3
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Sarafidou T, Galliopoulou E, Apostolopoulou D, Fragkiadakis GA, Moschonas NK. Reconstruction of a Comprehensive Interactome and Experimental Data Analysis of FRA10AC1 May Provide Insights into Its Biological Role in Health and Disease. Genes (Basel) 2023; 14:genes14030568. [PMID: 36980839 PMCID: PMC10048706 DOI: 10.3390/genes14030568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
FRA10AC1, the causative gene for the manifestation of the FRA10A fragile site, encodes a well-conserved nuclear protein characterized as a non-core spliceosomal component. Pre-mRNA splicing perturbations have been linked with neurodevelopmental diseases. FRA10AC1 variants have been, recently, causally linked with severe neuropathological and growth retardation phenotypes. To further elucidate the participation of FRA10AC1 in spliceosomal multiprotein complexes and its involvement in neurological phenotypes related to splicing, we exploited protein–protein interaction experimental data and explored network information and information deduced from transcriptomics. We confirmed the direct interaction of FRA10AC1with ESS2, a non-core spliceosomal protein, mapped their interacting domains, and documented their tissue co-localization and physical interaction at the level of intracellular protein stoichiometries. Although FRA10AC1 and SF3B2, a major core spliceosomal protein, were shown to interact under in vitro conditions, the endogenous proteins failed to co-immunoprecipitate. A reconstruction of a comprehensive, strictly binary, protein–protein interaction network of FRA10AC1 revealed dense interconnectivity with many disease-associated spliceosomal components and several non-spliceosomal regulatory proteins. The topological neighborhood of FRA10AC1 depicts an interactome associated with multiple severe monogenic and multifactorial neurodevelopmental diseases mainly referring to spliceosomopathies. Our results suggest that FRA10AC1 involvement in pre-mRNA processing might be strengthened by interconnecting splicing with transcription and mRNA export, and they propose the broader role(s) of FRA10AC1 in cell pathophysiology.
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Affiliation(s)
- Theologia Sarafidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece
- Correspondence: (T.S.); (N.K.M.)
| | - Eleni Galliopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece
| | | | - Georgios A. Fragkiadakis
- Department of Nutrition and Dietetics Sciences, Hellenic Mediterranean University, Tripitos, 72300 Siteia, Greece
| | - Nicholas K. Moschonas
- School of Medicine, University of Patras, 26500 Patras, Greece
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas (FORTH/ICE-HT), 26504 Patras, Greece
- Correspondence: (T.S.); (N.K.M.)
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4
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Gholami M, Zoughi M, Hasanzad M, Larijani B, Amoli MM. Haplotypic variants of COVID-19 related genes are associated with blood pressure and metabolites levels. J Med Virol 2023; 95:e28355. [PMID: 36443248 PMCID: PMC9877746 DOI: 10.1002/jmv.28355] [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: 12/25/2021] [Revised: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
The genetic association of coronavirus disease 2019 (COVID-19) with its complications has not been fully understood. This study aimed to identify variants and haplotypes of candidate genes implicated in COVID-19 related traits by combining the literature review and pathway analysis. To explore such genes, the protein-protein interactions and relevant pathways of COVID-19-associated genes were assessed. A number of variants on candidate genes were identified from Genome-wide association studies (GWASs) which were associated with COVID-19 related traits (p ˂ 10-6 ). Haplotypic blocks were assessed using haplotypic structures among the 1000 Genomes Project (r2 ≥ 0.8, D' ≥ 0.8). Further functional analyses were performed on the selected variants. The results demonstrated that a group of variants in ACE and AGT genes were significantly correlated with COVID-19 related traits. Three haplotypes were identified to be involved in the blood metabolites levels and the development of blood pressure. Functional analyses revealed that most GWAS index variants were expression quantitative trait loci and had transcription factor binding sites, exonic splicing enhancers or silencer activities. Furthermore, the proxy haplotype variants, rs4316, rs4353, rs4359, and three variants, namely rs2493133, rs2478543, and rs5051, were associated with blood metabolite and systolic blood pressure, respectively. These variants exerted more regulatory effects compared with other GWAS variants. The present study indicates that the genetic variants and candidate haplotypes of COVID-19 related genes are associated with blood pressure and blood metabolites. However, further observational studies are warranted to confirm these results.
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Affiliation(s)
- Morteza Gholami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Marziyeh Zoughi
- Metabolomics and genomics research center endocrinology and metabolism molecular‐cellular sciences instituteTehran University of medical sciencesTehranIran
| | - Mandana Hasanzad
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Mahsa M. Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran
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Bhatt IS, Wilson N, Dias R, Torkamani A. A genome-wide association study of tinnitus reveals shared genetic links to neuropsychiatric disorders. Sci Rep 2022; 12:22511. [PMID: 36581688 PMCID: PMC9800371 DOI: 10.1038/s41598-022-26413-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/14/2022] [Indexed: 12/30/2022] Open
Abstract
Tinnitus, a phantom perception of sound in the absence of any external sound source, is a prevalent health condition often accompanied by psychiatric comorbidities. Recent genome-wide association studies (GWAS) highlighted a polygenic nature of tinnitus susceptibility. A shared genetic component between tinnitus and psychiatric conditions remains elusive. Here we present a GWAS using the UK Biobank to investigate the genetic processes linked to tinnitus and tinnitus-related distress, followed by gene-set enrichment analyses. The UK Biobank sample comprised 132,438 individuals with tinnitus and genotype data. Among the study sample, 38,525 individuals reported tinnitus, and 26,889 participants mentioned they experienced tinnitus-related distress in daily living. The genome-wide association analyses were conducted on tinnitus and tinnitus-related distress. We conducted enrichment analyses using FUMA to further understand the genetic processes linked to tinnitus and tinnitus-related distress. A genome-wide significant locus (lead SNP: rs71595470) for tinnitus was obtained in the vicinity of GPM6A. Nineteen independent loci reached suggestive association with tinnitus. Fifteen independent loci reached suggestive association with tinnitus-related distress. The enrichment analysis revealed a shared genetic component between tinnitus and psychiatric traits, such as bipolar disorder, feeling worried, cognitive ability, fast beta electroencephalogram, and sensation seeking. Metabolic, cardiovascular, hematological, and pharmacological gene sets revealed a significant association with tinnitus. Anxiety and stress-related gene sets revealed a significant association with tinnitus-related distress. The GWAS signals for tinnitus were enriched in the hippocampus and cortex, and for tinnitus-related distress were enriched in the brain and spinal cord. This study provides novel insights into genetic processes associated with tinnitus and tinnitus-related distress and demonstrates a shared genetic component underlying tinnitus and psychiatric conditions. Further collaborative attempts are necessary to identify genetic components underlying the phenotypic heterogeneity in tinnitus and provide biological insight into the etiology.
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Affiliation(s)
- Ishan Sunilkumar Bhatt
- grid.214572.70000 0004 1936 8294Department of Communication Sciences & Disorders, University of Iowa, 250 Hawkins Dr, Iowa City, IA 52242 USA
| | - Nicholas Wilson
- Department of Integrative Structural and Computational Biology Scripps Science Institute, La Jolla, CA 92037 USA
| | - Raquel Dias
- grid.15276.370000 0004 1936 8091Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32608 USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology Scripps Science Institute, La Jolla, CA 92037 USA
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Grosjean I, Roméo B, Domdom MA, Belaid A, D’Andréa G, Guillot N, Gherardi RK, Gal J, Milano G, Marquette CH, Hung RJ, Landi MT, Han Y, Brest P, Von Bergen M, Klionsky DJ, Amos CI, Hofman P, Mograbi B. Autophagopathies: from autophagy gene polymorphisms to precision medicine for human diseases. Autophagy 2022; 18:2519-2536. [PMID: 35383530 PMCID: PMC9629091 DOI: 10.1080/15548627.2022.2039994] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/20/2022] [Accepted: 02/06/2022] [Indexed: 12/15/2022] Open
Abstract
At a time when complex diseases affect globally 280 million people and claim 14 million lives every year, there is an urgent need to rapidly increase our knowledge into their underlying etiologies. Though critical in identifying the people at risk, the causal environmental factors (microbiome and/or pollutants) and the affected pathophysiological mechanisms are not well understood. Herein, we consider the variations of autophagy-related (ATG) genes at the heart of mechanisms of increased susceptibility to environmental stress. A comprehensive autophagy genomic resource is presented with 263 single nucleotide polymorphisms (SNPs) for 69 autophagy-related genes associated with 117 autoimmune, inflammatory, infectious, cardiovascular, neurological, respiratory, and endocrine diseases. We thus propose the term 'autophagopathies' to group together a class of complex human diseases the etiology of which lies in a genetic defect of the autophagy machinery, whether directly related or not to an abnormal flux in autophagy, LC3-associated phagocytosis, or any associated trafficking. The future of precision medicine for common diseases will lie in our ability to exploit these ATG SNP x environment relationships to develop new polygenetic risk scores, new management guidelines, and optimal therapies for afflicted patients.Abbreviations: ATG, autophagy-related; ALS-FTD, amyotrophic lateral sclerosis-frontotemporal dementia; ccRCC, clear cell renal cell carcinoma; CD, Crohn disease; COPD, chronic obstructive pulmonary disease; eQTL, expression quantitative trait loci; HCC, hepatocellular carcinoma; HNSCC, head and neck squamous cell carcinoma; GTEx, genotype-tissue expression; GWAS, genome-wide association studies; LAP, LC3-associated phagocytosis; LC3-II, phosphatidylethanolamine conjugated form of LC3; LD, linkage disequilibrium; LUAD, lung adenocarcinoma; MAF, minor allele frequency; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NSCLC, non-small cell lung cancer; OS, overall survival; PtdIns3K CIII, class III phosphatidylinositol 3 kinase; PtdIns3P, phosphatidylinositol-3-phosphate; SLE, systemic lupus erythematosus; SNPs, single-nucleotide polymorphisms; mQTL, methylation quantitative trait loci; ULK, unc-51 like autophagy activating kinase; UTRs, untranslated regions; WHO, World Health Organization.
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Affiliation(s)
- Iris Grosjean
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Barnabé Roméo
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Marie-Angela Domdom
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Amine Belaid
- Université Côte d’Azur (UCA), INSERM U1065, C3M, Team 5, F-06204, France
| | - Grégoire D’Andréa
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
- ENT and Head and Neck surgery department, Institut Universitaire de la Face et du Cou, CHU de Nice, University Hospital, Côte d’Azur University, Nice, France
| | - Nicolas Guillot
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Romain K Gherardi
- INSERM U955 Team Relais, Faculty of Health, Paris Est University, France
| | - Jocelyn Gal
- University Côte d’Azur, Centre Antoine Lacassagne, Epidemiology and Biostatistics Department, Nice, France
| | - Gérard Milano
- Université Côte d’Azur, Centre Antoine Lacassagne, UPR7497, Nice, France
| | - Charles Hugo Marquette
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
- University Côte d’Azur, FHU-OncoAge, Department of Pulmonary Medicine and Oncology, CHU de Nice, Nice, France
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Patrick Brest
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Martin Von Bergen
- Helmholtz Centre for Environmental Research GmbH - UFZ, Dep. of Molecular Systems Biology; University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany
| | - Daniel J. Klionsky
- University of Michigan, Life Sciences Institute, Ann Arbor, MI, 48109, USA
| | - Christopher I. Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Paul Hofman
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
- University Côte d’Azur, FHU-OncoAge, CHU de Nice, Laboratory of Clinical and Experimental Pathology (LPCE) Biobank(BB-0033-00025), Nice, France
| | - Baharia Mograbi
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
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Fontanillas P, Kless A, Bothmer J, Tung JY. Genome-wide association study of pain sensitivity assessed by questionnaire and the cold pressor test. Pain 2022; 163:1763-1776. [PMID: 34924555 PMCID: PMC9393798 DOI: 10.1097/j.pain.0000000000002568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022]
Abstract
ABSTRACT We deployed an online pain sensitivity questionnaire (PSQ) and an at-home version of the cold pressor test (CPT) in a large genotyped cohort. We performed genome-wide association studies on the PSQ score (25,321 participants) and CPT duration (6853). We identified one new genome-wide significant locus associated with the PSQ score, which was located in the TSSC1 (also known as EIPR1 ) gene (rs58194899, OR = 0.950 [0.933-0.967], P -value = 1.9 × 10 -8 ). Although high pain sensitivity measured by both PSQ and CPT was associated with individual history of chronic and acute pains, genetic correlation analyses surprisingly suggested an opposite direction: PSQ score was inversely genetically correlated with neck and shoulder pain ( rg = -0.71), rheumatoid arthritis (-0.68), and osteoarthritis (-0.38), and with known risk factors, such as the length of working week (-0.65), smoking (-0.36), or extreme BMI (-0.23). Gene-based analysis followed by pathway analysis showed that genome-wide association studies results were enriched for genes expressed in the brain and involved in neuronal development and glutamatergic synapse signaling pathways. Finally, we confirmed that females with red hair were more sensitive to pain and found that genetic variation in the MC1R gene was associated with an increase in self-perceived pain sensitivity as assessed by the PSQ.
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Affiliation(s)
| | - Achim Kless
- Grünenthal Innovation, Grünenthal GmbH, Aachen, Germany. Kless is now with the Neuroscience Genetics, Eli Lilly and Company, United Kingdom
| | - John Bothmer
- Grünenthal Innovation, Grünenthal GmbH, Aachen, Germany. Kless is now with the Neuroscience Genetics, Eli Lilly and Company, United Kingdom
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8
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P.O.F.T. Guimarães J, Sprooten E, Beckmann CF, Franke B, Bralten J. Shared genetic influences on resting‐state functional networks of the brain. Hum Brain Mapp 2022; 43:1787-1803. [PMID: 35076988 PMCID: PMC8933256 DOI: 10.1002/hbm.25712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 11/17/2022] Open
Abstract
The amplitude of activation in brain resting state networks (RSNs), measured with resting‐state functional magnetic resonance imaging, is heritable and genetically correlated across RSNs, indicating pleiotropy. Recent univariate genome‐wide association studies (GWASs) explored the genetic underpinnings of individual variation in RSN activity. Yet univariate genomic analyses do not describe the pleiotropic nature of RSNs. In this study, we used a novel multivariate method called genomic structural equation modeling to model latent factors that capture the shared genomic influence on RSNs and to identify single nucleotide polymorphisms (SNPs) and genes driving this pleiotropy. Using summary statistics from GWAS of 21 RSNs reported in UK Biobank (N = 31,688), the genomic latent factor analysis was first conducted in a discovery sample (N = 21,081), and then tested in an independent sample from the same cohort (N = 10,607). In the discovery sample, we show that the genetic organization of RSNs can be best explained by two distinct but correlated genetic factors that divide multimodal association networks and sensory networks. Eleven of the 17 factor loadings were replicated in the independent sample. With the multivariate GWAS, we found and replicated nine independent SNPs associated with the joint architecture of RSNs. Further, by combining the discovery and replication samples, we discovered additional SNP and gene associations with the two factors of RSN amplitude. We conclude that modeling the genetic effects on brain function in a multivariate way is a powerful approach to learn more about the biological mechanisms involved in brain function.
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Affiliation(s)
- João P.O.F.T. Guimarães
- Department of Cognitive Neuroscience Radboud University Medical Center Nijmegen The Netherlands
- Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands
- Department of Human Genetics Radboud University Medical Center Nijmegen The Netherlands
| | - E. Sprooten
- Department of Cognitive Neuroscience Radboud University Medical Center Nijmegen The Netherlands
- Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands
- Department of Human Genetics Radboud University Medical Center Nijmegen The Netherlands
| | - C. F. Beckmann
- Department of Cognitive Neuroscience Radboud University Medical Center Nijmegen The Netherlands
- Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands
- Centre for Functional MRI of the Brain (FMRIB) University of Oxford Oxford UK
| | - B. Franke
- Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands
- Department of Human Genetics Radboud University Medical Center Nijmegen The Netherlands
- Department of Psychiatry Radboud University Medical Center Nijmegen The Netherlands
| | - J. Bralten
- Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands
- Department of Human Genetics Radboud University Medical Center Nijmegen The Netherlands
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9
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Li Q, Wang Z, Zong L, Ye L, Ye J, Ou H, Jiang T, Guo B, Yang Q, Liang W, Zhang J, Long Y, Zheng X, Hou Y, Wu F, Zhou L, Li S, Huang X, Zhao C. Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function. Mol Psychiatry 2021; 26:6630-6642. [PMID: 33963283 DOI: 10.1038/s41380-021-01126-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 12/26/2022]
Abstract
The non-Mendelian features of phenotypic variations within monozygotic twins are likely complicated by environmental modifiers of genetic effects that have yet to be elucidated. Here, we performed methylome and genome analyses of blood DNA from psychiatric disorder-discordant monozygotic twins to study how allele-specific methylation (ASM) mediates phenotypic variations. We identified that thousands of genetic variants with ASM imbalances exhibit phenotypic variation-associated switching at regulatory loci. These ASMs have plausible causal associations with psychiatric disorders through effects on interactions between transcription factors, DNA methylations, and other epigenomic markers and then contribute to dysregulated gene expression, which eventually increases disease susceptibility. Moreover, we also experimentally validated the model that the rs4854158 alternative C allele at an ASM switching regulatory locus of EIPR1 encoding endosome-associated recycling protein-interacting protein 1, is associated with demethylation and higher RNA expression and shows lower TF binding affinities in unaffected controls. An epigenetic ASM switching induces C allele hypermethylation and then recruits repressive Polycomb repressive complex 2 (PRC2), reinforces trimethylation of lysine 27 on histone 3 and inhibits its transcriptional activity, thus leading to downregulation of EIPR1 in schizophrenia. Moreover, disruption of rs4854158 induces gain of EIPR1 function and promotes neural development and vesicle trafficking. Our study provides a powerful framework for identifying regulatory risk variants and contributes to our understanding of the interplay between genetic and epigenetic variants in mediating psychiatric disorder susceptibility.
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Affiliation(s)
- Qiyang Li
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Lu Zong
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Linyan Ye
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Junping Ye
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Haiyan Ou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Tingyun Jiang
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Bo Guo
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Yang
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Wenquan Liang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Yong Long
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Xianzhen Zheng
- Guangdong General Hospital, Guangdong Academy of Medical Science and Guangdong Mental Health Center, Guangzhou, China
| | - Yu Hou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Fengchun Wu
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Lin Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Xingbing Huang
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China. .,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China.
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10
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Damotte V, van der Lee SJ, Chouraki V, Grenier‐Boley B, Simino J, Adams H, Tosto G, White C, Terzikhan N, Cruchaga C, Knol MJ, Li S, Schraen S, Grove ML, Satizabal C, Amin N, Berr C, Younkin S, Gottesman RF, Buée L, Beiser A, Knopman DS, Uitterlinden A, DeCarli C, Bressler J, DeStefano A, Dartigues J, Yang Q, Boerwinkle E, Tzourio C, Fornage M, Ikram MA, Amouyel P, de Jager P, Reitz C, Mosley TH, Lambert J, Seshadri S, van Duijn CM. Plasma amyloid β levels are driven by genetic variants near APOE, BACE1, APP, PSEN2: A genome-wide association study in over 12,000 non-demented participants. Alzheimers Dement 2021; 17:1663-1674. [PMID: 34002480 PMCID: PMC8597077 DOI: 10.1002/alz.12333] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 12/17/2020] [Accepted: 02/18/2021] [Indexed: 01/02/2023]
Abstract
INTRODUCTION There is increasing interest in plasma amyloid beta (Aβ) as an endophenotype of Alzheimer's disease (AD). Identifying the genetic determinants of plasma Aβ levels may elucidate important biological processes that determine plasma Aβ measures. METHODS We included 12,369 non-demented participants from eight population-based studies. Imputed genetic data and measured plasma Aβ1-40, Aβ1-42 levels and Aβ1-42/Aβ1-40 ratio were used to perform genome-wide association studies, and gene-based and pathway analyses. Significant variants and genes were followed up for their association with brain positron emission tomography Aβ deposition and AD risk. RESULTS Single-variant analysis identified associations with apolipoprotein E (APOE) for Aβ1-42 and Aβ1-42/Aβ1-40 ratio, and BACE1 for Aβ1-40. Gene-based analysis of Aβ1-40 additionally identified associations for APP, PSEN2, CCK, and ZNF397. There was suggestive evidence for interaction between a BACE1 variant and APOE ε4 on brain Aβ deposition. DISCUSSION Identification of variants near/in known major Aβ-processing genes strengthens the relevance of plasma-Aβ levels as an endophenotype of AD.
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Affiliation(s)
- Vincent Damotte
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de LilleLilleFrance
| | - Sven J. van der Lee
- Alzheimer Center Amsterdam, Department of NeurologyAmsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMCAmsterdamthe Netherlands
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
| | - Vincent Chouraki
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de LilleLilleFrance
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
| | | | - Jeannette Simino
- Gertrude C. Ford MIND CenterDepartment of Data ScienceJohn D. Bower School of Population HealthUniversity of Mississippi Medical CenterJacksonMississippiUSA
| | - Hieab Adams
- Departments of EpidemiologyNeurologyand Radiology and Nuclear MedicineErasmus Medical CenterRotterdamthe Netherlands
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew YorkUSA
- Gertrude H. Sergievsky CenterColumbia UniversityNew YorkNew YorkUSA
| | - Charles White
- Program in Translational NeuroPsychiatric GenomicsInstitute for the NeurosciencesDepartments of Neurology and PsychiatryBrigham and Women's HospitalBostonMassachusettsUSA
- Program in Medical and Population GeneticsBroad InstituteCambridgeMassachusettsUSA
| | - Natalie Terzikhan
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
- Department of Respiratory MedicineGhent University HospitalGhentBelgium
| | - Carlos Cruchaga
- Department of PsychiatryWashington University in St. LouisSaint LouisMissouriUSA
| | - Maria J. Knol
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
| | - Shuo Li
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
| | - Susanna Schraen
- Université Lille, CHU‐Lille, InsermUF de Neurobiologie, CBPGLilleFrance
| | - Megan L. Grove
- Human Genetics Center, Department of EpidemiologyHuman Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Claudia Satizabal
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
| | - Najaf Amin
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
| | - Claudine Berr
- INSERM U1061University of MontpellierMontpellierFrance
| | - Steven Younkin
- Department of NeuroscienceMayo Clinic, JacksonvilleFloridaUSA
| | | | - Rebecca F. Gottesman
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of EpidemiologyJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Luc Buée
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de LilleLilleFrance
- Institut National de la Santé et de la Recherche Medicale (INSERMUniversité de LilleLilleFrance
| | - Alexa Beiser
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
| | - David S. Knopman
- Department of NeurologyMayo Clinic College of MedicineRochesterMinnesotaUSA
| | - Andre Uitterlinden
- Department of Internal MedicineErasmus Medical CenterRotterdamthe Netherlands
| | - Charles DeCarli
- Department of NeurologyUniversity of California at DavisDavisCaliforniaUSA
| | - Jan Bressler
- Human Genetics Center, Department of EpidemiologyHuman Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Anita DeStefano
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
| | | | - Qiong Yang
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
| | - Eric Boerwinkle
- Human Genetics Center, Department of EpidemiologyHuman Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at HoustonHoustonTexasUSA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexasUSA
| | - Christophe Tzourio
- Bordeaux Population Health Research CenterINSERM, UMR1219Bordeaux UniversityBordeauxFrance
| | - Myriam Fornage
- Human Genetics Center, Department of EpidemiologyHuman Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at HoustonHoustonTexasUSA
- Brown Foundation Institute of Molecular MedicineMcGovern Medical SchoolThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - M. Arfan Ikram
- Departments of EpidemiologyNeurologyand Radiology and Nuclear MedicineErasmus Medical CenterRotterdamthe Netherlands
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de LilleLilleFrance
| | - Phil de Jager
- Program in Translational NeuroPsychiatric GenomicsInstitute for the NeurosciencesDepartments of Neurology and PsychiatryBrigham and Women's HospitalBostonMassachusettsUSA
- Program in Medical and Population GeneticsBroad InstituteCambridgeMassachusettsUSA
- Center for Translational & Systems NeuroimmunologyDepartment of NeurologyColumbia University Medical Center, New YorkNew YorkNew YorkUSA
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew YorkUSA
- Gertrude H. Sergievsky CenterColumbia UniversityNew YorkNew YorkUSA
- Department of NeurologyColumbia UniversityNew YorkNew YorkUSA
- Department of EpidemiologyColumbia UniversityNew YorkNew YorkUSA
| | - Thomas H. Mosley
- Department of MedicineGertrude C. Ford MIND CenterUniversity of Mississippi Medical CenterJacksonMississippiUSA
| | | | - Sudha Seshadri
- Department of NeurologyBoston University School of MedicineBostonMassachusettsUSA
- The Framingham Heart StudyFraminghamMassachusettsUSA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative DiseasesUT Health San AntonioSan AntonioTexasUSA
| | - Cornelia M. van Duijn
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
- Nuffield Department of Population HealthUniversity of OxfordOxfordUK
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11
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Recent ultra-rare inherited variants implicate new autism candidate risk genes. Nat Genet 2021; 53:1125-1134. [PMID: 34312540 DOI: 10.1038/s41588-021-00899-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/18/2021] [Indexed: 01/28/2023]
Abstract
Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation contributes significantly to risk. Using whole-genome sequencing data from 3,474 families, we investigate another source of large-effect risk variation, ultra-rare variants. We report and replicate a transmission disequilibrium of private, likely gene-disruptive (LGD) variants in probands but find that 95% of this burden resides outside of known DNM-enriched genes. This variant class more strongly affects multiplex family probands and supports a multi-hit model for autism. Candidate genes with private LGD variants preferentially transmitted to probands converge on the E3 ubiquitin-protein ligase complex, intracellular transport and Erb signaling protein networks. We estimate that these variants are approximately 2.5 generations old and significantly younger than other variants of similar type and frequency in siblings. Overall, private LGD variants are under strong purifying selection and appear to act on a distinct set of genes not yet associated with autism.
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12
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Horimoto ARVR, Xue D, Thornton TA, Blue EE. Admixture mapping reveals the association between Native American ancestry at 3q13.11 and reduced risk of Alzheimer's disease in Caribbean Hispanics. Alzheimers Res Ther 2021; 13:122. [PMID: 34217363 PMCID: PMC8254995 DOI: 10.1186/s13195-021-00866-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/20/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Genetic studies have primarily been conducted in European ancestry populations, identifying dozens of loci associated with late-onset Alzheimer's disease (AD). However, much of AD's heritability remains unexplained; as the prevalence of AD varies across populations, the genetic architecture of the disease may also vary by population with the presence of novel variants or loci. METHODS We conducted genome-wide analyses of AD in a sample of 2565 Caribbean Hispanics to better understand the genetic contribution to AD in this population. Statistical analysis included both admixture mapping and association testing. Evidence for differential gene expression within regions of interest was collected from independent transcriptomic studies comparing AD cases and controls in samples with primarily European ancestry. RESULTS Our genome-wide association study of AD identified no loci reaching genome-wide significance. However, a genome-wide admixture mapping analysis that tests for association between a haplotype's ancestral origin and AD status detected a genome-wide significant association with chromosome 3q13.11 (103.7-107.7Mb, P = 8.76E-07), driven by a protective effect conferred by the Native American ancestry (OR = 0.58, 95%CI = 0.47-0.73). Within this region, two variants were significantly associated with AD after accounting for the number of independent tests (rs12494162, P = 2.33E-06; rs1731642, P = 6.36E-05). The significant admixture mapping signal is composed of 15 haplotype blocks spanning 5 protein-coding genes (ALCAM, BBX, CBLB, CCDC54, CD47) and four brain-derived topologically associated domains, and includes markers significantly associated with the expression of ALCAM, BBX, CBLB, and CD47 in the brain. ALCAM and BBX were also significantly differentially expressed in the brain between AD cases and controls with European ancestry. CONCLUSION These results provide multiethnic evidence for a relationship between AD and multiple genes at 3q13.11 and illustrate the utility of leveraging genetic ancestry diversity via admixture mapping for new insights into AD.
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Affiliation(s)
| | - Diane Xue
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Elizabeth E Blue
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA.
- Division of Medical Genetics, University of Washington, BOX 357720, Seattle, WA, 98195-7720, USA.
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13
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Xi J, Ding D, Zhao Q, Liang X, Zheng L, Guo Q, Hong Z, Fu H, Xu J, Xiao Q. Joint Effect of ABCA7 rs4147929 and Body Mass Index on Progression from Mild Cognitive Impairment to Alzheimer's Disease: The Shanghai Aging Study. Curr Alzheimer Res 2021; 17:185-195. [PMID: 32183673 DOI: 10.2174/1567205017666200317095608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 01/15/2020] [Accepted: 02/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Approximately 40 independent Single Nucleotide Polymorphisms (SNPs) have been associated with Alzheimer's Disease (AD) or cognitive decline in genome-wide association studies. OBJECTIVE We aimed to evaluate the joint effect of genetic polymorphisms and environmental factors on the progression from Mild Cognitive Impairment (MCI) to AD (MCI-AD progression) in a Chinese community cohort. METHODS Demographic, DNA and incident AD diagnosis data were derived from the follow-up of 316 participants with MCI at baseline of the Shanghai Aging Study. The associations of 40 SNPs and environmental predictors with MCI-AD progression were assessed using the Kaplan-Meier method with the log-rank test and Cox regression model. RESULTS Rs4147929 at ATP-binding cassette family A member 7 (ABCA7) (AG/AA vs. GG, hazard ratio [HR] = 2.43, 95% confidence interval [CI] 1.24-4.76) and body mass index (BMI) (overweight vs. non-overweight, HR = 0.41, 95% CI 0.22-0.78) were independent predictors of MCI-AD progression. In the combined analyses, MCI participants with the copresence of non-overweight BMI and the ABCA7 rs4147929 (AG/AA) risk genotype had an approximately 6-fold higher risk of MCI-AD progression than those with an overweight BMI and a non-risk genotype (HR = 6.77, 95% CI 2.60-17.63). However, a nonsignificant result was found when participants carried only one of these two risk factors (nonoverweight BMI and AG/AA of ABCA7 rs4147929). CONCLUSION ABCA7 rs4147929 and BMI jointly affect MCI-AD progression. MCI participants with the rs4147929 risk genotype may benefit from maintaining an overweight BMI level with regard to their risk for incident AD.
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Affiliation(s)
- Jianxiong Xi
- Department of Preventive Medicine and Health Education, School of Public Health, Fudan University, Shanghai, China
| | - Ding Ding
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging Diseases, Shanghai, China
| | - Qianhua Zhao
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging Diseases, Shanghai, China
| | - Xiaoniu Liang
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging Diseases, Shanghai, China
| | - Li Zheng
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging Diseases, Shanghai, China
| | - Qihao Guo
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging Diseases, Shanghai, China
| | - Zhen Hong
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging Diseases, Shanghai, China
| | - Hua Fu
- Department of Preventive Medicine and Health Education, School of Public Health, Fudan University, Shanghai, China
| | - Jianfeng Xu
- Department of Preventive Medicine and Health Education, School of Public Health, Fudan University, Shanghai, China
| | - Qianyi Xiao
- Department of Preventive Medicine and Health Education, School of Public Health, Fudan University, Shanghai, China
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14
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Stocker H, Nabers A, Perna L, Möllers T, Rujescu D, Hartmann AM, Holleczek B, Schöttker B, Stockmann J, Gerwert K, Brenner H. Genetic predisposition, Aβ misfolding in blood plasma, and Alzheimer's disease. Transl Psychiatry 2021; 11:261. [PMID: 33934115 PMCID: PMC8088439 DOI: 10.1038/s41398-021-01380-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
Alzheimer's disease is highly heritable and characterized by amyloid plaques and tau tangles in the brain. The aim of this study was to investigate the association between genetic predisposition, Aβ misfolding in blood plasma, a unique marker of Alzheimer associated neuropathological changes, and Alzheimer's disease occurrence within 14 years. Within a German community-based cohort, two polygenic risk scores (clinical Alzheimer's disease and Aβ42 based) were calculated, APOE genotype was determined, and Aβ misfolding in blood plasma was measured by immuno-infrared sensor in 59 participants diagnosed with Alzheimer's disease during 14 years of follow-up and 581 participants without dementia diagnosis. Associations between each genetic marker and Aβ misfolding were assessed through logistic regression and the ability of each genetic marker and Aβ misfolding to predict Alzheimer's disease was determined. The Alzheimer's disease polygenic risk score and APOE ε4 presence were associated to Aβ misfolding (odds ratio, 95% confidence interval: per standard deviation increase of score: 1.25, 1.03-1.51; APOE ε4 presence: 1.61, 1.04-2.49). No association was evident for the Aβ polygenic risk score. All genetic markers were predictive of Alzheimer's disease diagnosis albeit much less so than Aβ misfolding (areas under the curve: Aβ polygenic risk score: 0.55; AD polygenic risk score: 0.59; APOE ε4: 0.63; Aβ misfolding: 0.84). Clinical Alzheimer's genetic risk was associated to early pathological changes (Aβ misfolding) measured in blood, however, predicted Alzheimer's disease less accurately than Aβ misfolding itself. Genetic predisposition may provide information regarding disease initiation, while Aβ misfolding could be important in clinical risk prediction.
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Affiliation(s)
- Hannah Stocker
- Network Aging Research, Heidelberg University, Heidelberg, Germany.
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany.
- Medical Faculty, Heidelberg University, Heidelberg, Germany.
| | - Andreas Nabers
- Department of Biophysics, Competence Center for Biospectroscopy, Ruhr-University Bochum, Bochum, Germany
- Faculty of Biology and Biotechnology, Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Laura Perna
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Tobias Möllers
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Halle, Halle, Germany
| | - Annette M Hartmann
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Halle, Halle, Germany
| | | | - Ben Schöttker
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Julia Stockmann
- Department of Biophysics, Competence Center for Biospectroscopy, Ruhr-University Bochum, Bochum, Germany
- Faculty of Biology and Biotechnology, Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, Competence Center for Biospectroscopy, Ruhr-University Bochum, Bochum, Germany
- Faculty of Biology and Biotechnology, Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Hermann Brenner
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
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15
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CAPS1 is involved in hippocampal synaptic plasticity and hippocampus-associated learning. Sci Rep 2021; 11:8656. [PMID: 33883618 PMCID: PMC8060421 DOI: 10.1038/s41598-021-88009-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/07/2021] [Indexed: 12/14/2022] Open
Abstract
Calcium-dependent activator protein for secretion 1 (CAPS1) is a key molecule in vesicular exocytosis, probably in the priming step. However, CAPS1's role in synaptic plasticity and brain function is elusive. Herein, we showed that synaptic plasticity and learning behavior were impaired in forebrain and/or hippocampus-specific Caps1 conditional knockout (cKO) mice by means of molecular, physiological, and behavioral analyses. Neonatal Caps1 cKO mice showed a decrease in the number of docked vesicles in the hippocampal CA3 region, with no detectable changes in the distribution of other major exocytosis-related molecules. Additionally, long-term potentiation (LTP) was partially and severely impaired in the CA1 and CA3 regions, respectively. CA1 LTP was reinforced by repeated high-frequency stimuli, whereas CA3 LTP was completely abolished. Accordingly, hippocampus-associated learning was severely impaired in adeno-associated virus (AAV) infection-mediated postnatal Caps1 cKO mice. Collectively, our findings suggest that CAPS1 is a key protein involved in the cellular mechanisms underlying hippocampal synaptic release and plasticity, which is crucial for hippocampus-associated learning.
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16
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Vogrinc D, Goričar K, Dolžan V. Genetic Variability in Molecular Pathways Implicated in Alzheimer's Disease: A Comprehensive Review. Front Aging Neurosci 2021; 13:646901. [PMID: 33815092 PMCID: PMC8012500 DOI: 10.3389/fnagi.2021.646901] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/16/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disease, affecting a significant part of the population. The majority of AD cases occur in the elderly with a typical age of onset of the disease above 65 years. AD presents a major burden for the healthcare system and since population is rapidly aging, the burden of the disease will increase in the future. However, no effective drug treatment for a full-blown disease has been developed to date. The genetic background of AD is extensively studied; numerous genome-wide association studies (GWAS) identified significant genes associated with increased risk of AD development. This review summarizes more than 100 risk loci. Many of them may serve as biomarkers of AD progression, even in the preclinical stage of the disease. Furthermore, we used GWAS data to identify key pathways of AD pathogenesis: cellular processes, metabolic processes, biological regulation, localization, transport, regulation of cellular processes, and neurological system processes. Gene clustering into molecular pathways can provide background for identification of novel molecular targets and may support the development of tailored and personalized treatment of AD.
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Affiliation(s)
| | | | - Vita Dolžan
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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17
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Li QS, Tian C, Hinds D, Seabrook GR. The association of clinical phenotypes to known AD/FTD genetic risk loci and their inter-relationship. PLoS One 2020; 15:e0241552. [PMID: 33152005 PMCID: PMC7644002 DOI: 10.1371/journal.pone.0241552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/18/2020] [Indexed: 11/25/2022] Open
Abstract
To elucidate how variants in genetic risk loci previously implicated in Alzheimer’s Disease (AD) and/or frontotemporal dementia (FTD) contribute to expression of disease phenotypes, a phenome-wide association study was performed in two waves. In the first wave, we explored clinical traits associated with thirteen genetic variants previously reported to be linked to disease risk using both the 23andMe and UKB cohorts. We tested 30 additional AD variants in UKB cohort only in the second wave. APOE variants defining ε2/ε3/ε4 alleles and rs646776 were identified to be significantly associated with metabolic/cardiovascular and longevity traits. APOE variants were also significantly associated with neurological traits. ABI3 variant rs28394864 was significantly associated with cardiovascular (e.g. (hypertension, ischemic heart disease, coronary atherosclerosis, angina) and immune-related trait asthma. Both APOE variants and CLU variant were significantly associated with nearsightedness. HLA- DRB1 variant was associated with diseases with immune-related traits. Additionally, variants from 10+ AD genes (BZRAP1-AS1, ADAMTS4, ADAM10, APH1B, SCIMP, ABI3, SPPL2A, ZNF232, GRN, CD2AP, and CD33) were associated with hematological measurements such as white blood cell (leukocyte) count, monocyte count, neutrophill count, platelet count, and/or mean platelet (thrombocyte) volume (an autoimmune disease biomarker). Many of these genes are expressed specifically in microglia. The associations of ABI3 variant with cardiovascular and immune-related traits are one of the novel findings from this study. Taken together, it is evidenced that at least some AD and FTD variants are associated with multiple clinical phenotypes and not just dementia. These findings were discussed in the context of causal relationship versus pleiotropy via Mendelian randomization analysis.
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Affiliation(s)
- Qingqin S. Li
- Janssen Research & Development, LLC, Titusville, NJ, United States of America
- * E-mail:
| | - Chao Tian
- 23andMe, Inc., Mountain View, CA, United States of America
| | | | - David Hinds
- 23andMe, Inc., Mountain View, CA, United States of America
| | - Guy R. Seabrook
- Johnson & Johnson Innovation, South San Francisco, CA, United States of America
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18
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Eze IC, Jeong A, Schaffner E, Rezwan FI, Ghantous A, Foraster M, Vienneau D, Kronenberg F, Herceg Z, Vineis P, Brink M, Wunderli JM, Schindler C, Cajochen C, Röösli M, Holloway JW, Imboden M, Probst-Hensch N. Genome-Wide DNA Methylation in Peripheral Blood and Long-Term Exposure to Source-Specific Transportation Noise and Air Pollution: The SAPALDIA Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:67003. [PMID: 32484729 PMCID: PMC7263738 DOI: 10.1289/ehp6174] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Few epigenome-wide association studies (EWAS) on air pollutants exist, and none have been done on transportation noise exposures, which also contribute to environmental burden of disease. OBJECTIVE We performed mutually independent EWAS on transportation noise and air pollution exposures. METHODS We used data from two time points of the Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults (SAPALDIA) from 1,389 participants contributing 2,542 observations. We applied multiexposure linear mixed-effects regressions with participant-level random intercept to identify significant Cytosine-phosphate-Guanine (CpG) sites and differentially methylated regions (DMRs) in relation to 1-y average aircraft, railway, and road traffic day-evening-night noise (Lden); nitrogen dioxide (NO 2 ); and particulate matter (PM) with aerodynamic diameter < 2.5 μ m (PM 2.5 ). We performed candidate (CpG-based; cross-systemic phenotypes, combined into "allostatic load") and agnostic (DMR-based) pathway enrichment tests, and replicated previously reported air pollution EWAS signals. RESULTS We found no statistically significant CpGs at false discovery rate < 0.05 . However, 14, 48, 183, 8, and 71 DMRs independently associated with aircraft, railway, and road traffic Lden; NO 2 ; and PM 2.5 , respectively, with minimally overlapping signals. Transportation Lden and air pollutants tendentially associated with decreased and increased methylation, respectively. We observed significant enrichment of candidate DNA methylation related to C-reactive protein and body mass index (aircraft, road traffic Lden, and PM 2.5 ), renal function and "allostatic load" (all exposures). Agnostic functional networks related to cellular immunity, gene expression, cell growth/proliferation, cardiovascular, auditory, embryonic, and neurological systems development were enriched. We replicated increased methylation in cg08500171 (NO 2 ) and decreased methylation in cg17629796 (PM 2.5 ). CONCLUSIONS Mutually independent DNA methylation was associated with source-specific transportation noise and air pollution exposures, with distinct and shared enrichments for pathways related to inflammation, cellular development, and immune responses. These findings contribute in clarifying the pathways linking these exposures and age-related diseases but need further confirmation in the context of mediation analyses. https://doi.org/10.1289/EHP6174.
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Affiliation(s)
- Ikenna C Eze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Emmanuel Schaffner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Maria Foraster
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
- Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona, Spain
| | - Danielle Vienneau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Mark Brink
- Federal Office for the Environment, Bern, Switzerland
| | - Jean-Marc Wunderli
- Empa Laboratory for Acoustics/Noise Control, Swiss Federal Laboratories for Material Science and Technology, Dübendorf, Switzerland
| | - Christian Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christian Cajochen
- Center for Chronobiology, Psychiatric Hospital of the University of Basel, and Transfaculty Research Platform Molecular and Cognitive Neurosciences (MCN), Basel, Switzerland
| | - Martin Röösli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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19
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Konki M, Malonzo M, Karlsson IK, Lindgren N, Ghimire B, Smolander J, Scheinin NM, Ollikainen M, Laiho A, Elo LL, Lönnberg T, Röyttä M, Pedersen NL, Kaprio J, Lähdesmäki H, Rinne JO, Lund RJ. Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease. Clin Epigenetics 2019; 11:130. [PMID: 31477183 PMCID: PMC6721173 DOI: 10.1186/s13148-019-0729-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alzheimer's disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. Environmental and lifestyle factors largely modulate the disease risk and may influence the pathogenesis through epigenetic mechanisms, such as DNA methylation. As environmental and lifestyle factors may affect multiple tissues of the body, we hypothesized that the disease-associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs. RESULTS Comparison of 23 disease discordant Finnish twin pairs with reduced representation bisulfite sequencing revealed peripheral blood DNA methylation differences in 11 genomic regions with at least 15.0% median methylation difference and FDR adjusted p value ≤ 0.05. Several of the affected genes are primarily associated with neuronal functions and pathologies and do not display disease-associated differences in gene expression in blood. The DNA methylation mark in ADARB2 gene was found to be differentially methylated also in the anterior hippocampus, including entorhinal cortex, of non-twin cases and controls. Targeted bisulfite pyrosequencing of the DNA methylation mark in ADARB2 gene in 62 Finnish and Swedish twin pairs revealed that, in addition to the disease status, DNA methylation of this region is influenced by gender, age, zygosity, APOE genotype, and smoking. Further analysis of 120 Swedish twin pairs indicated that this specific DNA methylation mark is not predictive for Alzheimer's disease and becomes differentially methylated after disease onset. CONCLUSIONS DNA methylation differences can be detected in the peripheral blood of twin pairs discordant for Alzheimer's disease. These DNA methylation signatures may have value as disease markers and provide insights into the molecular mechanisms of pathogenesis. We found no evidence that the DNA methylation marks would be associated with gene expression in blood. Further studies are needed to elucidate the potential importance of the associated genes in neuronal functions and to validate the prognostic or diagnostic value of the individual marks or marker panels.
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Affiliation(s)
- Mikko Konki
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, FI-20014, Turku, Finland
| | - Maia Malonzo
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Ida K Karlsson
- Institute of Gerontology and Aging Research Network-Jönköping (ARN-J), School of Health and Welfare, Jönköping University, SE-55111, Jönköping, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | - Noora Lindgren
- Drug Research Doctoral Program, University of Turku, FI-20014, Turku, Finland.,Turku PET Centre, University of Turku, FI-20520, Turku, Finland
| | - Bishwa Ghimire
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Noora M Scheinin
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Turku Brain and Mind Center, FinnBrain Birth Cohort Study, Institute of Clinical Medicine, University of Turku, FI-20014, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, FI-20014, Turku, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Matias Röyttä
- Department of Pathology/Neuropathology, Turku University Hospital, University of Turku, FI-20014, Turku, Finland
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden.,Department of Psychology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland.,Department of Public Health, University of Helsinki, FI-00271, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Juha O Rinne
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Division of Clinical Neurosciences, Turku University Hospital, FI-20014, Turku, Finland
| | - Riikka J Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.
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20
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Wu L, Shu X, Bao J, Guo X, Kote-Jarai Z, Haiman CA, Eeles RA, Zheng W. Analysis of Over 140,000 European Descendants Identifies Genetically Predicted Blood Protein Biomarkers Associated with Prostate Cancer Risk. Cancer Res 2019; 79:4592-4598. [PMID: 31337649 DOI: 10.1158/0008-5472.can-18-3997] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/21/2019] [Accepted: 07/17/2019] [Indexed: 12/24/2022]
Abstract
Several blood protein biomarkers have been associated with prostate cancer risk. However, most studies assessed only a small number of biomarkers and/or included a small sample size. To identify novel protein biomarkers of prostate cancer risk, we studied 79,194 cases and 61,112 controls of European ancestry, included in the PRACTICAL/ELLIPSE consortia, using genetic instruments of protein quantitative trait loci for 1,478 plasma proteins. A total of 31 proteins were associated with prostate cancer risk including proteins encoded by GSTP1, whose methylation level was shown previously to be associated with prostate cancer risk, and MSMB, SPINT2, IGF2R, and CTSS, which were previously implicated as potential target genes of prostate cancer risk variants identified in genome-wide association studies. A total of 18 proteins inversely correlated and 13 positively correlated with prostate cancer risk. For 28 of the identified proteins, gene somatic changes of short indels, splice site, nonsense, or missense mutations were detected in patients with prostate cancer in The Cancer Genome Atlas. Pathway enrichment analysis showed that relevant genes were significantly enriched in cancer-related pathways. In conclusion, this study identifies 31 candidates of protein biomarkers for prostate cancer risk and provides new insights into the biology and genetics of prostate tumorigenesis. SIGNIFICANCE: Integration of genomics and proteomics data identifies biomarkers associated with prostate cancer risk.
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Affiliation(s)
- Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii.,Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, California
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
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21
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Lai D, Wetherill L, Bertelsen S, Carey CE, Kamarajan C, Kapoor M, Meyers JL, Anokhin AP, Bennett DA, Bucholz KK, Chang KK, De Jager PL, Dick DM, Hesselbrock V, Kramer J, Kuperman S, Nurnberger JI, Raj T, Schuckit M, Scott DM, Taylor RE, Tischfield J, Hariri AR, Edenberg HJ, Agrawal A, Bogdan R, Porjesz B, Goate AM, Foroud T. Genome-wide association studies of alcohol dependence, DSM-IV criterion count and individual criteria. GENES, BRAIN, AND BEHAVIOR 2019; 18:e12579. [PMID: 31090166 PMCID: PMC6612573 DOI: 10.1111/gbb.12579] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/19/2019] [Accepted: 05/11/2019] [Indexed: 01/04/2023]
Abstract
Genome-wide association studies (GWAS) of alcohol dependence (AD) have reliably identified variation within alcohol metabolizing genes (eg, ADH1B) but have inconsistently located other signals, which may be partially attributable to symptom heterogeneity underlying the disorder. We conducted GWAS of DSM-IV AD (primary analysis), DSM-IV AD criterion count (secondary analysis), and individual dependence criteria (tertiary analysis) among 7418 (1121 families) European American (EA) individuals from the Collaborative Study on the Genetics of Alcoholism (COGA). Trans-ancestral meta-analyses combined these results with data from 3175 (585 families) African-American (AA) individuals from COGA. In the EA GWAS, three loci were genome-wide significant: rs1229984 in ADH1B for AD criterion count (P = 4.16E-11) and Desire to cut drinking (P = 1.21E-11); rs188227250 (chromosome 8, Drinking more than intended, P = 6.72E-09); rs1912461 (chromosome 15, Time spent drinking, P = 1.77E-08). In the trans-ancestral meta-analysis, rs1229984 was associated with multiple phenotypes and two additional loci were genome-wide significant: rs61826952 (chromosome 1, DSM-IV AD, P = 8.42E-11); rs7597960 (chromosome 2, Time spent drinking, P = 1.22E-08). Associations with rs1229984 and rs18822750 were replicated in independent datasets. Polygenic risk scores derived from the EA GWAS of AD predicted AD in two EA datasets (P < .01; 0.61%-1.82% of variance). Identified novel variants (ie, rs1912461, rs61826952) were associated with differential central evoked theta power (loss - gain; P = .0037) and reward-related ventral striatum reactivity (P = .008), respectively. This study suggests that studying individual criteria may unveil new insights into the genetic etiology of AD liability.
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Affiliation(s)
- Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
| | - Sarah Bertelsen
- Department of Neuroscience, Icahn School of Medicine at Mt.
Sinai, New York, NY
| | - Caitlin E. Carey
- BRAIN Lab, Department of Psychological and Brain Sciences,
Washington University School of Medicine, St. Louis, MO
| | - Chella Kamarajan
- Henri Begleiter Neurodynamics Lab, Department of
Psychiatry, State University of New York, Downstate Medical Center, Brooklyn,
NY
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt.
Sinai, New York, NY
| | - Jacquelyn L. Meyers
- Henri Begleiter Neurodynamics Lab, Department of
Psychiatry, State University of New York, Downstate Medical Center, Brooklyn,
NY
| | - Andrey P. Anokhin
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO
| | - David A. Bennett
- Rush Alzheimer's Disease Center, Rush University
Medical Center, Chicago, IL
| | - Kathleen K. Bucholz
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO
| | - Katharine K. Chang
- BRAIN Lab, Department of Psychological and Brain Sciences,
Washington University School of Medicine, St. Louis, MO
| | - Philip L. De Jager
- Departments of Neurology and Psychiatry, Brigham and
Women's Hospital, Boston, MA
| | - Danielle M. Dick
- Department of Psychology, Virginia Commonwealth University,
Richmond, VA
| | | | - John Kramer
- Department of Psychiatry, Roy Carver College of Medicine,
University of Iowa, Iowa City, IA
| | - Samuel Kuperman
- Department of Psychiatry, Roy Carver College of Medicine,
University of Iowa, Iowa City, IA
| | - John I. Nurnberger
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
- Department of Psychiatry, Indiana University School of
Medicine, Indianapolis, IN
| | - Towfique Raj
- Department of Neuroscience, Icahn School of Medicine at Mt.
Sinai, New York, NY
| | - Marc Schuckit
- Department of Psychiatry, University of California, San
Diego Medical School, San Diego, CA
| | - Denise M. Scott
- Departments of Pediatrics and Human Genetics, Howard
University, Washington, DC
| | | | | | - Ahmad R. Hariri
- Laboratory of NeuroGenetics, Department of Psychology and
Neuroscience, Duke University, Durham, NC, USA
| | - Howard J. Edenberg
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
- Department of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, IN
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO
| | - Ryan Bogdan
- BRAIN Lab, Department of Psychological and Brain Sciences,
Washington University School of Medicine, St. Louis, MO
| | - Bernice Porjesz
- Henri Begleiter Neurodynamics Lab, Department of
Psychiatry, State University of New York, Downstate Medical Center, Brooklyn,
NY
| | - Alison M. Goate
- Department of Neuroscience, Icahn School of Medicine at Mt.
Sinai, New York, NY
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
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22
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Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, Pallesen J, Agerbo E, Andreassen OA, Anney R, Awashti S, Belliveau R, Bettella F, Buxbaum JD, Bybjerg-Grauholm J, Bækvad-Hansen M, Cerrato F, Chambert K, Christensen JH, Churchhouse C, Dellenvall K, Demontis D, De Rubeis S, Devlin B, Djurovic S, Dumont AL, Goldstein JI, Hansen CS, Hauberg ME, Hollegaard MV, Hope S, Howrigan DP, Huang H, Hultman CM, Klei L, Maller J, Martin J, Martin AR, Moran JL, Nyegaard M, Nærland T, Palmer DS, Palotie A, Pedersen CB, Pedersen MG, dPoterba T, Poulsen JB, Pourcain BS, Qvist P, Rehnström K, Reichenberg A, Reichert J, Robinson EB, Roeder K, Roussos P, Saemundsen E, Sandin S, Satterstrom FK, Davey Smith G, Stefansson H, Steinberg S, Stevens CR, Sullivan PF, Turley P, Walters GB, Xu X, Stefansson K, Geschwind DH, Nordentoft M, Hougaard DM, Werge T, Mors O, Mortensen PB, Neale BM, Daly MJ, Børglum AD. Identification of common genetic risk variants for autism spectrum disorder. Nat Genet 2019; 51:431-444. [PMID: 30804558 PMCID: PMC6454898 DOI: 10.1038/s41588-019-0344-8] [Citation(s) in RCA: 1228] [Impact Index Per Article: 245.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/12/2018] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample-size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 individuals with ASD and 27,969 controls that identified five genome-wide-significant loci. Leveraging GWAS results from three phenotypes with significantly overlapping genetic architectures (schizophrenia, major depression, and educational attainment), we identified seven additional loci shared with other traits at equally strict significance levels. Dissecting the polygenic architecture, we found both quantitative and qualitative polygenic heterogeneity across ASD subtypes. These results highlight biological insights, particularly relating to neuronal function and corticogenesis, and establish that GWAS performed at scale will be much more productive in the near term in ASD.
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Affiliation(s)
- Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Thomas D Als
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Manuel Mattheisen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonatan Pallesen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Ole A Andreassen
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Richard Anney
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Swapnil Awashti
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Rich Belliveau
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Francesco Bettella
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Felecia Cerrato
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jane H Christensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Claire Churchhouse
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Karin Dellenvall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Srdjan Djurovic
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ashley L Dumont
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jacqueline I Goldstein
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Christine S Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Institute of Biological Psychiatry, MHC SctHans, Mental Health Services, Copenhagen, Denmark
| | - Mads Engel Hauberg
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Mads V Hollegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Sigrun Hope
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Department of Neurohabilitation, Oslo University Hospital, Oslo, Norway
| | - Daniel P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Julian Maller
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Genomics plc, Oxford, UK
- Vertex Pharmaceuticals, Abingdon, UK
| | - Joanna Martin
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mette Nyegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Terje Nærland
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- NevSom, Department of Rare Disorders and Disabilities, , Oslo University Hospital, Oslo, Norway
| | - Duncan S Palmer
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Carsten Bøcker Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Marianne Giørtz Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Timothy dPoterba
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jesper Buchhave Poulsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Per Qvist
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | | | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer Reichert
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elise B Robinson
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kathryn Roeder
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | | | - Christine R Stevens
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick Turley
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - G Bragi Walters
- deCODE genetics/Amgen, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment and Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC SctHans, Mental Health Services, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.
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Patel R, Scheinfeldt LB, Sanderford MD, Lanham TR, Tamura K, Platt A, Glicksberg BS, Xu K, Dudley JT, Kumar S. Adaptive Landscape of Protein Variation in Human Exomes. Mol Biol Evol 2018; 35:2015-2025. [PMID: 29846678 PMCID: PMC6063297 DOI: 10.1093/molbev/msy107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The human genome contains hundreds of thousands of missense mutations. However, only a handful of these variants are known to be adaptive, which implies that adaptation through protein sequence change is an extremely rare phenomenon in human evolution. Alternatively, existing methods may lack the power to pinpoint adaptive variation. We have developed and applied an Evolutionary Probability Approach (EPA) to discover candidate adaptive polymorphisms (CAPs) through the discordance between allelic evolutionary probabilities and their observed frequencies in human populations. EPA reveals thousands of missense CAPs, which suggest that a large number of previously optimal alleles experienced a reversal of fortune in the human lineage. We explored nonadaptive mechanisms to explain CAPs, including the effects of demography, mutation rate variability, and negative and positive selective pressures in modern humans. Many nonadaptive hypotheses were tested, but failed to explain the data, which suggests that a large proportion of CAP alleles have increased in frequency due to beneficial selection. This suggestion is supported by the fact that a vast majority of adaptive missense variants discovered previously in humans are CAPs, and hundreds of CAP alleles are protective in genotype-phenotype association data. Our integrated phylogenomic and population genetic EPA approach predicts the existence of thousands of nonneutral candidate variants in the human proteome. We expect this collection to be enriched in beneficial variation. The EPA approach can be applied to discover candidate adaptive variation in any protein, population, or species for which allele frequency data and reliable multispecies alignments are available.
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Affiliation(s)
- Ravi Patel
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
| | - Laura B Scheinfeldt
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Coriell Institute for Medical Research, Camden, NJ
| | - Maxwell D Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Tamera R Lanham
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Koichiro Tamura
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
| | - Alexander Platt
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ke Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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24
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Guerreiro R, Ross OA, Kun-Rodrigues C, Hernandez DG, Orme T, Eicher JD, Shepherd CE, Parkkinen L, Darwent L, Heckman MG, Scholz SW, Troncoso JC, Pletnikova O, Ansorge O, Clarimon J, Lleo A, Morenas-Rodriguez E, Clark L, Honig LS, Marder K, Lemstra A, Rogaeva E, St George-Hyslop P, Londos E, Zetterberg H, Barber I, Braae A, Brown K, Morgan K, Troakes C, Al-Sarraj S, Lashley T, Holton J, Compta Y, Van Deerlin V, Serrano GE, Beach TG, Lesage S, Galasko D, Masliah E, Santana I, Pastor P, Diez-Fairen M, Aguilar M, Tienari PJ, Myllykangas L, Oinas M, Revesz T, Lees A, Boeve BF, Petersen RC, Ferman TJ, Escott-Price V, Graff-Radford N, Cairns NJ, Morris JC, Pickering-Brown S, Mann D, Halliday GM, Hardy J, Trojanowski JQ, Dickson DW, Singleton A, Stone DJ, Bras J. Investigating the genetic architecture of dementia with Lewy bodies: a two-stage genome-wide association study. Lancet Neurol 2018; 17:64-74. [PMID: 29263008 PMCID: PMC5805394 DOI: 10.1016/s1474-4422(17)30400-3] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/17/2017] [Accepted: 11/03/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND Dementia with Lewy bodies is the second most common form of dementia in elderly people but has been overshadowed in the research field, partly because of similarities between dementia with Lewy bodies, Parkinson's disease, and Alzheimer's disease. So far, to our knowledge, no large-scale genetic study of dementia with Lewy bodies has been done. To better understand the genetic basis of dementia with Lewy bodies, we have done a genome-wide association study with the aim of identifying genetic risk factors for this disorder. METHODS In this two-stage genome-wide association study, we collected samples from white participants of European ancestry who had been diagnosed with dementia with Lewy bodies according to established clinical or pathological criteria. In the discovery stage (with the case cohort recruited from 22 centres in ten countries and the controls derived from two publicly available database of Genotypes and Phenotypes studies [phs000404.v1.p1 and phs000982.v1.p1] in the USA), we performed genotyping and exploited the recently established Haplotype Reference Consortium panel as the basis for imputation. Pathological samples were ascertained following autopsy in each individual brain bank, whereas clinical samples were collected after participant examination. There was no specific timeframe for collection of samples. We did association analyses in all participants with dementia with Lewy bodies, and also only in participants with pathological diagnosis. In the replication stage, we performed genotyping of significant and suggestive results from the discovery stage. Lastly, we did a meta-analysis of both stages under a fixed-effects model and used logistic regression to test for association in each stage. FINDINGS This study included 1743 patients with dementia with Lewy bodies (1324 with pathological diagnosis) and 4454 controls (1216 patients with dementia with Lewy bodies vs 3791 controls in the discovery stage; 527 vs 663 in the replication stage). Results confirm previously reported associations: APOE (rs429358; odds ratio [OR] 2·40, 95% CI 2·14-2·70; p=1·05 × 10-48), SNCA (rs7681440; OR 0·73, 0·66-0·81; p=6·39 × 10-10), an GBA (rs35749011; OR 2·55, 1·88-3·46; p=1·78 × 10-9). They also provide some evidence for a novel candidate locus, namely CNTN1 (rs7314908; OR 1·51, 1·27-1·79; p=2·32 × 10-6); further replication will be important. Additionally, we estimate the heritable component of dementia with Lewy bodies to be about 36%. INTERPRETATION Despite the small sample size for a genome-wide association study, and acknowledging the potential biases from ascertaining samples from multiple locations, we present the most comprehensive and well powered genetic study in dementia with Lewy bodies so far. These data show that common genetic variability has a role in the disease. FUNDING The Alzheimer's Society and the Lewy Body Society.
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Affiliation(s)
- Rita Guerreiro
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Department of Medical Sciences and Institute of Biomedicine, iBiMED, University of Aveiro, Aveiro, Portugal
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Celia Kun-Rodrigues
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA; German Center for Neurodegenerative Diseases, Tubingen, Germany
| | - Tatiana Orme
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | | | - Claire E Shepherd
- Neuroscience Research Australia, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Lee Darwent
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Jordi Clarimon
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Alberto Lleo
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Estrella Morenas-Rodriguez
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Lorraine Clark
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Lawrence S Honig
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Karen Marder
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Afina Lemstra
- Department of Neurology and Alzheimer Center, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Elisabet Londos
- Clinical Memory Research Unit, Institution of Clinical Sciences Malmo, Lund University, Sweden
| | - Henrik Zetterberg
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Molndal, Sweden
| | - Imelda Barber
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Anne Braae
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Kristelle Brown
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Safa Al-Sarraj
- Department of Basic and Clinical Neuroscience and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Janice Holton
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Yaroslau Compta
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Parkinson's Disease & Movement Disorders Unit, Neurology Service, Hospital Clinic, IDIBAPS, CIBERNED, Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Vivianna Van Deerlin
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Suzanne Lesage
- Inserm U1127, CNRS UMR7225, Sorbonne Universites, UPMC Univ Paris 06, UMR, Paris, France; S1127, Institut du Cerveau et de la Moelle epiniere, Paris, France
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA
| | - Eliezer Masliah
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA; Division of Neurosciences, National Institutes of Health, Bethesda, MD, USA
| | - Isabel Santana
- Neurology Service, University of Coimbra Hospital, Coimbra, Portugal
| | - Pau Pastor
- Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Barcelona, Spain; Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Monica Diez-Fairen
- Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Barcelona, Spain; Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Miquel Aguilar
- Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Barcelona, Spain; Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Pentti J Tienari
- Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Myllykangas
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland; HUSLAB, Helsinki, Finland
| | - Minna Oinas
- Department of Neurosurgery, University of Helsinki, Helsinki, Finland; Department of Neuropathology and Neurosurgery, Helsinki University Hospital, Helsinki, Finland
| | - Tamas Revesz
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Andrew Lees
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Brad F Boeve
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | - Tanis J Ferman
- Department of Psychiatry, Mayo Clinic, Jacksonville, FL, USA
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Nigel J Cairns
- Knight Alzheimer's Disease Research Center, Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John C Morris
- Knight Alzheimer's Disease Research Center, Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Stuart Pickering-Brown
- Institute of Brain, Behaviour and Mental Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - David Mann
- Institute of Brain, Behaviour and Mental Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Glenda M Halliday
- Neuroscience Research Australia, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Brain and Mind Centre, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - John Hardy
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Andrew Singleton
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Jose Bras
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Department of Medical Sciences and Institute of Biomedicine, iBiMED, University of Aveiro, Aveiro, Portugal.
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25
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Li J, Zhang Q, Chen F, Meng X, Liu W, Chen D, Yan J, Kim S, Wang L, Feng W, Saykin AJ, Liang H, Shen L. Genome-wide association and interaction studies of CSF T-tau/Aβ 42 ratio in ADNI cohort. Neurobiol Aging 2017. [PMID: 28641921 DOI: 10.1016/j.neurobiolaging.2017.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß42 (Aß42) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß42 ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability". Linear regression method was used to detect SNP-SNP interactions among SNPs with uncorrected p-value ≤0.01 from the GWAS. Age, gender, and diagnosis were considered as covariates in both studies. The GWAS results replicated the previously reported AD-related genes APOE, APOC1, and TOMM40, as well as identified 14 novel genes, which showed genome-wide statistical significance. Genome-wide interaction study revealed 7 pairs of SNPs meeting the cell-size criteria and with bonferroni-corrected p-value ≤0.05. As we expect, these interaction pairs all had marginal main effects but explained a relatively high-level variance of T-tau/Aß42, demonstrating their potential association with AD pathology.
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Affiliation(s)
- Jin Li
- College of Automation, Harbin Engineering University, Harbin, China
| | - Qiushi Zhang
- College of Automation, Harbin Engineering University, Harbin, China; College of Information Engineering, Northeast Dianli University, Jilin, China
| | - Feng Chen
- College of Automation, Harbin Engineering University, Harbin, China
| | - Xianglian Meng
- College of Automation, Harbin Engineering University, Harbin, China
| | - Wenjie Liu
- College of Automation, Harbin Engineering University, Harbin, China
| | - Dandan Chen
- College of Automation, Harbin Engineering University, Harbin, China; College of Information Engineering, Northeast Dianli University, Jilin, China
| | - Jingwen Yan
- 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; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lei Wang
- College of Automation, Harbin Engineering University, Harbin, China
| | - Weixing Feng
- College of Automation, Harbin Engineering University, Harbin, China
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hong Liang
- College of Automation, Harbin Engineering University, Harbin, China.
| | - Li Shen
- 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; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA.
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Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, Carrell D, Cai Y, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Huang KL, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, De Jager PL, Albert M, Moghekar A, O'Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, Lee VMY, Shaw LM, Trojanowski JQ, Schellenberg G, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Peskind ER, Li G, Di Narzo AF, Kauwe JSK, Goate AM, Cruchaga C. Genome-wide association study identifies four novel loci associated with Alzheimer's endophenotypes and disease modifiers. Acta Neuropathol 2017; 133:839-856. [PMID: 28247064 PMCID: PMC5613285 DOI: 10.1007/s00401-017-1685-y] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/08/2017] [Accepted: 02/14/2017] [Indexed: 01/20/2023]
Abstract
More than 20 genetic loci have been associated with risk for Alzheimer's disease (AD), but reported genome-wide significant loci do not account for all the estimated heritability and provide little information about underlying biological mechanisms. Genetic studies using intermediate quantitative traits such as biomarkers, or endophenotypes, benefit from increased statistical power to identify variants that may not pass the stringent multiple test correction in case-control studies. Endophenotypes also contain additional information helpful for identifying variants and genes associated with other aspects of disease, such as rate of progression or onset, and provide context to interpret the results from genome-wide association studies (GWAS). We conducted GWAS of amyloid beta (Aβ42), tau, and phosphorylated tau (ptau181) levels in cerebrospinal fluid (CSF) from 3146 participants across nine studies to identify novel variants associated with AD. Five genome-wide significant loci (two novel) were associated with ptau181, including loci that have also been associated with AD risk or brain-related phenotypes. Two novel loci associated with Aβ42 near GLIS1 on 1p32.3 (β = -0.059, P = 2.08 × 10-8) and within SERPINB1 on 6p25 (β = -0.025, P = 1.72 × 10-8) were also associated with AD risk (GLIS1: OR = 1.105, P = 3.43 × 10-2), disease progression (GLIS1: β = 0.277, P = 1.92 × 10-2), and age at onset (SERPINB1: β = 0.043, P = 4.62 × 10-3). Bioinformatics indicate that the intronic SERPINB1 variant (rs316341) affects expression of SERPINB1 in various tissues, including the hippocampus, suggesting that SERPINB1 influences AD through an Aβ-associated mechanism. Analyses of known AD risk loci suggest CLU and FERMT2 may influence CSF Aβ42 (P = 0.001 and P = 0.009, respectively) and the INPP5D locus may affect ptau181 levels (P = 0.009); larger studies are necessary to verify these results. Together the findings from this study can be used to inform future AD studies.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Manav Kapoor
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Yefei Cai
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Shengmei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kuan-Lin Huang
- Department of Medicine, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Sarah Bertelsen
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne M Fagan
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., 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
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., 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
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., 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
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Sungeun Kim
- Indiana Alzheimer Disease Center and Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Electrical and Computer Engineering, State University of New York, Oswego, NY, 13126, USA
| | - Andrew J Saykin
- Indiana Alzheimer Disease Center and Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard University and M.I.T., Cambridge, MA, 02142, USA
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard O'Brien
- Department of Neurology, Duke Medical Center, Box 2900, Durham, NC, 27710, USA
| | | | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, University of Gothenburg, Mölndal, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Lennart Minthon
- Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia Man-Yee Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan L Haines
- Department of Molecular Physiology and Biophysics, Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
| | - Richard Mayeux
- Department of Neurology, Taub Institute on Alzheimer's Disease and the Aging Brain, and Gertrude H. Sergievsky Center, 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, Epidemiology, and Neurology, Boston University, Boston, MA, USA
| | - Elaine R Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- VISN-20 Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Ge Li
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- VISN-20 Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Alison M Goate
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA.
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.
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27
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Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Green RC, Harvey D, Jack CR, Jagust W, Morris JC, Petersen RC, Saykin AJ, Shaw LM, Toga AW, Trojanowski JQ. Recent publications from the Alzheimer's Disease Neuroimaging Initiative: Reviewing progress toward improved AD clinical trials. Alzheimers Dement 2017; 13:e1-e85. [PMID: 28342697 DOI: 10.1016/j.jalz.2016.11.007] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/21/2016] [Accepted: 11/28/2016] [Indexed: 01/31/2023]
Abstract
INTRODUCTION The Alzheimer's Disease Neuroimaging Initiative (ADNI) has continued development and standardization of methodologies for biomarkers and has provided an increased depth and breadth of data available to qualified researchers. This review summarizes the over 400 publications using ADNI data during 2014 and 2015. METHODS We used standard searches to find publications using ADNI data. RESULTS (1) Structural and functional changes, including subtle changes to hippocampal shape and texture, atrophy in areas outside of hippocampus, and disruption to functional networks, are detectable in presymptomatic subjects before hippocampal atrophy; (2) In subjects with abnormal β-amyloid deposition (Aβ+), biomarkers become abnormal in the order predicted by the amyloid cascade hypothesis; (3) Cognitive decline is more closely linked to tau than Aβ deposition; (4) Cerebrovascular risk factors may interact with Aβ to increase white-matter (WM) abnormalities which may accelerate Alzheimer's disease (AD) progression in conjunction with tau abnormalities; (5) Different patterns of atrophy are associated with impairment of memory and executive function and may underlie psychiatric symptoms; (6) Structural, functional, and metabolic network connectivities are disrupted as AD progresses. Models of prion-like spreading of Aβ pathology along WM tracts predict known patterns of cortical Aβ deposition and declines in glucose metabolism; (7) New AD risk and protective gene loci have been identified using biologically informed approaches; (8) Cognitively normal and mild cognitive impairment (MCI) subjects are heterogeneous and include groups typified not only by "classic" AD pathology but also by normal biomarkers, accelerated decline, and suspected non-Alzheimer's pathology; (9) Selection of subjects at risk of imminent decline on the basis of one or more pathologies improves the power of clinical trials; (10) Sensitivity of cognitive outcome measures to early changes in cognition has been improved and surrogate outcome measures using longitudinal structural magnetic resonance imaging may further reduce clinical trial cost and duration; (11) Advances in machine learning techniques such as neural networks have improved diagnostic and prognostic accuracy especially in challenges involving MCI subjects; and (12) Network connectivity measures and genetic variants show promise in multimodal classification and some classifiers using single modalities are rivaling multimodal classifiers. DISCUSSION Taken together, these studies fundamentally deepen our understanding of AD progression and its underlying genetic basis, which in turn informs and improves clinical trial design.
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Affiliation(s)
- Michael W Weiner
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA; Department of Radiology, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, CA, USA.
| | - Dallas P Veitch
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA
| | - Paul S Aisen
- Alzheimer's Therapeutic Research Institute, University of Southern California, San Diego, CA, USA
| | - Laurel A Beckett
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Nigel J Cairns
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, Saint Louis, MO, USA; Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Danielle Harvey
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | | | - William Jagust
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - John C Morris
- Alzheimer's Therapeutic Research Institute, University of Southern California, San Diego, CA, USA
| | | | - Andrew J Saykin
- 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
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, Institute of Neuroimaging and Informatics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Alzheimer's Disease Core Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Udall Parkinson's Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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28
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Feng W, Chakraborty A. Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:489-526. [PMID: 29357071 DOI: 10.1007/978-981-10-6955-0_21] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome fragile sites are a fascinating cytogenetic phenomenon now widely implicated in a slew of human diseases ranging from neurological disorders to cancer. Yet, the paths leading to these revelations were far from direct, and the number of fragile sites that have been molecularly cloned with known disease-associated genes remains modest. Moreover, as more fragile sites were being discovered, research interests in some of the earliest discovered fragile sites ebbed away, leaving a number of unsolved mysteries in chromosome biology. In this review we attempt to recount some of the early discoveries of fragile sites and highlight those phenomena that have eluded intense scrutiny but remain extremely relevant in our understanding of the mechanisms of chromosome fragility. We then survey the literature for disease association for a comprehensive list of fragile sites. We also review recent studies addressing the underlying cause of chromosome fragility while highlighting some ongoing debates. We report an observed enrichment for R-loop forming sequences in fragile site-associated genes than genomic average. Finally, we will leave the reader with some lingering questions to provoke discussion and inspire further scientific inquiries.
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Affiliation(s)
- Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
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